From 9b25c16a75d8d9bebf4ba11e606e7772b2b339ff Mon Sep 17 00:00:00 2001
From: "marcin p. joachimiak" <4625870+realmarcin@users.noreply.github.com>
Date: Mon, 6 Jul 2026 06:25:26 -0700
Subject: [PATCH] Add growth conditions to 10 records + fix dark-mode contrast
 + regen pages
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Deep-research growth-conditions sweep over the 45 records lacking any
growth_media/cultivation_setup (via the add-growth-conditions skill + the new
sweep runner). One agent per record extracted only source-backed conditions
with verbatim evidence snippets; 35 records were correctly left unchanged
(uncultured/metagenomic/computational/paywalled — no fabrication).

Enriched (10):
- ANME_SRB_Marine_Methane_Seep_Consortium (OA full text: anaerobic seawater
  microcosm, CH4 ± HPG, 4/24/50 C)
- Chromium_Sulfur_Reduction_Enrichment (aerobic, pH 8, 30-37 C; dominant strain)
- Phylogenetically_Diverse_Denitrifying_SynCom (marine broth 2216 + 20 mM NaNO3,
  anaerobic, 25 C; OA companion study, attributed)
- BioModels_MODEL2209060002_DPigrum_SAureus (in silico SNM3 medium, COMPUTATIONAL)
- Aerobic_Denitrification_Disturbance_SynCom, Aerobic_Denitrification_QQ_SynCom,
  Shewanella_Pseudomonas_Fe0_*, BSFL_Gut_SynCom, SynCom_BsBv_Cigar_*,
  Thermophilic_Lignocellulose_Composting_* (abstract-level conditions)

Dark-mode contrast fix (community.html): preparation_notes, .interaction-flow,
.evidence-item, and inline code hardcoded light backgrounds with no text color,
rendering invisible (light-on-light) in dark mode — switched to theme variables.

Regenerated all 295 community pages (+ browser/index): bakes in the dark-mode
fix and syncs page content with already-merged #185 (GTDB), #187 (GO-term
cleanup) and #189 (growth media) data that predated the last render.

reports/growth_conditions_sweep/INDEX.md: sweep prep/progress report
(24 OA full text, 21 abstract-only).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---
 docs/browser.html                             |  946 +++++++++-
 .../AMD_Acidophile_Heterotroph_Network.html   |   48 +-
 .../AMD_Nitrososphaerota_Archaeal.html        |   35 +-
 ...c_Methanotrophic_Syntrophic_Consortia.html | 1385 +++++++++++++++
 ...ME_SRB_Marine_Methane_Seep_Consortium.html |  168 +-
 ...alborg_East_Full_Scale_EBPR_Community.html |   86 +-
 ...lostridium_CO2_Electrolysis_Coculture.html |   10 +-
 ...Dechlorination_Groundwater_Enrichment.html |    8 +-
 ...ic_Denitrification_Disturbance_SynCom.html |   76 +-
 .../Aerobic_Denitrification_QQ_SynCom.html    |   63 +-
 ...undra_Permafrost_Iron_Redox_Community.html |   76 +-
 ...ler_Flora_Gnotobiotic_Mouse_Community.html |  102 +-
 ...eactor_DNRA_Destabilization_Community.html |    8 +-
 ...anule_Metabolic_Interaction_Community.html |   10 +-
 ...lasmata_CuMMO_Soil_Sediment_Community.html |   23 +-
 .../Arabidopsis_Coumarin_Root_SynCom.html     |   71 +-
 .../Arabidopsis_Phyllosphere_SynCom7.html     |  106 +-
 ...il_Methanogenesis_Substrate_Community.html |    8 +-
 docs/communities/At_RSPHERE_SynCom.html       |   20 +-
 .../Australian_Lead_Zinc_Polymetallic.html    |   71 +-
 ...hizosphere_CrossKingdom_SIP_Community.html |    8 +-
 ...sphere_Detritusphere_Niche_Succession.html |    8 +-
 ...m_Bacillus_Lactobacillus_Issatchenkia.html | 1150 ++++++++++++
 ...dyrhizobium_Straw_Humification_SynCom.html |    8 +-
 ...des_Eubacterium_Gnotobiotic_Gut_Model.html |   58 +-
 ...evibacter_Gnotobiotic_Mouse_Mutualism.html |   71 +-
 .../Banana_Fusarium_Biocontrol_SynCom12.html  |   76 +-
 ...wage_SARS_CoV2_Surveillance_Community.html |    8 +-
 .../Bayan_Obo_REE_Tailings_Consortium.html    |   20 +-
 ..._Ruminococcus_Infant_HMO_CrossFeeding.html |    8 +-
 ...L1806250003_Spittlebug_Sulcia_Sodalis.html |    8 +-
 ...6250004_Sharpshooter_Sulcia_Baumannia.html |    8 +-
 ...DEL1806250005_Cicada_Sulcia_Hodgkinia.html |    8 +-
 ...MODEL2204300001_Kefir_Community_Model.html |   76 +-
 ...L2209060002_DPigrum_SAureus_Community.html |  160 +-
 ...EL2310020001_Mouse_Metaorganism_Model.html |    8 +-
 ...MODEL2405300001_Infant_Gut_HMO_SynCom.html |   99 +-
 ...EL2407300002_Sponge_Holobiont_Network.html |    8 +-
 ...ung_Root_Rhizosphere_EcoFAB_Community.html |    8 +-
 ..._Cinara_Cedri_Endosymbiont_Consortium.html |    8 +-
 ...us_Lignocellulolytic_Rumen_Consortium.html | 1053 +++++++++++
 .../CRC_Fusobacterium_Control_SynCom.html     |   76 +-
 ...teria_Photosynthetic_Biofilm_Sediment.html |  105 +-
 ...dium_Aerotolerant_Cellulose_Coculture.html |   10 +-
 ...iruptor_TwoSpecies_Hydrogen_Coculture.html |   10 +-
 ...d_Precipitation_Legacy_Soil_Community.html |   16 +-
 ...ilosis_Hospitalized_Infant_Microbiome.html |    8 +-
 ...bio_Caenorhabditis_Elegans_Microbiome.html |   16 +-
 ...ter_Cellulose_Photohydrogen_Coculture.html |   10 +-
 ...Cellulose_Methane_Quad_Culture_SynCom.html |   94 +-
 ...e_Rind_InSitu_InVitro_Model_Community.html |   10 +-
 ...Chlamydomonas_Bacterial_H2_Consortium.html |   20 +-
 ...amydomonas_Methylobacterium_Mutualism.html |   10 +-
 ...ella_Azospirillum_Synthetic_Mutualism.html |   10 +-
 ...a_Ecoli_Mixotrophic_Biofuel_Coculture.html |   10 +-
 .../Chlorella_Rhizobium_Bioflocculation.html  |   71 +-
 ...um_Aggregatum_Phototrophic_Consortium.html |   10 +-
 .../Chromium_Sulfur_Reduction_Enrichment.html |  172 +-
 .../Cinnamate_Degradation_Consortium.html     |   88 +-
 ...ethanogenum_Kluyveri_Syngas_Coculture.html |   10 +-
 ...lulosiruptor_Minimal_Medium_Coculture.html |   10 +-
 ...luyveri_CO_Chain_Elongation_Coculture.html |   10 +-
 ...cum_Geobacter_Cellulose_MFC_Coculture.html |   10 +-
 ...nosarcina_Cellulose_Methane_Coculture.html |   10 +-
 ...monas_Cellulose_Biohydrogen_Coculture.html |   10 +-
 ...lii_Kluyveri_Syngas_Alcohol_Coculture.html |   10 +-
 ...s_Ecoli_Cellobiose_Biofilm_Consortium.html |   10 +-
 ...haromyces_Cellulose_Ethanol_Coculture.html |   10 +-
 ...acter_Cellulosic_Bioethanol_Coculture.html |   10 +-
 ...JN4_GD17_Cellulosic_Biofuel_Coculture.html |   10 +-
 ...etonicum_Cellulosic_Butanol_Coculture.html |   10 +-
 ...land_Seawater_Ion_Microcosm_Community.html |   16 +-
 ...nCom_Lignocellulose_Degradation_Humus.html |  977 +++++++++++
 ...um_Citrobacter_Wheat_Straw_Consortium.html |   10 +-
 .../Copper_Biomining_Heap_Leach.html          |   64 +-
 ...la_oneidensis_Succinic_Acid_Coculture.html | 1036 +++++++++++
 .../Coscinodiscus_Synthetic_Community.html    |   18 +-
 ...an_Carp_Gut_Disease_Resistance_SynCom.html | 1033 +++++++++++
 ...eyser_CO2_Aquifer_CPR_Lipid_Community.html |    8 +-
 ...opper_Sulphide_Bioleaching_Consortium.html |    8 +-
 ...nocellulose_to_Methane_DIET_Consortia.html | 1246 +++++++++++++
 docs/communities/DVM_Triculture.html          |   94 +-
 docs/communities/Dangl_SynComm_35.html        |   12 +-
 ...Horizon_Deep_Sea_Oil_Plume_Succession.html |   76 +-
 ...ined_Multispecies_Enamel_Caries_Model.html |   71 +-
 ...s_Desulfovibrio_Lactate_TCE_Syntrophy.html |   10 +-
 ...vibrio_Pelosinus_Corrinoid_Triculture.html |   10 +-
 ...ethanosarcina_DMB_Cobalamin_Coculture.html |   10 +-
 ...es_Pelobacter_Acetylene_TCE_Coculture.html |   10 +-
 ...phomonas_TCE_Dechlorination_Coculture.html |   10 +-
 ...cartyi_CWV2_Dechlorinating_Consortium.html |  949 ++++++++++
 .../Desert_Tomato_Salt_Stress_SynCom5.html    |   63 +-
 ...Desulfovibrio_Methanococcus_Syntrophy.html |   10 +-
 ...brio_Methanosarcina_Lactate_Syntrophy.html |   10 +-
 ...iveSpecies_Gnotobiotic_Gut_Microbiota.html |   10 +-
 ...osphere_Iron_Actinobacteria_Community.html |    8 +-
 ...udomonas_putida_Lactic_Acid_Coculture.html | 1256 ++++++++++++++
 .../ENIGMA_Denitrifying_SynCom.html           |   86 +-
 .../Early_Dental_Biofilm_FiveSpecies.html     |   81 +-
 ...East_River_Floodplain_Core_Microbiome.html |   24 +-
 ...Hillslope_Riparian_Transect_Community.html |   23 +-
 .../EcoFAB_Ring_Trial_SynCom17.html           |   76 +-
 ...um_Infant_gut_HMO_Mutualism_Coculture.html | 1141 ++++++++++++
 ...c_VFA_Producing_Enrichment_Consortium.html | 1021 +++++++++++
 ...la_Clostridium_Acetobacterium_Acetate.html | 1178 +++++++++++++
 ...iania_Phaeobacter_Dynamic_Interaction.html |   10 +-
 ...ut_Amino_Acid_CrossFeeding_Consortium.html |   10 +-
 ..._Y2_Polyethylene_Degrading_Consortium.html | 1111 ++++++++++++
 ...iotic_CPR_DPANN_Groundwater_Community.html |    8 +-
 .../Ewaste_Bioleaching_Consortium.html        |  125 +-
 .../Ferroplasma_Leptospirillum_Syntrophy.html |   64 +-
 .../GLBRC_Exometabolite_Transwell_SynCom.html |   76 +-
 .../GLBRC_Populus_Variovorax_SynCom28.html    |   76 +-
 .../GLBRC_UFMP_Fermentation_Community.html    |   86 +-
 .../GOM_Oil_Degrading_Consortium.html         |   83 +-
 .../Garlic_Pseudomonas_SynCom6.html           |   63 +-
 .../Geobacter_Clostridium_DIET.html           |   10 +-
 .../Geobacter_Methanosaeta_DIET.html          |   10 +-
 .../Geobacter_Methanosarcina_DIET.html        |   10 +-
 ...mate_Fumarate_Electroactive_Coculture.html |   10 +-
 ...sland_Soil_WetUp_Virus_Host_Community.html |    8 +-
 ...ter_Elusimicrobia_Diverse_Metabolisms.html |   23 +-
 ...300_Area_Unconfined_Aquifer_Community.html |   31 +-
 ...s_Switchgrass_Methanogenic_Microbiome.html |   10 +-
 .../Honeybee_Core20_Defined_Microbiota.html   |   68 +-
 ...be_Mizunami_URL_Subsurface_Microbiome.html |    8 +-
 ...Iberian_Pit_Lake_Stratified_Community.html |   24 +-
 .../Industrial_Bioreactor_Consortium.html     |  227 ++-
 ...l_Milk_Line_FourSpecies_Model_Biofilm.html |   10 +-
 ...nt_Gut_DNA_Phage_Succession_Community.html |    8 +-
 .../Infant_Gut_Prebiotic_Response_SynCom.html | 1281 ++++++++++++++
 ...Strain_Persistence_Maternal_Community.html |    8 +-
 ...n_Adsorption_REE_Indigenous_Community.html |  121 +-
 docs/communities/Jala_Maize_PGPB_SynCom.html  |   76 +-
 ...ated_Ethene_Dechlorinating_Consortium.html |   10 +-
 ...ase_Models_for_Zahmeeth_Original_PLOS.html |    8 +-
 .../KBase_ORT_Workflow_Community_Model.html   |    8 +-
 ...ase_Synthetic_Bacterial_Community_R2A.html |   81 +-
 ...ucha_KMC_IMBG1_Fermentation_Community.html |   10 +-
 .../LBNL_Brachypodium_Drought_SynCom15.html   |   76 +-
 .../LBNL_Human_Gut_Interaction_SynCom.html    |   81 +-
 .../LBNL_Switchgrass_Soil_SynCom16.html       |   81 +-
 .../Lac_Pavin_Stratified_Lake_Community.html  |    8 +-
 ...Methane_Oxygen_Methylotroph_Community.html |   10 +-
 docs/communities/Lotus_LjSC3.html             |   16 +-
 docs/communities/MAMC_M48_Lignocellulose.html |   10 +-
 docs/communities/MSC1_Dominant_Core.html      |   76 +-
 .../MSC2_Model_Soil_Consortium.html           |   76 +-
 ...ter_Wetland_Methane_Network_Community.html |    8 +-
 ...ze_Benzoxazinoid_Metabolizing_SynComs.html |   76 +-
 .../Maize_Drought_Response_SynCom.html        |   71 +-
 .../Maize_Root_Simplified_Community.html      |  120 +-
 .../Medicago_Nodule_Biofertilizer_SynCom.html |   84 +-
 ...ean_Grassland_qSIP_Rainfall_Community.html |    8 +-
 .../Mercury_SFA_EFPC_Sediment_Community.html  |    8 +-
 ...thane_Oxidation_CrVI_Reduction_SynCom.html |   76 +-
 ...Galdieria_Thermoacidophilic_Coculture.html |   10 +-
 ...ethane_Acetate_Crossfeeding_Coculture.html |   10 +-
 ...bacter_Methane_Crossfeeding_Coculture.html |   10 +-
 ...hodococcus_Methane_VFA_PHBV_Coculture.html |   10 +-
 ...rella_Methane_Sequestration_Coculture.html |   10 +-
 ...Synechococcus_Gas_Feedstock_Coculture.html |   10 +-
 ...s_Massilia_Cyanosphere_Urea_Mutualism.html |   10 +-
 ...anthus_REE_Tailings_Nitrogen_SynCom10.html |    8 +-
 ...Mixed_Gallium_LED_Recovery_Consortium.html |  115 +-
 ...nobacterial_Consortia_Core_Microbiome.html |   10 +-
 ...e_Formaldehyde_Crossfeeding_Community.html |   10 +-
 ...bic_Digestion_SynCom_YSJ_and_SynCom_J.html |  989 +++++++++++
 ...tiomics_Corn_Straw_Degradation_SynCom.html |   58 +-
 ...Hot_Spring_Phototrophic_Mat_Community.html |    8 +-
 ...ycle_Bioflocculation_Model_Consortium.html |   63 +-
 .../Naica_Deep_Subsurface_Thermophilic.html   |   54 +-
 ...ix_Methanobrevibacter_Xylan_Coculture.html |   10 +-
 ..._Geothermal_Mercury_Cycling_Community.html |    8 +-
 ...OMM12_Gnotobiotic_Mouse_Gut_Community.html |   67 +-
 ...Desulfovibrio_Geobacter_Trophic_Model.html |   40 +-
 .../ORNL_PMI_Populus_PD10_SynCom.html         |   63 +-
 ...Uranium_Nitrate_Groundwater_Community.html |   16 +-
 .../Okeke_Lu_Cellulolytic_Consortium.html     |   10 +-
 ...us_Dinoroseobacter_BVitamin_Mutualism.html |   10 +-
 ...al_FourSpecies_Degradation_Consortium.html |   43 +-
 .../PGM_Spent_Catalyst_Bioleaching.html       |  110 +-
 ...Variovorax_Thermotolerance_Collection.html |   63 +-
 ...ic_Rice_Rhizosphere_Methane_Community.html |    8 +-
 .../Panzhihua_Vanadium_Titanium_Tailings.html |  113 +-
 ...a_Saccharomyces_Mutualistic_Coculture.html | 1174 +++++++++++++
 .../Peanut_Seed_Bacterial_CS_SynCom.html      |    8 +-
 ...hanocella_Propionate_RNASeq_Coculture.html |   10 +-
 ...maculum_Methanothermobacter_Syntrophy.html |   10 +-
 .../Pepper_Growth_Rhizosphere_SynCom.html     |   76 +-
 .../Pepper_Phytophthora_SynCom5.html          |   76 +-
 .../Phenol_Carboxylation_Consortium.html      |   90 +-
 .../Phormidium_Alkaline_Consortium.html       |  100 +-
 ...us_Lithosyntrophy_Phosphite_Coculture.html | 1038 +++++++++++
 ...netically_Diverse_Denitrifying_SynCom.html |  131 +-
 ...armandii_Endophytic_Biocontrol_SynCom.html | 1105 ++++++++++++
 ...rading_Artificial_Consortium_5_Strain.html | 1099 ++++++++++++
 ...aromonas_Vanadium_Reduction_Community.html |   44 +-
 .../Populus_Salt_Tolerant_SynComs.html        |    8 +-
 ...Wetland_Sulfur_Carbon_Virus_Community.html |   12 +-
 ...Escherichia_Diametric_Ratio_Community.html |    8 +-
 ...rococcus_Alteromonas_Helper_Coculture.html |   76 +-
 ...inated_Ethene_Cometabolism_Enrichment.html |  107 +-
 ...Pedobacter_Social_Spreading_Coculture.html |   10 +-
 ...dococcus_Chloronitrobenzene_Coculture.html |   41 +-
 ...us_RDK17_Terephthalic_Acid_Consortium.html | 1091 ++++++++++++
 ...thalene_Biochar_Engineered_Consortium.html | 1040 +++++++++++
 ...donitzschia_Sulfitobacter_Association.html |   14 +-
 .../Rammelsberg_Cobalt_Nickel_Tailings.html   |   39 +-
 ...udomonas_Ecoli_CrossFeeding_Coculture.html |   94 +-
 ...s_Geobacter_Magnetite_Redox_Coculture.html |   49 +-
 .../Rice_Acid_Soil_Bioinoculant_SynCom.html   |    8 +-
 .../Rice_Duckweed_Bacillus_SynCom.html        |   63 +-
 .../Rice_P_Uptake_Intercropping_SynCom4.html  |   63 +-
 .../Richmond_Mine_AMD_Biofilm.html            |   59 +-
 .../Rifle_Aquifer_Bioanode_EET_Community.html |    8 +-
 .../Rifle_Uranium_Reducing_Community.html     |  145 +-
 .../communities/SF356_Cellulose_Degrader.html |   10 +-
 ...UMIx_Human_Intestinal_Model_Community.html |   10 +-
 .../SMutans_CAlbicans_ECC_Biofilm.html        |   81 +-
 .../SMutans_SSputigena_ECC_Pathobiont.html    |   81 +-
 .../SMutans_VParvula_ASC_Biofilm.html         |   81 +-
 ...CE_Peatland_Methane_Cycling_Community.html |    8 +-
 ...ch_Inlet_OMZ_Redox_Gradient_Community.html |   32 +-
 ...bacter_Lignocellulose_Detox_Coculture.html |   81 +-
 ..._Chlamydomonas_Fungal_Algal_Mutualism.html |   10 +-
 ...Salar_Atacama_Lithium_Brine_Community.html |   92 +-
 ...wanella_Denitrifying_Richness_SynComs.html |   81 +-
 ...ter_Exoelectrogenic_Biofilm_Community.html |   38 +-
 ...trosyntrophic_Denitrifying_Consortium.html | 1102 ++++++++++++
 ...eptococcus_Starch_Microbial_Fuel_Cell.html |   10 +-
 ...palustris_Electrosyntrophic_Coculture.html |  949 ++++++++++
 .../SkinCom_Synthetic_Skin_Community.html     |   76 +-
 ...BGC_Phylum_Depth_Vegetation_Community.html |    8 +-
 ..._Nanoarchaea_Rare_Biosphere_Community.html |    8 +-
 ...oil_Corrinoid_B12_Reservoir_Community.html |    8 +-
 docs/communities/Sorghum_SRC1_Subset.html     |   58 +-
 ...lt_Pond_Methane_Restoration_Community.html |    8 +-
 ...rophyll_Selected_Biofertilizer_SynCom.html |   84 +-
 .../Soybean_N_Fixation_sfSynCom.html          |   14 +-
 ...s_Lignin_Dimer_Valorization_Coculture.html |   40 +-
 ...thylotrophic_Methanogenesis_Community.html |   12 +-
 ...e_Carboxydocella_CO_Aquifer_Community.html |   23 +-
 ...ulfide_Spring_Autotrophic_CPR_Biofilm.html |    8 +-
 ...SynComBac10_Chicken_Intestinal_SynCom.html |   81 +-
 ..._BsBv_Cigar_Tobacco_Leaf_Fermentation.html | 1064 ++++++++++++
 ...kiniana_Biogas_Slurry_Coupling_System.html |  997 +++++++++++
 ...obacteria_Sugarcane_Stress_Resilience.html | 1023 +++++++++++
 ...s_Rahnella_Artemisia_Phytoremediation.html |  941 ++++++++++
 ...Com_Sesame_Flavor_Baijiu_Fuqu_13Genus.html | 1541 +++++++++++++++++
 ...Bacillus_Biofilm_Biocontrol_Coculture.html | 1233 +++++++++++++
 ...Azotobacter_Photoproduction_Mutualism.html |   10 +-
 .../Synechococcus_Bacillus_SPC.html           |   86 +-
 docs/communities/Synechococcus_Ecoli_SPC.html |   86 +-
 ..._Halomonas_Light_Driven_PHB_Coculture.html |   10 +-
 ...us_Pseudomonas_PhotoPHA_DNT_Coculture.html |   10 +-
 ...a_Dlactate_Biophotovoltaic_Consortium.html |   10 +-
 .../Synechococcus_Yarrowia_SPC.html           |   81 +-
 ...n_Synechococcus_Rhodotorula_Coculture.html |   10 +-
 ...nthetic_Periphyton_Freshwater_Biofilm.html |   89 +-
 ...ophobacter_Methanobacterium_Syntrophy.html |   98 +-
 ...ophobacter_Methanospirillum_Syntrophy.html |   14 +-
 ...utyrate_Growth_Coordination_Coculture.html |   10 +-
 ...rophomonas_Methanospirillum_Syntrophy.html |   10 +-
 .../Syntrophus_Benzoate_Degrader.html         |  102 +-
 ...pirillum_Gentianae_Benzoate_Coculture.html |   10 +-
 .../THOR_Rhizosphere_Model_Community.html     |   63 +-
 .../TYQ1_Nematode_Biocontrol_SynCom.html      |   63 +-
 .../Teosinte_Maize_Biofertilizer_SynCom7.html |   63 +-
 ...ra_Marinobacter_Marine_Snow_Coculture.html |   10 +-
 ...iosira_Ruegeria_Phycosphere_Coculture.html |   10 +-
 ...rmobacter_Acetate_Oxidation_Coculture.html |   10 +-
 ...ose_Composting_SynCom_Biosanitization.html | 1223 +++++++++++++
 .../Thermophilic_Pyrite_QS_Consortium.html    |  134 +-
 ...ldococcus_Hyperthermophilic_Syntrophy.html |   10 +-
 ...pia_Thiobacillus_Bioreactor_Community.html |    8 +-
 .../Tinto_River_Iron_Cycling_Community.html   |   61 +-
 ...Tobacco_Chemotactic_Biocontrol_SynCom.html |   63 +-
 docs/communities/Tomato_Oxylipin_SynCom3.html |    8 +-
 ...henol_Anaerobic_Bioremediation_SynCom.html |   76 +-
 ...s_Methanospirillum_Butyrate_Coculture.html |   10 +-
 ...Ecoli_Cellulosic_Isobutanol_Coculture.html |   10 +-
 .../Trichoderma_Lactate_Platform.html         |   81 +-
 ...myces_Filamentous_Cellulose_Coculture.html |   10 +-
 ...desmium_Alteromonas_Marine_Consortium.html |   78 +-
 .../Urine_Nitrification_SynCom.html           |   71 +-
 ...ptococcus_Vitamin_Mutualism_Microcosm.html |   10 +-
 ...termelon_Rhizosphere_Fusarium_SynCom8.html |  102 +-
 ...xygen_Sulfate_GHG_Microcosm_Community.html |   12 +-
 docs/communities/Wheat_Consortium_C1.html     |   76 +-
 docs/communities/Wheat_Consortium_C6.html     |   76 +-
 ...heat_Straw_Biogas_Pretreatment_SynCom.html |    8 +-
 .../Yogurt_TwoSpecies_Starter_Culture.html    |   12 +-
 ...li_Exometabolomics_Obligate_Mutualism.html |   10 +-
 .../hCom2_Complex_Gut_Microbiome.html         |  102 +-
 docs/communities/mCAFEs_Brachypodium_RCC.html |   94 +-
 ...ME_SRB_Marine_Methane_Seep_Consortium.yaml |   51 +
 ...ic_Denitrification_Disturbance_SynCom.yaml |   17 +
 .../Aerobic_Denitrification_QQ_SynCom.yaml    |   13 +
 ...m_Bacillus_Lactobacillus_Issatchenkia.yaml |   32 +
 ...L2209060002_DPigrum_SAureus_Community.yaml |   46 +
 .../Chromium_Sulfur_Reduction_Enrichment.yaml |   36 +
 ...netically_Diverse_Denitrifying_SynCom.yaml |   37 +
 ...trosyntrophic_Denitrifying_Consortium.yaml |   26 +
 ..._BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml |   19 +
 ...ose_Composting_SynCom_Biosanitization.yaml |   26 +
 reports/growth_conditions_sweep/INDEX.md      |   56 +
 src/communitymech/templates/community.html    |   10 +-
 308 files changed, 43285 insertions(+), 2376 deletions(-)
 create mode 100644 docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html
 create mode 100644 docs/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.html
 create mode 100644 docs/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.html
 create mode 100644 docs/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html
 create mode 100644 docs/communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html
 create mode 100644 docs/communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.html
 create mode 100644 docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html
 create mode 100644 docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
 create mode 100644 docs/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.html
 create mode 100644 docs/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html
 create mode 100644 docs/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.html
 create mode 100644 docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
 create mode 100644 docs/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html
 create mode 100644 docs/communities/Infant_Gut_Prebiotic_Response_SynCom.html
 create mode 100644 docs/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html
 create mode 100644 docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
 create mode 100644 docs/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.html
 create mode 100644 docs/communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html
 create mode 100644 docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html
 create mode 100644 docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
 create mode 100644 docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
 create mode 100644 docs/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.html
 create mode 100644 docs/communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.html
 create mode 100644 docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html
 create mode 100644 docs/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.html
 create mode 100644 docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html
 create mode 100644 docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html
 create mode 100644 docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
 create mode 100644 docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
 create mode 100644 docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
 create mode 100644 reports/growth_conditions_sweep/INDEX.md

diff --git a/docs/browser.html b/docs/browser.html
index cb9216c6..0b9f4d3d 100644
--- a/docs/browser.html
+++ b/docs/browser.html
@@ -512,7 +512,7 @@ <h1>CommunityMech</h1>
                     <button id="search-clear" class="clear-btn" title="Clear search">✕</button>
                 </div>
                 <div class="search-results-count">
-                    Showing <span id="results-count">265</span> of 265 communities
+                    Showing <span id="results-count">295</span> of 295 communities
                 </div>
 
                 <!-- Active filters summary -->
@@ -664,6 +664,35 @@ <h2>AMD Nitrososphaerota Archaeal Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html"
+                       class="community-card"
+                       data-id="ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia"
+                       data-name="anme/srb anaerobic methanotrophic syntrophic consortia"
+                       data-description="marine syntrophic consortia of anaerobic methanotrophic archaea (anme) and sulfate-reducing bacteria (srb) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. sediment-free enrichment cultures of three consortium types (anme-1/desulfofervidus, anme-2a/seep-srb1, and anme-2a+2c/seep-srb1+2) exhibited high dry conductance close to that of electrogenic biofilms. cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners."
+                       data-category="SYNTROPHY"
+                       data-state="STABLE"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="6">
+                        <h2>ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia</h2>
+                        <p class="description">Marine syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. Sediment-free enrichment cultures of three consortium types (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2) exhibited high dry conductance close to that of electrogenic biofilms. Cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    6
+                                </span>
+                                <span class="badge badge-STABLE">STABLE</span>
+                            </div>
+                            <span class="badge badge-category">SYNTROPHY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/ANME_SRB_Marine_Methane_Seep_Consortium.html"
                        class="community-card"
                        data-id="ANME_SRB_Marine_Methane_Seep_Consortium"
@@ -1208,6 +1237,35 @@ <h2>Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds</
                         </div>
                     </a>
                     
+                    <a href="communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.html"
+                       class="community-card"
+                       data-id="BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia"
+                       data-name="black soldier fly larvae gut syncom (bacillus + lactobacillus + issatchenkia)"
+                       data-description="a tripartite synthetic microbial community (syncom) engineered from the core gut microbiota of black soldier fly larvae (bsfl) to enhance protein bioconversion from organic wastes. the syncom combines the bacteria bacillus and lactobacillus with the yeast issatchenkia and was assembled and tested in germ-free (gnotobiotic) larval hosts using multi-omics. bacillus provides direct proteolytic activity, whereas lactobacillus and issatchenkia are associated with improved protein-conversion performance and amino-acid metabolic responses. the tripartite syncom showed the highest protein conversion performance and distinct spatiotemporal distribution along the gut ph gradient, increasing final larval protein content by 63%."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia)</h2>
+                        <p class="description">A tripartite synthetic microbial community (SynCom) engineered from the core gut microbiota of black soldier fly larvae (BSFL) to enhance protein bioconversion from organic wastes. The SynCom combines the bacteria Bacillus and Lactobacillus with the yeast Issatchenkia and was assembled and tested in germ-free (gnotobiotic) larval hosts using multi-omics. Bacillus provides direct proteolytic activity, whereas Lactobacillus and Issatchenkia are associated with improved protein-conversion performance and amino-acid metabolic responses. The tripartite SynCom showed the highest protein conversion performance and distinct spatiotemporal distribution along the gut pH gradient, increasing final larval protein content by 63%.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.html"
                        class="community-card"
                        data-id="Bacillus_Bradyrhizobium_Straw_Humification_SynCom"
@@ -1713,6 +1771,35 @@ <h2>Buchnera-Serratia Cinara cedri Endosymbiont Consortium</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.html"
+                       class="community-card"
+                       data-id="Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium"
+                       data-name="butyrivibrio fibrisolvens + selenomonas ruminantium + ruminococcus albus lignocellulolytic rumen consortium"
+                       data-description="a synthetic lignocellulolytic bacterial consortium designed from six bovine rumen microbial strains to enhance lignocellulose degradation for biofuel and enzyme production. genome-scale community metabolic models were used with flux-based parameters (pairwise metabolic assistance, pma; growth support index, pgsi) to predict compatible, mutualistic pairs, which were validated in experimentally grown cocultures. the strongest pairwise enzymatic synergism was observed for butyrivibrio fibrisolvens with selenomonas ruminantium (a 41% increase in endoglucanase activity), and a three-membered community of b. fibrisolvens, s. ruminantium, and ruminococcus albus showed synergistic activity across all lignocellulosic substrates, indicating strong metabolic interplay among compatible species."
+                       data-category="LIGNOCELLULOSE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium</h2>
+                        <p class="description">A synthetic lignocellulolytic bacterial consortium designed from six bovine rumen microbial strains to enhance lignocellulose degradation for biofuel and enzyme production. Genome-scale community metabolic models were used with flux-based parameters (pairwise metabolic assistance, PMA; growth support index, PGSI) to predict compatible, mutualistic pairs, which were validated in experimentally grown cocultures. The strongest pairwise enzymatic synergism was observed for Butyrivibrio fibrisolvens with Selenomonas ruminantium (a 41% increase in endoglucanase activity), and a three-membered community of B. fibrisolvens, S. ruminantium, and Ruminococcus albus showed synergistic activity across all lignocellulosic substrates, indicating strong metabolic interplay among compatible species.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">LIGNOCELLULOSE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/CRC_Fusobacterium_Control_SynCom.html"
                        class="community-card"
                        data-id="CRC_Fusobacterium_Control_SynCom"
@@ -2668,6 +2755,35 @@ <h2>Coastal Forested Wetland Seawater-Ion Microcosm Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html"
+                       class="community-card"
+                       data-id="Composting_SynCom_Lignocellulose_Degradation_Humus"
+                       data-name="five-member bacterial-fungal composting syncom for lignocellulose degradation"
+                       data-description="a rationally designed five-member bacterial-fungal synthetic microbial community (syncom) used to bioaugment the co-composting of cattle manure and mulberry branches. inoculation acts as an ecological engineer that elevates pile temperatures, shortens the maturation period by roughly 7 days, and enhances degradation of lignin, cellulose, and hemicellulose while boosting humus content. metagenomics shows the syncom restructures the native microbiome, enriching key lignocellulose-degrading functional genera such as thermobifida and actinomadura and increasing the abundance of carbohydrate-active enzymes (cellulases, hemicellulases, and lignin-modifying auxiliary-activity enzymes)."
+                       data-category="LIGNOCELLULOSE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Five-member bacterial-fungal composting SynCom for lignocellulose degradation</h2>
+                        <p class="description">A rationally designed five-member bacterial-fungal synthetic microbial community (SynCom) used to bioaugment the co-composting of cattle manure and mulberry branches. Inoculation acts as an ecological engineer that elevates pile temperatures, shortens the maturation period by roughly 7 days, and enhances degradation of lignin, cellulose, and hemicellulose while boosting humus content. Metagenomics shows the SynCom restructures the native microbiome, enriching key lignocellulose-degrading functional genera such as Thermobifida and Actinomadura and increasing the abundance of carbohydrate-active enzymes (cellulases, hemicellulases, and lignin-modifying auxiliary-activity enzymes).</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">LIGNOCELLULOSE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.html"
                        class="community-card"
                        data-id="Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium"
@@ -2730,6 +2846,35 @@ <h2>Copper Biomining Heap Leach Consortium</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html"
+                       class="community-card"
+                       data-id="Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture"
+                       data-name="corynebacterium glutamicum + shewanella oneidensis succinic-acid co-culture"
+                       data-description="engineered two-member co-culture pairing the succinic-acid producer corynebacterium glutamicum (including an ldha-deleted, lactate-deficient strain k1) with the electroactive bacterium shewanella oneidensis to enhance anaerobic succinic acid biosynthesis through interspecies interactions. co-cultivation raised succinic acid yield markedly over monoculture without altering glucose consumption, and supplementation with riboflavin (the most effective of five screened redox-active additives) further improved production. transcriptomics showed co-culture reprogrammed c. glutamicum metabolism, reinforcing its electron transport system and redistributing carbon flux toward the reductive tca pathway."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture</h2>
+                        <p class="description">Engineered two-member co-culture pairing the succinic-acid producer Corynebacterium glutamicum (including an ldhA-deleted, lactate-deficient strain K1) with the electroactive bacterium Shewanella oneidensis to enhance anaerobic succinic acid biosynthesis through interspecies interactions. Co-cultivation raised succinic acid yield markedly over monoculture without altering glucose consumption, and supplementation with riboflavin (the most effective of five screened redox-active additives) further improved production. Transcriptomics showed co-culture reprogrammed C. glutamicum metabolism, reinforcing its electron transport system and redistributing carbon flux toward the reductive TCA pathway.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Coscinodiscus_Synthetic_Community.html"
                        class="community-card"
                        data-id="Coscinodiscus_Synthetic_Community"
@@ -2761,6 +2906,35 @@ <h2>Coscinodiscus Synthetic Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.html"
+                       class="community-card"
+                       data-id="Crucian_Carp_Gut_Disease_Resistance_SynCom"
+                       data-name="crucian carp gut disease-resistance syncom"
+                       data-description="a simplified synthetic microbial community of three gut genera (cetobacterium, paraclostridium, and pseudomonas) assembled from the intestinal microbiota of crucian carp (carassius auratus). these genera were enriched in fish that displayed mild symptoms after aeromonas hydrophila infection, and fecal microbiota transplantation from mild-symptom fish conferred enhanced resistance to the pathogen. the reconstituted syncom significantly reduced a. hydrophila abundance by activating intestinal immune responses and reinforcing the gut barrier, supporting microbiome-based disease prevention in aquaculture."
+                       data-category="OTHER"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Crucian Carp Gut Disease-resistance SynCom</h2>
+                        <p class="description">A simplified synthetic microbial community of three gut genera (Cetobacterium, Paraclostridium, and Pseudomonas) assembled from the intestinal microbiota of crucian carp (Carassius auratus). These genera were enriched in fish that displayed mild symptoms after Aeromonas hydrophila infection, and fecal microbiota transplantation from mild-symptom fish conferred enhanced resistance to the pathogen. The reconstituted SynCom significantly reduced A. hydrophila abundance by activating intestinal immune responses and reinforcing the gut barrier, supporting microbiome-based disease prevention in aquaculture.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">OTHER</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html"
                        class="community-card"
                        data-id="Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community"
@@ -2823,6 +2997,35 @@ <h2>Cyprus Copper Sulphide Bioleaching Consortium</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html"
+                       class="community-card"
+                       data-id="DIETsimp_Lignocellulose_to_Methane_DIET_Consortia"
+                       data-name="diet-based simplified lignocellulose-to-methane consortia (dietsimp)"
+                       data-description="two simplified methanogenic consortia (dietsimp) constructed by top-down selection from cow manure combined with paddy soil or marine sediment inocula for high-efficiency conversion of lignocellulose to methane via direct interspecies electron transfer (diet). metagenomic analysis identified methanosarcina mazei, capable of accepting electrons via diet, as the dominant archaeon, and the electroactive bacteria sphaerochaeta globosa and clostridium aceticum as the dominant bacteria. the proposed diet-based methanogenic pathway has s. globosa and c. aceticum metabolizing intermediates (xylose, glucose, pyruvate, acetate) and transferring electrons to m. mazei for reduction of co2 to methane. both consortia shortened methanogenesis periods and increased methane production rates relative to conventional anaerobic digestion."
+                       data-category="LIGNOCELLULOSE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)</h2>
+                        <p class="description">Two simplified methanogenic consortia (DIETsimp) constructed by top-down selection from cow manure combined with paddy soil or marine sediment inocula for high-efficiency conversion of lignocellulose to methane via direct interspecies electron transfer (DIET). Metagenomic analysis identified Methanosarcina mazei, capable of accepting electrons via DIET, as the dominant archaeon, and the electroactive bacteria Sphaerochaeta globosa and Clostridium aceticum as the dominant bacteria. The proposed DIET-based methanogenic pathway has S. globosa and C. aceticum metabolizing intermediates (xylose, glucose, pyruvate, acetate) and transferring electrons to M. mazei for reduction of CO2 to methane. Both consortia shortened methanogenesis periods and increased methane production rates relative to conventional anaerobic digestion.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">LIGNOCELLULOSE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/DVM_Triculture.html"
                        class="community-card"
                        data-id="DVM_Triculture"
@@ -3100,6 +3303,35 @@ <h2>Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html"
+                       class="community-card"
+                       data-id="Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium"
+                       data-name="dehalococcoides mccartyi cwv2 dechlorinating consortium"
+                       data-description="a native groundwater microbial consortium enriched in dehalococcoides mccartyi (dhc) strain cwv2, a strain capable of completely dechlorinating vinyl chloride (vc) to non-toxic ethene. the consortium remediates trichloroethene (tce)-contaminated groundwater; amendment with biochar (bc600) derived from zizania latifolia husks enhances microbial colonization and activity, accelerating tce degradation and reducing vc accumulation. community analysis indicates biochar promotes syntrophic hydrogen producers and electroactive bacteria that supply reducing equivalents and ensure long-term dechlorination stability."
+                       data-category="BIOREMEDIATION"
+                       data-state="STABLE"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="1">
+                        <h2>Dehalococcoides mccartyi CWV2 Dechlorinating Consortium</h2>
+                        <p class="description">A native groundwater microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2, a strain capable of completely dechlorinating vinyl chloride (VC) to non-toxic ethene. The consortium remediates trichloroethene (TCE)-contaminated groundwater; amendment with biochar (BC600) derived from Zizania latifolia husks enhances microbial colonization and activity, accelerating TCE degradation and reducing VC accumulation. Community analysis indicates biochar promotes syntrophic hydrogen producers and electroactive bacteria that supply reducing equivalents and ensure long-term dechlorination stability.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    1
+                                </span>
+                                <span class="badge badge-STABLE">STABLE</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Desert_Tomato_Salt_Stress_SynCom5.html"
                        class="community-card"
                        data-id="Desert_Tomato_Salt_Stress_SynCom5"
@@ -3253,6 +3485,35 @@ <h2>Drought-Induced Rhizosphere Iron-Enriched Actinobacteria Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.html"
+                       class="community-card"
+                       data-id="Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture"
+                       data-name="dual bacillus coagulans + pseudomonas putida lactic-acid co-culture"
+                       data-description="engineered artificial microbial consortium for l-lactic acid (la) fermentation directly from undetoxified lignocellulosic (corncob) hydrolysates. a dual bacillus coagulans (heyndrickxia coagulans) system pairs a phenolic acid decarboxylase (pad)-overexpressing biodetoxifying strain, dsm1-25280, with a high-yield la producer, cc17b-1, and reaches 124.72 g/l la from undetoxified hydrolysate via a sequential-inoculation division of labor. multidimensional analysis supports a niche-succession model transitioning from biodetoxification-mediated commensalism to competitive exclusion. a sugar-metabolism-deficient engineered pseudomonas putida kt2440 zl added as a heterologous aromatic scavenger reinforces the system, raising the la titer to 146.00 g/l at 98.9% yield."
+                       data-category="LIGNOCELLULOSE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture</h2>
+                        <p class="description">Engineered artificial microbial consortium for L-lactic acid (LA) fermentation directly from undetoxified lignocellulosic (corncob) hydrolysates. A dual Bacillus coagulans (Heyndrickxia coagulans) system pairs a phenolic acid decarboxylase (PAD)-overexpressing biodetoxifying strain, DSM1-25280, with a high-yield LA producer, CC17B-1, and reaches 124.72 g/L LA from undetoxified hydrolysate via a sequential-inoculation division of labor. Multidimensional analysis supports a niche-succession model transitioning from biodetoxification-mediated commensalism to competitive exclusion. A sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL added as a heterologous aromatic scavenger reinforces the system, raising the LA titer to 146.00 g/L at 98.9% yield.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">LIGNOCELLULOSE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/ENIGMA_Denitrifying_SynCom.html"
                        class="community-card"
                        data-id="ENIGMA_Denitrifying_SynCom"
@@ -3402,21 +3663,19 @@ <h2>EcoFAB 2.0 Root Microbiome Ring Trial SynCom17</h2>
                         </div>
                     </a>
                     
-                    <a href="communities/Emiliania_Phaeobacter_Dynamic_Interaction.html"
+                    <a href="communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html"
                        class="community-card"
-                       data-id="Emiliania_Phaeobacter_Dynamic_Interaction"
-                       data-name="emiliania huxleyi-phaeobacter inhibens dynamic interaction"
-                       data-description="a defined marine algal-bacterial co-culture model between the coccolithophore emiliania huxleyi ccmp3266 and the roseobacter-group bacterium phaeobacter inhibens dsm 17395. the interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan.
-"
-                       data-category="PHYTOPLANKTON"
+                       data-id="Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture"
+                       data-name="escherichia coli + bifidobacterium bifidum infant-gut mutualistic co-culture"
+                       data-description="two-member infant-gut co-culture of escherichia coli and bifidobacterium bifidum. in healthy, term-born, breastfed infants these genera co-exist despite differing ecological strategies and share evolutionary adaptations for lactose acquisition. in vitro co-culture demonstrates a mutualistic cross-feeding interaction in which e. coli supplies cysteine to its auxotrophic partner b. bifidum, facilitating cooperative degradation of 2&#39;-fucosyllactose (the predominant human milk oligosaccharide), and the liberated monosaccharides in turn sustain e. coli growth, potentially helping regulate e. coli abundance in the infant gut."
+                       data-category="DIET"
                        data-state="ENGINEERED"
                        data-metals=""
                        data-ree=""
                        data-relevance="NOT_APPLICABLE"
                        data-member-count="2">
-                        <h2>Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction</h2>
-                        <p class="description">A defined marine algal-bacterial co-culture model between the coccolithophore Emiliania huxleyi CCMP3266 and the Roseobacter-group bacterium Phaeobacter inhibens DSM 17395. The interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. Evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan.
-</p>
+                        <h2>Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture</h2>
+                        <p class="description">Two-member infant-gut co-culture of Escherichia coli and Bifidobacterium bifidum. In healthy, term-born, breastfed infants these genera co-exist despite differing ecological strategies and share evolutionary adaptations for lactose acquisition. In vitro co-culture demonstrates a mutualistic cross-feeding interaction in which E. coli supplies cysteine to its auxotrophic partner B. bifidum, facilitating cooperative degradation of 2&#39;-fucosyllactose (the predominant human milk oligosaccharide), and the liberated monosaccharides in turn sustain E. coli growth, potentially helping regulate E. coli abundance in the infant gut.</p>
                         <div class="card-footer">
                             <div class="card-footer-left">
                                 <span class="badge badge-member-count" title="Number of member taxa">
@@ -3429,25 +3688,23 @@ <h2>Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction</h2>
                                 </span>
                                 <span class="badge badge-ENGINEERED">ENGINEERED</span>
                             </div>
-                            <span class="badge badge-category">PHYTOPLANKTON</span>
+                            <span class="badge badge-category">DIET</span>
                         </div>
                     </a>
                     
-                    <a href="communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html"
+                    <a href="communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.html"
                        class="community-card"
-                       data-id="Engineered_Gut_Amino_Acid_CrossFeeding_Consortium"
-                       data-name="engineered gut amino acid cross-feeding consortium"
-                       data-description="a four-species engineered mammalian-gut consortium in which escherichia coli, salmonella enterica serovar typhimurium, bacteroides thetaiotaomicron, and bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. the design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.
-"
+                       data-id="Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium"
+                       data-name="electrostimulated mixotrophic vfa-producing enrichment consortium"
+                       data-description="a specialized mixotrophic microbial consortium enriched in a continuous electrostimulated bioreactor operated at a constant potential of 300 mv for co2 conversion into volatile fatty acids. decreasing hydraulic retention time (hrt) selected for a spatially organized community in which enterococcus and clostridium dominated the planktonic phase while desulfovibrio and enterococcus were enriched in the electrode biofilm. this syntrophic organization enhanced biomass-specific inorganic carbon removal and redirected carbon flux toward acetate, a key product of acetogenic pathways, with electrode-associated taxa contributing reducing equivalents that supported autotrophic co2/hco3- fixation."
                        data-category="BIOTECHNOLOGY"
                        data-state="ENGINEERED"
                        data-metals=""
                        data-ree=""
                        data-relevance="NOT_APPLICABLE"
-                       data-member-count="4">
-                        <h2>Engineered Gut Amino Acid Cross-Feeding Consortium</h2>
-                        <p class="description">A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.
-</p>
+                       data-member-count="3">
+                        <h2>Electrostimulated Mixotrophic VFA-producing Enrichment Consortium</h2>
+                        <p class="description">A specialized mixotrophic microbial consortium enriched in a continuous electrostimulated bioreactor operated at a constant potential of 300 mV for CO2 conversion into volatile fatty acids. Decreasing hydraulic retention time (HRT) selected for a spatially organized community in which Enterococcus and Clostridium dominated the planktonic phase while Desulfovibrio and Enterococcus were enriched in the electrode biofilm. This syntrophic organization enhanced biomass-specific inorganic carbon removal and redirected carbon flux toward acetate, a key product of acetogenic pathways, with electrode-associated taxa contributing reducing equivalents that supported autotrophic CO2/HCO3- fixation.</p>
                         <div class="card-footer">
                             <div class="card-footer-left">
                                 <span class="badge badge-member-count" title="Number of member taxa">
@@ -3456,7 +3713,7 @@ <h2>Engineered Gut Amino Acid Cross-Feeding Consortium</h2>
                                         <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
                                         <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
                                     </svg>
-                                    4
+                                    3
                                 </span>
                                 <span class="badge badge-ENGINEERED">ENGINEERED</span>
                             </div>
@@ -3464,21 +3721,19 @@ <h2>Engineered Gut Amino Acid Cross-Feeding Consortium</h2>
                         </div>
                     </a>
                     
-                    <a href="communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html"
+                    <a href="communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html"
                        class="community-card"
-                       data-id="Episymbiotic_CPR_DPANN_Groundwater_Community"
-                       data-name="episymbiotic cpr bacteria and dpann archaea groundwater community"
-                       data-description="a groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 candidate phyla radiation (cpr) bacterial and dpann archaeal genomes. pristine sites, which serve as local sources of drinking water, contained up to 31 percent cpr bacteria and 4 percent dpann archaea. little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that cpr and dpann communities are differentiated according to physicochemical conditions and host populations. cryogenic transmission electron microscopy and genomic analysis identified cpr and dpann lineages that reproducibly attach to host cells, with attachment apparently stimulating cpr bacterial growth.
-"
-                       data-category="EXTREME_ENVIRONMENT"
-                       data-state="STABLE"
+                       data-id="Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate"
+                       data-name="shewanella-acetogen electrosynthetic consortia for co2-to-acetate"
+                       data-description="defined synthetic microbial electrosynthesis (mes) consortia constructed by pairing the model bidirectional electroactive bacterium shewanella oneidensis mr-1 with either the electroactive acetogen clostridium aceticum or the nonelectroactive acetogen acetobacterium woodii, mimicking functional guilds of natural mes communities. co-cultivation boosts co2-to-acetate production by up to 88%. the two pairings use distinct interspecies electron transfer (iet) modes, namely direct interspecies electron transfer (diet) via cytochrome c and riboflavin at the biofilm-electrode interface in the s. oneidensis-c. aceticum consortium, versus h2/formate-mediated iet in the planktonic phase for the s. oneidensis-a. woodii consortium. this metabolic stratification lets s. oneidensis act as an &#34;ecosystem engineer&#34; orchestrating electron flow across biofilm and suspension niches."
+                       data-category="CARBON_SEQUESTRATION"
+                       data-state="ENGINEERED"
                        data-metals=""
                        data-ree=""
                        data-relevance="NOT_APPLICABLE"
                        data-member-count="3">
-                        <h2>Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community</h2>
-                        <p class="description">A groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 Candidate Phyla Radiation (CPR) bacterial and DPANN archaeal genomes. Pristine sites, which serve as local sources of drinking water, contained up to 31 percent CPR bacteria and 4 percent DPANN archaea. Little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that CPR and DPANN communities are differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy and genomic analysis identified CPR and DPANN lineages that reproducibly attach to host cells, with attachment apparently stimulating CPR bacterial growth.
-</p>
+                        <h2>Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate</h2>
+                        <p class="description">Defined synthetic microbial electrosynthesis (MES) consortia constructed by pairing the model bidirectional electroactive bacterium Shewanella oneidensis MR-1 with either the electroactive acetogen Clostridium aceticum or the nonelectroactive acetogen Acetobacterium woodii, mimicking functional guilds of natural MES communities. Co-cultivation boosts CO2-to-acetate production by up to 88%. The two pairings use distinct interspecies electron transfer (IET) modes, namely direct interspecies electron transfer (DIET) via cytochrome c and riboflavin at the biofilm-electrode interface in the S. oneidensis-C. aceticum consortium, versus H2/formate-mediated IET in the planktonic phase for the S. oneidensis-A. woodii consortium. This metabolic stratification lets S. oneidensis act as an &#34;ecosystem engineer&#34; orchestrating electron flow across biofilm and suspension niches.</p>
                         <div class="card-footer">
                             <div class="card-footer-left">
                                 <span class="badge badge-member-count" title="Number of member taxa">
@@ -3489,19 +3744,141 @@ <h2>Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community</h2>
                                     </svg>
                                     3
                                 </span>
-                                <span class="badge badge-STABLE">STABLE</span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
                             </div>
-                            <span class="badge badge-category">EXTREME_ENVIRONMENT</span>
+                            <span class="badge badge-category">CARBON_SEQUESTRATION</span>
                         </div>
                     </a>
                     
-                    <a href="communities/Ewaste_Bioleaching_Consortium.html"
+                    <a href="communities/Emiliania_Phaeobacter_Dynamic_Interaction.html"
                        class="community-card"
-                       data-id="Ewaste_Bioleaching_Consortium"
-                       data-name="e-waste bioleaching consortium"
-                       data-description="an engineered acidophilic microbial consortium adapted for recovering valuable metals from electronic waste, particularly printed circuit boards (pcbs). this consortium consists primarily of iron-oxidizing bacteria dominated by leptospirillum ferriphilum with sulfobacillus benefaciens, acidithiobacillus ferrooxidans, and acidithiobacillus thiooxidans contributing to metal solubilization. the community operates at extremely low ph (1.2 ± 0.1) and moderate temperature (35°c), oxidizing ferrous iron to generate ferric iron (fe³⁺) that dissolves base metals (copper, zinc, nickel) and mobilizes precious metals (gold, silver, palladium) from pcb components. metal recovery is exceptional: 100% copper dissolution (2.6-4.2 g/l), 100% zinc (303-543 mg/l), and 70% nickel (30-52 mg/l). however, pcb materials are toxic to the consortium, delaying the pre-oxidation phase from 11 days at 1% pcb load to 18 days at 2% load, with no growth above 8% pcb. successive subculturing adapts the consortium to pcb toxicity, reducing lag phase by 2.6-fold. this biotechnological approach offers an environmentally-friendly alternative to pyrometallurgical e-waste processing (smelting), avoiding toxic emissions while recovering critical materials including copper for electrical applications and precious metals for electronics manufacturing. the two-step process may include subsequent cyanide-producing heterotrophs (pseudomonas fluorescens, p. putida) for enhanced gold and silver extraction.
+                       data-id="Emiliania_Phaeobacter_Dynamic_Interaction"
+                       data-name="emiliania huxleyi-phaeobacter inhibens dynamic interaction"
+                       data-description="a defined marine algal-bacterial co-culture model between the coccolithophore emiliania huxleyi ccmp3266 and the roseobacter-group bacterium phaeobacter inhibens dsm 17395. the interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan.
 "
-                       data-category="BIOMINING"
+                       data-category="PHYTOPLANKTON"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction</h2>
+                        <p class="description">A defined marine algal-bacterial co-culture model between the coccolithophore Emiliania huxleyi CCMP3266 and the Roseobacter-group bacterium Phaeobacter inhibens DSM 17395. The interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. Evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan.
+</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">PHYTOPLANKTON</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html"
+                       class="community-card"
+                       data-id="Engineered_Gut_Amino_Acid_CrossFeeding_Consortium"
+                       data-name="engineered gut amino acid cross-feeding consortium"
+                       data-description="a four-species engineered mammalian-gut consortium in which escherichia coli, salmonella enterica serovar typhimurium, bacteroides thetaiotaomicron, and bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. the design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.
+"
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="4">
+                        <h2>Engineered Gut Amino Acid Cross-Feeding Consortium</h2>
+                        <p class="description">A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.
+</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    4
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html"
+                       class="community-card"
+                       data-id="Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium"
+                       data-name="ensifer yf2 + sphingobacterium y2 polyethylene-degrading consortium"
+                       data-description="synthetic bacterial consortium for polyethylene (pe) biodegradation, built from three strains-ensifer sp. yf2, sphingobacterium sp. y2, and chryseobacterium sp. mf1-isolated from plastic-contaminated agricultural soils. a dual-strain consortium of yf2 and y2 degraded pe more efficiently than individual strains or the full three-strain combination, using pe as the sole carbon source and inducing oxidative modifications and physical erosion of the polymer. genomic analysis showed a complementary enzymatic division of labor - yf2 (oxidases lada, alkb, cyp450) performs backbone cleavage as the primary degrader, while y2 (esterases and lipases) carries out intermediate metabolism through cross-feeding."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading Consortium</h2>
+                        <p class="description">Synthetic bacterial consortium for polyethylene (PE) biodegradation, built from three strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-isolated from plastic-contaminated agricultural soils. A dual-strain consortium of YF2 and Y2 degraded PE more efficiently than individual strains or the full three-strain combination, using PE as the sole carbon source and inducing oxidative modifications and physical erosion of the polymer. Genomic analysis showed a complementary enzymatic division of labor - YF2 (oxidases LadA, AlkB, CYP450) performs backbone cleavage as the primary degrader, while Y2 (esterases and lipases) carries out intermediate metabolism through cross-feeding.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html"
+                       class="community-card"
+                       data-id="Episymbiotic_CPR_DPANN_Groundwater_Community"
+                       data-name="episymbiotic cpr bacteria and dpann archaea groundwater community"
+                       data-description="a groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 candidate phyla radiation (cpr) bacterial and dpann archaeal genomes. pristine sites, which serve as local sources of drinking water, contained up to 31 percent cpr bacteria and 4 percent dpann archaea. little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that cpr and dpann communities are differentiated according to physicochemical conditions and host populations. cryogenic transmission electron microscopy and genomic analysis identified cpr and dpann lineages that reproducibly attach to host cells, with attachment apparently stimulating cpr bacterial growth.
+"
+                       data-category="EXTREME_ENVIRONMENT"
+                       data-state="STABLE"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="3">
+                        <h2>Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community</h2>
+                        <p class="description">A groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 Candidate Phyla Radiation (CPR) bacterial and DPANN archaeal genomes. Pristine sites, which serve as local sources of drinking water, contained up to 31 percent CPR bacteria and 4 percent DPANN archaea. Little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that CPR and DPANN communities are differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy and genomic analysis identified CPR and DPANN lineages that reproducibly attach to host cells, with attachment apparently stimulating CPR bacterial growth.
+</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    3
+                                </span>
+                                <span class="badge badge-STABLE">STABLE</span>
+                            </div>
+                            <span class="badge badge-category">EXTREME_ENVIRONMENT</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Ewaste_Bioleaching_Consortium.html"
+                       class="community-card"
+                       data-id="Ewaste_Bioleaching_Consortium"
+                       data-name="e-waste bioleaching consortium"
+                       data-description="an engineered acidophilic microbial consortium adapted for recovering valuable metals from electronic waste, particularly printed circuit boards (pcbs). this consortium consists primarily of iron-oxidizing bacteria dominated by leptospirillum ferriphilum with sulfobacillus benefaciens, acidithiobacillus ferrooxidans, and acidithiobacillus thiooxidans contributing to metal solubilization. the community operates at extremely low ph (1.2 ± 0.1) and moderate temperature (35°c), oxidizing ferrous iron to generate ferric iron (fe³⁺) that dissolves base metals (copper, zinc, nickel) and mobilizes precious metals (gold, silver, palladium) from pcb components. metal recovery is exceptional: 100% copper dissolution (2.6-4.2 g/l), 100% zinc (303-543 mg/l), and 70% nickel (30-52 mg/l). however, pcb materials are toxic to the consortium, delaying the pre-oxidation phase from 11 days at 1% pcb load to 18 days at 2% load, with no growth above 8% pcb. successive subculturing adapts the consortium to pcb toxicity, reducing lag phase by 2.6-fold. this biotechnological approach offers an environmentally-friendly alternative to pyrometallurgical e-waste processing (smelting), avoiding toxic emissions while recovering critical materials including copper for electrical applications and precious metals for electronics manufacturing. the two-step process may include subsequent cyanide-producing heterotrophs (pseudomonas fluorescens, p. putida) for enhanced gold and silver extraction.
+"
+                       data-category="BIOMINING"
                        data-state="ENGINEERED"
                        data-metals="COPPER,GOLD,IRON,NICKEL,PALLADIUM,SILVER,ZINC"
                        data-ree=""
@@ -4136,6 +4513,35 @@ <h2>Infant Gut DNA Phageome Succession Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Infant_Gut_Prebiotic_Response_SynCom.html"
+                       class="community-card"
+                       data-id="Infant_Gut_Prebiotic_Response_SynCom"
+                       data-name="infant-gut prebiotic-response syncom"
+                       data-description="a defined synthetic microbial community (syncom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. human milk oligosaccharides (hmos) and galacto-oligosaccharides (gos) robustly promote bifidobacterial expansion, while bacteroides/phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. the syncom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters escherichia coli metabolic activity. competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk ph."
+                       data-category="DIET"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="4">
+                        <h2>Infant-gut Prebiotic-response SynCom</h2>
+                        <p class="description">A defined synthetic microbial community (SynCom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. Human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promote bifidobacterial expansion, while Bacteroides/Phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. The SynCom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with Phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters Escherichia coli metabolic activity. Competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk pH.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    4
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">DIET</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Infant_Gut_Strain_Persistence_Maternal_Community.html"
                        class="community-card"
                        data-id="Infant_Gut_Strain_Persistence_Maternal_Community"
@@ -5224,6 +5630,35 @@ <h2>Model Lignocellulose Formaldehyde Cross-Feeding Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html"
+                       class="community-card"
+                       data-id="Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J"
+                       data-name="multi-stage anaerobic-digestion syncom-ysj and syncom-j"
+                       data-description="two function-driven synthetic microbial communities (syncoms) constructed for bioaugmentation of food-waste anaerobic digestion. syncom-j is a methanogen-only consortium, whereas syncom-ysj is a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members. both were introduced into semi-continuous reactors already harboring a metabolically complete native microbiome. the multi-stage syncom-ysj increased methane yield by 22% (vs 8% for syncom-j), nearly eliminated the start-up lag phase, reduced propionate accumulation, and reshaped the digester microenvironment (elevated acetate, reduced propionate), upregulating genes for hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. individual member species are not named in the source abstract, so no ncbitaxon-grounded members are asserted here."
+                       data-category="METHANOGENESIS"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="0">
+                        <h2>Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J</h2>
+                        <p class="description">Two function-driven synthetic microbial communities (SynComs) constructed for bioaugmentation of food-waste anaerobic digestion. SynCom-J is a methanogen-only consortium, whereas SynCom-YSJ is a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members. Both were introduced into semi-continuous reactors already harboring a metabolically complete native microbiome. The multi-stage SynCom-YSJ increased methane yield by 22% (vs 8% for SynCom-J), nearly eliminated the start-up lag phase, reduced propionate accumulation, and reshaped the digester microenvironment (elevated acetate, reduced propionate), upregulating genes for hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Individual member species are not named in the source abstract, so no NCBITaxon-grounded members are asserted here.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    0
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">METHANOGENESIS</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Multiomics_Corn_Straw_Degradation_SynCom.html"
                        class="community-card"
                        data-id="Multiomics_Corn_Straw_Degradation_SynCom"
@@ -5739,6 +6174,35 @@ <h2>Panzhihua Vanadium Titanium Tailings Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html"
+                       class="community-card"
+                       data-id="Parachlorella_Saccharomyces_Mutualistic_Coculture"
+                       data-name="parachlorella kessleri + saccharomyces cerevisiae mutualistic co-culture"
+                       data-description="two-member engineered co-culture of the green microalga parachlorella kessleri and the yeast saccharomyces cerevisiae, established to enhance microalgal lipid productivity. the partners form a mutualistic relationship based on reciprocal oxygen/carbon dioxide gas exchange. under co-culture, biomass and lipid production increased 4-fold relative to microalgal monoculture. yeast sustained microalgal growth during the transition to phototrophy after glucose depletion and promoted lipid accumulation through nutrient competition, while microalgae are inferred to provide metabolic support to the yeast via exopolysaccharide (eps)-derived molecules. nanomechanical analyses (afm, fluidfm) showed increased eps production and stronger, longer microalga-yeast cell-cell interactions in co-culture."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture</h2>
+                        <p class="description">Two-member engineered co-culture of the green microalga Parachlorella kessleri and the yeast Saccharomyces cerevisiae, established to enhance microalgal lipid productivity. The partners form a mutualistic relationship based on reciprocal oxygen/carbon dioxide gas exchange. Under co-culture, biomass and lipid production increased 4-fold relative to microalgal monoculture. Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion and promoted lipid accumulation through nutrient competition, while microalgae are inferred to provide metabolic support to the yeast via exopolysaccharide (EPS)-derived molecules. Nanomechanical analyses (AFM, FluidFM) showed increased EPS production and stronger, longer microalga-yeast cell-cell interactions in co-culture.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Peanut_Seed_Bacterial_CS_SynCom.html"
                        class="community-card"
                        data-id="Peanut_Seed_Bacterial_CS_SynCom"
@@ -5950,6 +6414,35 @@ <h2>Phormidium Alkaline Consortium</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.html"
+                       class="community-card"
+                       data-id="Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture"
+                       data-name="phosphitivorax-methanoculleus lithosyntrophic phosphite-oxidizing methanogenic culture"
+                       data-description="an anoxic, methanogenic enrichment culture defining &#34;lithosyntrophy,&#34; an obligate syntrophic interaction in which the electrons driving hydrogenotrophic methanogenesis originate from an inorganic compound. candidatus phosphitivorax anaerolimi phox-21 oxidizes phosphite (oxidation state +3) to phosphate coupled to hydrogenogenesis, in an obligate energetic dependency on a hydrogenotrophic methanogen, methanoculleus sp. electrons derived from phosphite drive h2 production via an electron-confurcating hydrogenase; the methanogen consumes the h2 to keep the reaction thermodynamically favorable, establishing interspecies electron transfer that links the phosphorus and carbon redox cycles in anoxic ecosystems."
+                       data-category="SYNTROPHY"
+                       data-state="STABLE"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture</h2>
+                        <p class="description">An anoxic, methanogenic enrichment culture defining &#34;lithosyntrophy,&#34; an obligate syntrophic interaction in which the electrons driving hydrogenotrophic methanogenesis originate from an inorganic compound. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (oxidation state +3) to phosphate coupled to hydrogenogenesis, in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase; the methanogen consumes the H2 to keep the reaction thermodynamically favorable, establishing interspecies electron transfer that links the phosphorus and carbon redox cycles in anoxic ecosystems.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-STABLE">STABLE</span>
+                            </div>
+                            <span class="badge badge-category">SYNTROPHY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Phylogenetically_Diverse_Denitrifying_SynCom.html"
                        class="community-card"
                        data-id="Phylogenetically_Diverse_Denitrifying_SynCom"
@@ -5979,6 +6472,64 @@ <h2>Phylogenetically Diverse Denitrifying SynCom</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Pinus_armandii_Endophytic_Biocontrol_SynCom.html"
+                       class="community-card"
+                       data-id="Pinus_armandii_Endophytic_Biocontrol_SynCom"
+                       data-name="pinus armandii endophytic biocontrol syncom"
+                       data-description="a five-strain synthetic bacterial community (syncom) assembled from endophytic bacteria isolated from multiple tissues of pinus armandii to promote seedling growth and prime blister rust-associated defense responses. the optimized, functionally complementary syncom comprises pseudomonas koreensis rc1, paenibacillus terrae re7, bacillus velezensis ob3 and na3, and bacillus subtilis na11, selected for plant growth-promoting traits (nitrogen fixation, phosphate and potassium solubilization, iaa production) and antagonism of the rust pathogen. in pot experiments the syncom increased seedling height and biomass and raised defense-related polyphenol oxidase and peroxidase activities relative to the control."
+                       data-category="RHIZOSPHERE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="5">
+                        <h2>Pinus armandii Endophytic Biocontrol SynCom</h2>
+                        <p class="description">A five-strain synthetic bacterial community (SynCom) assembled from endophytic bacteria isolated from multiple tissues of Pinus armandii to promote seedling growth and prime blister rust-associated defense responses. The optimized, functionally complementary SynCom comprises Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, selected for plant growth-promoting traits (nitrogen fixation, phosphate and potassium solubilization, IAA production) and antagonism of the rust pathogen. In pot experiments the SynCom increased seedling height and biomass and raised defense-related polyphenol oxidase and peroxidase activities relative to the control.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    5
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">RHIZOSPHERE</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html"
+                       class="community-card"
+                       data-id="Pleuromutilin_Degrading_Artificial_Consortium_5_Strain"
+                       data-name="pleuromutilin-degrading artificial consortium (5-strain)"
+                       data-description="a defined five-strain artificial microbial consortium constructed to degrade the antibiotic pleuromutilin, assembled from bacteria isolated out of a natural consortium (en4) that was itself developed by gradient enrichment and domestication under pleuromutilin stress. the consortium comprises stenotrophomonas pavanii, stenotrophomonas maltophilia, lysinibacillus sphaericus, lysinibacillus mangiferihumi, and pseudomonas songnenensis, and achieves a pleuromutilin degradation rate of 91.97%. in the parent natural community, pleuromutilin stress reduced microbial diversity and selected core taxa with functional specialization (notably proteobacteria, and enriched pollutant-degrading genera such as allorhizobium-neorhizobium-pararhizobium-rhizobium and cupriavidus), and potential degradation products and metabolic pathways were proposed for the artificial consortium."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="5">
+                        <h2>Pleuromutilin-degrading Artificial Consortium (5-strain)</h2>
+                        <p class="description">A defined five-strain artificial microbial consortium constructed to degrade the antibiotic pleuromutilin, assembled from bacteria isolated out of a natural consortium (En4) that was itself developed by gradient enrichment and domestication under pleuromutilin stress. The consortium comprises Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis, and achieves a pleuromutilin degradation rate of 91.97%. In the parent natural community, pleuromutilin stress reduced microbial diversity and selected core taxa with functional specialization (notably Proteobacteria, and enriched pollutant-degrading genera such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Cupriavidus), and potential degradation products and metabolic pathways were proposed for the artificial consortium.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    5
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Polaromonas_Vanadium_Reduction_Community.html"
                        class="community-card"
                        data-id="Polaromonas_Vanadium_Reduction_Community"
@@ -6223,6 +6774,64 @@ <h2>Pseudomonas-Rhodococcus Chloronitrobenzene Coculture</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html"
+                       class="community-card"
+                       data-id="Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium"
+                       data-name="pseudomonas putida pp-te + rhodococcus sp. rdk17 terephthalic-acid consortium"
+                       data-description="two-strain synthetic consortium of an engineered degrader (pseudomonas putida strain pp-te) and a native degrader (rhodococcus sp. strain rdk17) grown with terephthalic acid (tpa), a primary polyethylene terephthalate (pet) monomer, as the sole carbon and energy source. although both strains utilize tpa at comparable rates in monoculture, pp-te consistently outcompetes rdk17 in batch and multitransfer coculture fermentations. dominance is driven jointly by exploitative competition for tpa and by interference competition through the pp-te type vi secretion system, which impairs rdk17 growth via contact-dependent inhibition. loss of tpa metabolism in pp-te abolishes its dominance, illustrating how interspecies interaction and metabolic capability co-determine consortium structure and overall tpa degradation."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium</h2>
+                        <p class="description">Two-strain synthetic consortium of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) grown with terephthalic acid (TPA), a primary polyethylene terephthalate (PET) monomer, as the sole carbon and energy source. Although both strains utilize TPA at comparable rates in monoculture, Pp-TE consistently outcompetes RDK17 in batch and multitransfer coculture fermentations. Dominance is driven jointly by exploitative competition for TPA and by interference competition through the Pp-TE type VI secretion system, which impairs RDK17 growth via contact-dependent inhibition. Loss of TPA metabolism in Pp-TE abolishes its dominance, illustrating how interspecies interaction and metabolic capability co-determine consortium structure and overall TPA degradation.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html"
+                       class="community-card"
+                       data-id="Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium"
+                       data-name="pseudomonas stutzeri + rhodococcus naphthalene-degrading biochar-bridged engineered consortium"
+                       data-description="two-member engineered bioremediation consortium in which genetically engineered pseudomonas stutzeri (overexpressing nahac and nahb) and a rhodococcus strain (overexpressing nahh and cata) are co-anchored on s-n-doped biochar to mineralize naphthalene. pseudomonas stutzeri acts as an oxidative bio-anode that initiates naphthalene degradation and releases electrons, while the conductive biochar matrix mediates direct interspecies electron transfer (diet) and extracellular electron transfer (eet) to rhodococcus, which serves as a reductive bio-cathode driving oxygenolytic ring-cleavage catalysis. the resulting bioelectrochemical syntrophic circuit achieved &gt;98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium</h2>
+                        <p class="description">Two-member engineered bioremediation consortium in which genetically engineered Pseudomonas stutzeri (overexpressing nahAc and nahB) and a Rhodococcus strain (overexpressing nahH and catA) are co-anchored on S-N-doped biochar to mineralize naphthalene. Pseudomonas stutzeri acts as an oxidative bio-anode that initiates naphthalene degradation and releases electrons, while the conductive biochar matrix mediates direct interspecies electron transfer (DIET) and extracellular electron transfer (EET) to Rhodococcus, which serves as a reductive bio-cathode driving oxygenolytic ring-cleavage catalysis. The resulting bioelectrochemical syntrophic circuit achieved &gt;98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Pseudonitzschia_Sulfitobacter_Association.html"
                        class="community-card"
                        data-id="Pseudonitzschia_Sulfitobacter_Association"
@@ -6885,6 +7494,35 @@ <h2>Shewanella-Geobacter Three-Species Exoelectrogenic Biofilm Community</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.html"
+                       class="community-card"
+                       data-id="Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium"
+                       data-name="shewanella oneidensis + pseudomonas aeruginosa fe0-dependent electro-syntrophic denitrifying consortium"
+                       data-description="engineered two-member denitrifying consortium of the electroactive bacterium shewanella oneidensis and the denitrifier pseudomonas aeruginosa, operated in anaerobic conditions with metallic iron (fe0) as the sole electron donor. s. oneidensis acts as a bio-engine, using its membrane-bound cyma-omca-mtrc complexes to harvest electrons from fe0 biocorrosion and transfer them to p. aeruginosa. p. aeruginosa accepts these electrons for nitrate reduction, accomplishing microbial denitrification via a fe0-s. oneidensis-p. aeruginosa electron-transfer system. this fe0-dependent electro-syntrophy defines a metabolic window for denitrifier growth relevant to nitrate removal in water/wastewater treatment and the global nitrogen cycle."
+                       data-category="SYNTROPHY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium</h2>
+                        <p class="description">Engineered two-member denitrifying consortium of the electroactive bacterium Shewanella oneidensis and the denitrifier Pseudomonas aeruginosa, operated in anaerobic conditions with metallic iron (Fe0) as the sole electron donor. S. oneidensis acts as a bio-engine, using its membrane-bound CymA-OmcA-MtrC complexes to harvest electrons from Fe0 biocorrosion and transfer them to P. aeruginosa. P. aeruginosa accepts these electrons for nitrate reduction, accomplishing microbial denitrification via a Fe0-S. oneidensis-P. aeruginosa electron-transfer system. This Fe0-dependent electro-syntrophy defines a metabolic window for denitrifier growth relevant to nitrate removal in water/wastewater treatment and the global nitrogen cycle.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">SYNTROPHY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.html"
                        class="community-card"
                        data-id="Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell"
@@ -6916,6 +7554,35 @@ <h2>Shewanella-Streptococcus Starch-Fueled Microbial Fuel Cell Coculture</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.html"
+                       class="community-card"
+                       data-id="Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture"
+                       data-name="shewanella oneidensis mr-1 - rhodopseudomonas palustris electro-syntrophic co-culture"
+                       data-description="engineered two-species electro-syntrophic co-culture of shewanella oneidensis mr-1 (the electron-donating partner) and rhodopseudomonas palustris (the electron-accepting partner) built to study and enhance artificial interspecies electron transfer (iet). in-situ polydopamine (pda) nano-encapsulation of the s. oneidensis mr-1 surface created a conductive, adhesive cell-to-cell interface that promoted stable coaggregation of the two partners and shifted the dominant iet mode from h2-mediated miet toward contact-dependent direct electron transfer involving outer-membrane c-type cytochromes. nitrogenase-derived ch4, used as a quantitative indicator of iet efficiency, increased by roughly 380% in the engineered community."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture</h2>
+                        <p class="description">Engineered two-species electro-syntrophic co-culture of Shewanella oneidensis MR-1 (the electron-donating partner) and Rhodopseudomonas palustris (the electron-accepting partner) built to study and enhance artificial interspecies electron transfer (IET). In-situ polydopamine (PDA) nano-encapsulation of the S. oneidensis MR-1 surface created a conductive, adhesive cell-to-cell interface that promoted stable coaggregation of the two partners and shifted the dominant IET mode from H2-mediated MIET toward contact-dependent direct electron transfer involving outer-membrane c-type cytochromes. Nitrogenase-derived CH4, used as a quantitative indicator of IET efficiency, increased by roughly 380% in the engineered community.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/SkinCom_Synthetic_Skin_Community.html"
                        class="community-card"
                        data-id="SkinCom_Synthetic_Skin_Community"
@@ -7313,6 +7980,180 @@ <h2>SynComBac10 Chicken Intestinal SynCom</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html"
+                       class="community-card"
+                       data-id="SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation"
+                       data-name="syncom bsbv cigar tobacco leaf fermentation"
+                       data-description="two-species synthetic microbial community (the bsbv syncom) of bacillus safensis and bacillus velezensis, screened for high extracellular cellulase, amylase and protease activities and applied to cigar tobacco leaves (cultivar qx204) during a 42-day fermentation. the consortium accelerated degradation of cellulose, protein, and starch, shifted the leaf bacterial community toward firmicutes/bacillus, and modulated the volatile flavor metabolite profile (e.g. phenylacetic acid, phytol, farnesol) to enhance honey, floral, and baked aromas while reducing irritancy, thereby directionally improving cigar tobacco leaf quality."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>SynCom BsBv Cigar Tobacco Leaf Fermentation</h2>
+                        <p class="description">Two-species synthetic microbial community (the BsBv SynCom) of Bacillus safensis and Bacillus velezensis, screened for high extracellular cellulase, amylase and protease activities and applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation. The consortium accelerated degradation of cellulose, protein, and starch, shifted the leaf bacterial community toward Firmicutes/Bacillus, and modulated the volatile flavor metabolite profile (e.g. phenylacetic acid, phytol, farnesol) to enhance honey, floral, and baked aromas while reducing irritancy, thereby directionally improving cigar tobacco leaf quality.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.html"
+                       class="community-card"
+                       data-id="SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System"
+                       data-name="syncom + chlorella sorokiniana biogas-slurry coupling system"
+                       data-description="a sequential synthetic microbial community (syncom)-microalga coupling system engineered to treat livestock biogas slurry. an autochthonous microalga, chlorella sorokiniana, isolated from the slurry is coupled with a syncom pretreatment stage. the system operated stably for 60 days, achieving 94.41% nitrate-nitrogen removal, 81.84% total-phosphorus removal, and 6.31% chemical oxygen demand removal. syncom pretreatment increased the biomass and soluble protein content of c. sorokiniana (by 27.15% and 488.10% vs the bg11 control), upregulating rubisco and glutamine synthetase, providing a strategy for simultaneous pollutant abatement and resource recovery."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>SynCom + Chlorella sorokiniana Biogas-slurry Coupling System</h2>
+                        <p class="description">A sequential synthetic microbial community (SynCom)-microalga coupling system engineered to treat livestock biogas slurry. An autochthonous microalga, Chlorella sorokiniana, isolated from the slurry is coupled with a SynCom pretreatment stage. The system operated stably for 60 days, achieving 94.41% nitrate-nitrogen removal, 81.84% total-phosphorus removal, and 6.31% chemical oxygen demand removal. SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana (by 27.15% and 488.10% vs the BG11 control), upregulating Rubisco and glutamine synthetase, providing a strategy for simultaneous pollutant abatement and resource recovery.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html"
+                       class="community-card"
+                       data-id="SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience"
+                       data-name="syncom metg2 rhizobacteria sugarcane stress resilience"
+                       data-description="a rhizobacteria synthetic community (syncom) named metg2 inoculated onto sugarcane in a greenhouse experiment to enhance stress resilience through targeted modulation of plant-microbe interactions. shotgun metagenome and metatranscriptome sequencing revealed temporal shifts in the rhizosphere microbial community, with up-regulation of genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation (particularly within proteobacteria), indicating active microbial movement toward root surfaces, alongside enrichment of genes for nutrient acquisition, hormone synthesis, siderophore production, and voc synthesis. sugarcane responded with up-regulation of hormone-related and nutrient-transporter genes and induction of stress-resistance genes, supporting metg2 as a sustainable strategy to enhance crop productivity and resilience."
+                       data-category="RHIZOSPHERE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience</h2>
+                        <p class="description">A rhizobacteria synthetic community (SynCom) named MetG2 inoculated onto sugarcane in a greenhouse experiment to enhance stress resilience through targeted modulation of plant-microbe interactions. Shotgun metagenome and metatranscriptome sequencing revealed temporal shifts in the rhizosphere microbial community, with up-regulation of genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation (particularly within Proteobacteria), indicating active microbial movement toward root surfaces, alongside enrichment of genes for nutrient acquisition, hormone synthesis, siderophore production, and VOC synthesis. Sugarcane responded with up-regulation of hormone-related and nutrient-transporter genes and induction of stress-resistance genes, supporting MetG2 as a sustainable strategy to enhance crop productivity and resilience.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">RHIZOSPHERE</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html"
+                       class="community-card"
+                       data-id="SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation"
+                       data-name="pseudomonas-rahnella native rhizosphere syncom for artemisia argyi phytoremediation"
+                       data-description="a simplified, native rhizosphere synthetic microbial community (syncom) pairing a pseudomonas isolate with a rahnella isolate, assembled by a top-down design from rhizobacteria isolated from cadmium (cd)-contaminated agricultural soil to partner with the perennial medicinal plant artemisia argyi. the pseudomonas-rahnella pair shows strong cd tolerance (~2 mm), plant growth-promotion (pgp) traits, and carbon fixation capacity, and was chosen for functional complementarity with minimal antagonism. under cd stress the syncom establishes stable endophytic colonization (10-15%) rather than rhizoplane colonization, improving root biomass, cd uptake, soil organic carbon accumulation, and essential-oil precursors, thereby coupling phytoremediation, productivity, and carbon sequestration."
+                       data-category="BIOREMEDIATION"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation</h2>
+                        <p class="description">A simplified, native rhizosphere synthetic microbial community (SynCom) pairing a Pseudomonas isolate with a Rahnella isolate, assembled by a top-down design from rhizobacteria isolated from cadmium (Cd)-contaminated agricultural soil to partner with the perennial medicinal plant Artemisia argyi. The Pseudomonas-Rahnella pair shows strong Cd tolerance (~2 mM), plant growth-promotion (PGP) traits, and carbon fixation capacity, and was chosen for functional complementarity with minimal antagonism. Under Cd stress the SynCom establishes stable endophytic colonization (10-15%) rather than rhizoplane colonization, improving root biomass, Cd uptake, soil organic carbon accumulation, and essential-oil precursors, thereby coupling phytoremediation, productivity, and carbon sequestration.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOREMEDIATION</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html"
+                       class="community-card"
+                       data-id="SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus"
+                       data-name="sesame-flavor baijiu fuqu syncom (13-genus)"
+                       data-description="thirteen-genus synthetic microbial community (syncom) designed for fuqu, the fermentation starter used in sesame flavor-type baijiu (chinese liquor) production. multi-omics analysis identified 13 core genera - the fungal/yeast genera aspergillus, pichia, saccharomyces, trichosporon, candida, torulaspora, clavispora and wickerhamomyces and the bacterial genera bacillus, lactobacillus, leuconostoc, pediococcus and weissella - as the core microbiota driving flavor-compound formation. assembled into a syncom, these members yielded the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, and outperformed commercial fuqu at large scale. the community represents an engineered strategy to enhance sulfur-containing flavor compounds during baijiu fermentation."
+                       data-category="BIOTECHNOLOGY"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="13">
+                        <h2>Sesame-flavor Baijiu Fuqu SynCom (13-genus)</h2>
+                        <p class="description">Thirteen-genus synthetic microbial community (SynCom) designed for Fuqu, the fermentation starter used in sesame flavor-type baijiu (Chinese liquor) production. Multi-omics analysis identified 13 core genera - the fungal/yeast genera Aspergillus, Pichia, Saccharomyces, Trichosporon, Candida, Torulaspora, Clavispora and Wickerhamomyces and the bacterial genera Bacillus, Lactobacillus, Leuconostoc, Pediococcus and Weissella - as the core microbiota driving flavor-compound formation. Assembled into a SynCom, these members yielded the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, and outperformed commercial Fuqu at large scale. The community represents an engineered strategy to enhance sulfur-containing flavor compounds during baijiu fermentation.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    13
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">BIOTECHNOLOGY</span>
+                        </div>
+                    </a>
+                    
+                    <a href="communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html"
+                       class="community-card"
+                       data-id="SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture"
+                       data-name="syncom y agrobacterium-bacillus biofilm biocontrol co-culture"
+                       data-description="two-species synthetic bacterial community (syncom y) of agrobacterium deltaense lsq16 and bacillus velezensis wb, simplified from a larger biocontrol syncom q by stepwise strain omission. co-cultivation synergistically enhances multispecies biofilm formation, extracellular polysaccharide production, and metabolic activity, improving suppression of watermelon fusarium wilt. genome-scale modeling predicts interspecies metabolite exchange (amino acids, purines, phosphates); exogenous l-ornithine and guanine enhance b. velezensis biofilm formation, consistent with cross-feeding-supported cooperation."
+                       data-category="RHIZOSPHERE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="2">
+                        <h2>SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture</h2>
+                        <p class="description">Two-species synthetic bacterial community (SynCom Y) of Agrobacterium deltaense LSQ16 and Bacillus velezensis WB, simplified from a larger biocontrol SynCom Q by stepwise strain omission. Co-cultivation synergistically enhances multispecies biofilm formation, extracellular polysaccharide production, and metabolic activity, improving suppression of watermelon Fusarium wilt. Genome-scale modeling predicts interspecies metabolite exchange (amino acids, purines, phosphates); exogenous L-ornithine and guanine enhance B. velezensis biofilm formation, consistent with cross-feeding-supported cooperation.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    2
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">RHIZOSPHERE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html"
                        class="community-card"
                        data-id="Synechococcus_Azotobacter_Photoproduction_Mutualism"
@@ -7960,6 +8801,35 @@ <h2>Thermacetogenium-Methanothermobacter Acetate Oxidation Coculture</h2>
                         </div>
                     </a>
                     
+                    <a href="communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html"
+                       class="community-card"
+                       data-id="Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization"
+                       data-name="thermophilic lignocellulose-degrading composting syncom"
+                       data-description="a five-member thermophilic lignocellulose-degrading synthetic microbial community (syncom) designed for manure composting, comprising the bacteria bacillus cereus, achromobacter sp., and pseudomonas sp. together with the fungi cladosporium sp. and trichoderma harzianum. inoculation drives a metabolic reprogramming from a biofilm-dependent defense-survival mode toward an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), which restricts horizontal gene transfer opportunities. by intensifying thermophilic fermentation, lowering the carbon/nitrogen ratio, and enhancing humification, the syncom attenuates antibiotic resistance genes and virulence factors, collapses high-risk arg-mobilome interactomes, and achieves deep bio-sanitization by eliminating high-risk pathogens such as pseudomonas aeruginosa."
+                       data-category="LIGNOCELLULOSE"
+                       data-state="ENGINEERED"
+                       data-metals=""
+                       data-ree=""
+                       data-relevance="NOT_APPLICABLE"
+                       data-member-count="5">
+                        <h2>Thermophilic Lignocellulose-degrading Composting SynCom</h2>
+                        <p class="description">A five-member thermophilic lignocellulose-degrading synthetic microbial community (SynCom) designed for manure composting, comprising the bacteria Bacillus cereus, Achromobacter sp., and Pseudomonas sp. together with the fungi Cladosporium sp. and Trichoderma harzianum. Inoculation drives a metabolic reprogramming from a biofilm-dependent defense-survival mode toward an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), which restricts horizontal gene transfer opportunities. By intensifying thermophilic fermentation, lowering the carbon/nitrogen ratio, and enhancing humification, the SynCom attenuates antibiotic resistance genes and virulence factors, collapses high-risk ARG-mobilome interactomes, and achieves deep bio-sanitization by eliminating high-risk pathogens such as Pseudomonas aeruginosa.</p>
+                        <div class="card-footer">
+                            <div class="card-footer-left">
+                                <span class="badge badge-member-count" title="Number of member taxa">
+                                    <svg width="12" height="12" viewBox="0 0 12 12" style="vertical-align: middle; margin-right: 3px;">
+                                        <circle cx="6" cy="3" r="2" fill="currentColor"/>
+                                        <circle cx="3" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                        <circle cx="9" cy="8" r="1.5" fill="currentColor" opacity="0.7"/>
+                                    </svg>
+                                    5
+                                </span>
+                                <span class="badge badge-ENGINEERED">ENGINEERED</span>
+                            </div>
+                            <span class="badge badge-category">LIGNOCELLULOSE</span>
+                        </div>
+                    </a>
+                    
                     <a href="communities/Thermophilic_Pyrite_QS_Consortium.html"
                        class="community-card"
                        data-id="Thermophilic_Pyrite_QS_Consortium"
diff --git a/docs/communities/AMD_Acidophile_Heterotroph_Network.html b/docs/communities/AMD_Acidophile_Heterotroph_Network.html
index 523c53fc..d8db4a06 100644
--- a/docs/communities/AMD_Acidophile_Heterotroph_Network.html
+++ b/docs/communities/AMD_Acidophile_Heterotroph_Network.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>AMD Acidophile Heterotroph Network</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000001</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000001</code>
                     </span>
                 </div>
 
@@ -849,12 +851,6 @@ <h3>Organic Carbon Scavenging and Remineralization</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         aerobic respiration
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0009060"
@@ -946,12 +942,6 @@ <h3>Ferric Iron Reduction and Ferrous Iron Regeneration</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1048,12 +1038,6 @@ <h3>Heterotrophic Iron Oxidation by Ferrimicrobium</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1236,12 +1220,6 @@ <h3>Photoheterotrophic Carbon Cycling</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
                     </li>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1310,12 +1288,6 @@ <h3>Complex Polysaccharide Degradation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0000272</a>)
                     </li>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1668,8 +1640,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("aerobic respiration");
             
             processes.push("nitrogen compound metabolic process");
@@ -1720,8 +1690,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("anaerobic respiration");
@@ -1770,8 +1738,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("heterotrophy");
@@ -1870,8 +1836,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("photosynthesis");
             
-            processes.push("organic substance catabolic process");
-            
             
             var evidenceCount = 1;
 
@@ -1918,8 +1882,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("polysaccharide catabolic process");
             
-            processes.push("organic substance catabolic process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/AMD_Nitrososphaerota_Archaeal.html b/docs/communities/AMD_Nitrososphaerota_Archaeal.html
index 077b1750..c5d4f723 100644
--- a/docs/communities/AMD_Nitrososphaerota_Archaeal.html
+++ b/docs/communities/AMD_Nitrososphaerota_Archaeal.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>AMD Nitrososphaerota Archaeal Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000002</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000002</code>
                     </span>
                 </div>
 
@@ -873,8 +875,8 @@ <h3>Nitrite Oxidation to Nitrate by Nitrospira</h3>
                     
                     <li>
                         nitrite oxidoreductase activity
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0050151"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0050151</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0016661"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0016661</a>)
                     </li>
                     
                 </ul>
@@ -954,23 +956,6 @@ <h3>Organic Matter Detoxification by Ferroplasma</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1578,12 +1563,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html b/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html
new file mode 100644
index 00000000..c44b61d4
--- /dev/null
+++ b/docs/communities/ANME_SRB_Anaerobic_Methanotrophic_Syntrophic_Consortia.html
@@ -0,0 +1,1385 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
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+        h1 {
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+            font-size: 2rem;
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+        h2 {
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+            margin: 2rem 0 1rem;
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+
+        h3 {
+            color: var(--text);
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+            margin: 1.5rem 0 0.75rem;
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+        .metadata {
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+            border-radius: 8px;
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+        .metadata-grid {
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+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
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+        .metadata-item {
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+        .badge {
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+            border-radius: 8px;
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+            border: 1px solid var(--border);
+            margin: 1rem 0;
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+
+        th, td {
+            padding: 0.75rem 1rem;
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+        th {
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+            font-weight: 600;
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+        tr:not(:last-child) td {
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+        .term-link {
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+            text-decoration: none;
+            font-family: 'Courier New', monospace;
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+        .term-link:hover {
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+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
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+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
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+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
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+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
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+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
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+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
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+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
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+            pointer-events: none;
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+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
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+
+        .network-tooltip strong {
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+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000276</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-natural">
+                            STABLE
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        marine sediment
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_03000033"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:03000033
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Marine syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. Sediment-free enrichment cultures of three consortium types (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2) exhibited high dry conductance close to that of electrogenic biofilms. Cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>ANME-1 (anaerobic methanotrophic archaea, clade 1)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=588814"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:588814
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Desulfofervidus (sulfate-reducing bacterial partner of ANME-1)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1902583"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1902583
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>ANME-2a (anaerobic methanotrophic archaea, clade 2a)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=588816"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:588816
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>ANME-2c (anaerobic methanotrophic archaea, clade 2c)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3386252"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:3386252
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Seep-SRB1 (sulfate-reducing bacterial partner of ANME-2a)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=213119"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:213119
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Seep-SRB2 (additional sulfate-reducing bacterial partner)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=213118"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:213118
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Cyclic voltammetry revealed redox activity centered at 28 ± 11, 94 ± 6, and 24 ± 7 millivolts for ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2 consortia, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>ANME-1/Desulfofervidus syntrophy via direct interspecies electron transport</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> ANME-1</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Desulfofervidus</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) form syntrophic partnerships in marine sediments to consume greenhouse gas methane."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Collectively, our results establish that marine ANME/SRB symbiosis uses redox conduction, consistent with multiheme cytochrome c, for direct interspecies electron transport."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>ANME-2a/Seep-SRB1 syntrophy via direct interspecies electron transport</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> ANME-2a</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Seep-SRB1</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Generator-collector measurements further demonstrated that these redox components facilitate electron transport over micrometer-scale distances, sufficient to link archaeal and bacterial partners."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>ANME-2a+2c/Seep-SRB1+2 syntrophy via direct interspecies electron transport</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> ANME-2c</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Seep-SRB2</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/40845095/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40845095</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Diverse ANME/SRB consortia exhibited high dry conductance close to electrogenic biofilms."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    anoxic artificial seawater medium (defined HEPES-buffered marine mineral medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">7.3</span>
+                    </div>
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Per liter Milli-Q water: 5.67 g MgCl2·6H2O, 0.22 g CaCl2·2H2O, 26.37 g NaCl, 0.6 g KCl, 1.5 g Na2SO4, 0.174 g K2HPO4, 0.107 g NH4Cl, 25 mM HEPES; trace elements added, no vitamins. ANME-1/Desulfofervidus grown at 50°C, ANME-2a/Seep-SRB1 at 10°C, ANME-2a+2c/Seep-SRB1+2 at 20°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40845095"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40845095
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"grown at 50°C, ANME-2a partnered with Seep-SRB1 (ANME-2a/Seep-SRB1 consortia) grown at 10°C, and ANME-2a and ANME-2c partnered with Seep-SRB1 and Seep-SRB2 grown at 20°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40845095"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40845095
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the pH of the medium was adjusted to 7.3, filter sterilized through a 0.22-μm filter, and sparged anoxic using N 2 gas for at least 20 min"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["ANME-1 (anaerobic methanotrophic archaea, clade 1)"] = {
+            id: "NCBITaxon:588814",
+            label: "ANME-1 (anaerobic methanotrophic archaea, clade 1)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_DONOR"]
+        };
+        
+        taxonData["Desulfofervidus (sulfate-reducing bacterial partner of ANME-1)"] = {
+            id: "NCBITaxon:1902583",
+            label: "Desulfofervidus (sulfate-reducing bacterial partner of ANME-1)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_ACCEPTOR"]
+        };
+        
+        taxonData["ANME-2a (anaerobic methanotrophic archaea, clade 2a)"] = {
+            id: "NCBITaxon:588816",
+            label: "ANME-2a (anaerobic methanotrophic archaea, clade 2a)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_DONOR"]
+        };
+        
+        taxonData["ANME-2c (anaerobic methanotrophic archaea, clade 2c)"] = {
+            id: "NCBITaxon:3386252",
+            label: "ANME-2c (anaerobic methanotrophic archaea, clade 2c)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_DONOR"]
+        };
+        
+        taxonData["Seep-SRB1 (sulfate-reducing bacterial partner of ANME-2a)"] = {
+            id: "NCBITaxon:213119",
+            label: "Seep-SRB1 (sulfate-reducing bacterial partner of ANME-2a)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_ACCEPTOR"]
+        };
+        
+        taxonData["Seep-SRB2 (additional sulfate-reducing bacterial partner)"] = {
+            id: "NCBITaxon:213118",
+            label: "Seep-SRB2 (additional sulfate-reducing bacterial partner)",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_ACCEPTOR"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "ANME-1/Desulfofervidus syntrophy via direct interspecies electron transport",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "ANME-1";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Desulfofervidus";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "ANME-2a/Seep-SRB1 syntrophy via direct interspecies electron transport",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "ANME-2a";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Seep-SRB1";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "ANME-2a+2c/Seep-SRB1+2 syntrophy via direct interspecies electron transport",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "ANME-2c";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Seep-SRB2";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 9;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html b/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html
index cd56beb4..3cc78f74 100644
--- a/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html
+++ b/docs/communities/ANME_SRB_Marine_Methane_Seep_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>ANME-SRB Marine Methane Seep Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000134</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000134</code>
                     </span>
                 </div>
 
@@ -835,6 +837,166 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Anaerobic artificial seawater sediment/rock microcosm (methane seep AOM incubation)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">variable by sample (4, 24, or 50 degrees C) °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>methane</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>sulfate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>pyruvate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Samples were stored under an N2 atmosphere at 4°C prior to microcosm incubation. ANME-SRB consortia were incubated in (anaerobic) artificial seawater; sediment horizons received CH4 plus 250 μM L-Homopropargylglycine (HPG) at 4°C, and metabolic activity was confirmed by sulfide accumulation and BONCAT/HPG incorporation. Rock and push-core variants were incubated with CH4 (50°C), with pyruvate (24°C), or without added electron donor (24°C). Single active ANME:SRB aggregates were subsequently FACS-sorted for metagenomics.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37747940"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37747940
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"was incubated in anaerobic artificial sea water without electron donor at 24°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37747940"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37747940
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"artificial sea water supplemented with pyruvate at 24°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37747940"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37747940
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"250 μM L-Homopropargylglycine (HPG) at 4°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37747940"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37747940
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"atmosphere at 4°C for sediment microcosm incubations"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37747940"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37747940
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Push-core samples of seafloor sediment were collected from different locations on the Costa Rica margin"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Aalborg_East_Full_Scale_EBPR_Community.html b/docs/communities/Aalborg_East_Full_Scale_EBPR_Community.html
index b59e6471..ed1d29d2 100644
--- a/docs/communities/Aalborg_East_Full_Scale_EBPR_Community.html
+++ b/docs/communities/Aalborg_East_Full_Scale_EBPR_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Aalborg East Full-Scale EBPR Activated Sludge Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000139</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000139</code>
                     </span>
                 </div>
 
@@ -761,17 +763,6 @@ <h3>Flanking-Community Substrate Provision To PAOs</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -984,6 +975,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    domestic wastewater (full-scale EBPR activated sludge)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Municipal EBPR plant fed mainly domestic wastewater; influent phosphorus 10-20 mg P/L with &gt;95% removal and effluent below 0.5 mg P/L. No incubation temperature, pH, or defined atmosphere reported for this full-scale in situ community.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/22170425"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:22170425
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Activated sludge was taken from the aeration tank at Aalborg East WWTP, Denmark (57.044565° N, 10.047598° E) on 4 August 2009."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/22170425"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:22170425
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The plant had stable EBPR performance for several years prior to the time of sampling removing &gt;95% of the incoming P (10-20 mg P l-1) resulting in effluent concentrations below 0.5 mg P l-1."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1110,10 +1164,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.html b/docs/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.html
index 906c5d50..b185811e 100644
--- a/docs/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.html
+++ b/docs/communities/Acetobacterium_Clostridium_CO2_Electrolysis_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Acetobacterium woodii-Clostridium drakei CO2 Electrolysis Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000173</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000173</code>
                     </span>
                 </div>
 
@@ -1126,7 +1128,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Mineral medium details are not curated here; the source-backed conditions are CO2/H2 supply, anaerobic cultivation, and comparison of in situ electrolysis with direct H2 sparging.
                 </p>
                 
diff --git a/docs/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.html b/docs/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.html
index fde9c29d..cb6167fe 100644
--- a/docs/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.html
+++ b/docs/communities/Acetylene_Fueled_TCE_Dechlorination_Groundwater_Enrichment.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Acetylene-Fueled Trichloroethene Dechlorination Groundwater Enrichment</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000238</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000238</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Aerobic_Denitrification_Disturbance_SynCom.html b/docs/communities/Aerobic_Denitrification_Disturbance_SynCom.html
index ae84bd0b..5d4ba337 100644
--- a/docs/communities/Aerobic_Denitrification_Disturbance_SynCom.html
+++ b/docs/communities/Aerobic_Denitrification_Disturbance_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Aerobic Denitrification Disturbance-Stable SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000116</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000116</code>
                     </span>
                 </div>
 
@@ -702,6 +704,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified (aerobic denitrification medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Three-member aerobic denitrification synthetic microbial community cultivated under dibutyl phthalate (DBP) and levofloxacin (LOFX) disturbance treatments; medium composition, temperature and pH are not reported in the accessible (subscription-only) abstract.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40020349"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40020349
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"aerobic denitrification efficiency could be maintained at about 93 %"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40020349"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40020349
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"dibutyl phthalate (DBP) and levofloxacin (LOFX) were used as environmental disturbances"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Aerobic_Denitrification_QQ_SynCom.html b/docs/communities/Aerobic_Denitrification_QQ_SynCom.html
index 8f29aa71..08bd5ed5 100644
--- a/docs/communities/Aerobic_Denitrification_QQ_SynCom.html
+++ b/docs/communities/Aerobic_Denitrification_QQ_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Aerobic Denitrification Quorum-Quenching SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000115</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000115</code>
                     </span>
                 </div>
 
@@ -702,6 +704,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    nitrate wastewater (aerobic denitrification medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Synthetic microbial community cultivated under aerobic conditions for aerobic denitrification of nitrate wastewater. Medium composition, temperature, and pH are not reported in the accessible (paywalled) abstract.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38277828"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38277828
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the application of aerobic denitrification technology in wastewater treatment"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.html b/docs/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.html
index a0b5adf6..114904d1 100644
--- a/docs/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.html
+++ b/docs/communities/Alaska_Tundra_Permafrost_Iron_Redox_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Alaska Tundra Permafrost Iron-Redox Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000262</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000262</code>
                     </span>
                 </div>
 
@@ -661,12 +663,6 @@ <h3>Fe(III) Reduction Coupled to Organic Acid Oxidation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0006826</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -902,6 +898,66 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    wet sedge tundra organic soil thaw incubation
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">4 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Anaerobic slurry incubation under reducing conditions to mimic an extended permafrost thaw.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37996661"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37996661
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Organic soils from the tundra active-layer (0-50 cm), transition-zone (50-70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -995,8 +1051,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("iron ion transport");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
diff --git a/docs/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.html b/docs/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.html
index 7e32dffb..7057fac1 100644
--- a/docs/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.html
+++ b/docs/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Altered Schaedler Flora Gnotobiotic Mouse Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000144</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000144</code>
                     </span>
                 </div>
 
@@ -901,6 +903,100 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    brain heart infusion medium or Schaedler&#39;s medium supplemented with bovine serum
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> The eight ASF members are cultivated in vitro in complex media (BHI plus serum or Schaedler&#39;s medium plus serum); only the two lactobacilli grow aerobically, while the remaining members are obligate anaerobes, and no defined medium exists for the EOS members (ASF356, 492, 500, 502). In vivo the community is maintained in gnotobiotic mice continually bred in isolator facilities.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/26323627"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:26323627
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"each of the ASF is cultivable in complex media including brain heart infusion medium or Schaedler&#39;s medium supplemented with bovine serum"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/26323627"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:26323627
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"consisted of eight anaerobic bacteria of which only the two lactobacilli could grow aerobically"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/26323627"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:26323627
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"all members of the ASF community can be cultivated in vitro (e.g., BHI plus serum or Schaedler&#39;s medium plus serum)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/26323627"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:26323627
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"stably passed through multiple generations (at least 15 years or more by the authors) in gnotobiotic mice continually bred in isolator facilities"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.html b/docs/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.html
index e80af653..42d21655 100644
--- a/docs/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.html
+++ b/docs/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Anammox Bioreactor DNRA Destabilization Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000244</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000244</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Anammox_Granule_Metabolic_Interaction_Community.html b/docs/communities/Anammox_Granule_Metabolic_Interaction_Community.html
index a808591f..70f7b413 100644
--- a/docs/communities/Anammox_Granule_Metabolic_Interaction_Community.html
+++ b/docs/communities/Anammox_Granule_Metabolic_Interaction_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Anammox Granule Metabolic Interaction Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000146</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000146</code>
                     </span>
                 </div>
 
@@ -1005,7 +1007,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Laboratory-scale anammox bioreactor biomass maintained as granular sludge; exact influent recipe is not asserted in this record because the curated claims focus on community metagenomics and metatranscriptomics.
                 </p>
                 
diff --git a/docs/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.html b/docs/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.html
index e00f07b1..38a5e05d 100644
--- a/docs/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.html
+++ b/docs/communities/Angelarchaeales_Thermoplasmata_CuMMO_Soil_Sediment_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Angelarchaeales Thermoplasmata CuMMO Soil and Sediment Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000234</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000234</code>
                     </span>
                 </div>
 
@@ -553,17 +555,6 @@ <h3>Archaeal CuMMO-Driven Aerobic Oxidation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -867,10 +858,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Arabidopsis_Coumarin_Root_SynCom.html b/docs/communities/Arabidopsis_Coumarin_Root_SynCom.html
index f9c0cab1..2ad9edb3 100644
--- a/docs/communities/Arabidopsis_Coumarin_Root_SynCom.html
+++ b/docs/communities/Arabidopsis_Coumarin_Root_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Arabidopsis Coumarin Root SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000094</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000094</code>
                     </span>
                 </div>
 
@@ -618,6 +620,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    quarter-strength tryptic soy broth (root-isolate SynCom inoculum); hydroponic Murashige and Skoog medium for the Arabidopsis host
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom strains were grown to saturation in quarter-strength tryptic soy broth and washed with phosphate-buffered saline before root inoculation; the Arabidopsis host was grown hydroponically, with the medium around 13-day-old seedlings inoculated with the SynCom and the root community profiled at 20 days; iron-deficient Murashige and Skoog media were used to test the coumarin-dependent community shift.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31152139"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31152139
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All SynCom strains were grown to saturation in quarter-strength tryptic soy broth and washed with phosphate-buffered saline before root inoculation."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31152139"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31152139
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The media surrounding hydroponically grown 13-d-old A. thaliana seedlings was inoculated with a 22-member SynCom"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Arabidopsis_Phyllosphere_SynCom7.html b/docs/communities/Arabidopsis_Phyllosphere_SynCom7.html
index aee1d3d5..cf93a158 100644
--- a/docs/communities/Arabidopsis_Phyllosphere_SynCom7.html
+++ b/docs/communities/Arabidopsis_Phyllosphere_SynCom7.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Arabidopsis Phyllosphere SynCom7</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000093</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000093</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Arabidopsis Phyllosphere SynCom7</h1>
                     <span class="metadata-value">
                         phyllosphere
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001442"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001001"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:01001442
+                            ENVO:01001001
                         </a>
                     </span>
                 </div>
@@ -618,6 +620,100 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    nutrient broth (NB) / mineral salt medium (seven-strain phyllosphere SynCom); half-strength MS medium for the gnotobiotic Arabidopsis host
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Bacterial members grown on nutrient broth (both Methylobacterium strains on mineral salt medium with 0.5% succinate) at 28°C for one to three days, washed and resuspended in 10 mM MgCl2, adjusted to OD600 0.2, mixed 1:1 across the seven strains and diluted to OD600 0.02 for spray inoculation; the Arabidopsis host was cultivated on half-strength MS nutrient medium with vitamins, 0.55% plant agar and 1% sucrose, with seeds stratified for 3 days at 4°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24743269"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24743269
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Strains were grown at 28°C for three days (both Methylobacterium strains), two days (Rhodococcus sp., Variovorax sp., Arthrobacter sp. and S. phyllosphaerae), or one day (Sphingomonas sp. Fr1)."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24743269"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24743269
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All other strains were grown on nutrient broth (NB) without additional NaCl"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24743269"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24743269
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Plants were grown under short-day conditions (a 9-h photoperiod) in a standard growth chamber, as previously described."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24743269"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24743269
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"This solution was then diluted to an OD600 of 0.02."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.html b/docs/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.html
index ab56ea55..11e1028c 100644
--- a/docs/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.html
+++ b/docs/communities/Asgard_Wetland_Soil_Methanogenesis_Substrate_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Asgard Archaea Wetland Soil Methanogenesis-Substrate Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000219</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000219</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/At_RSPHERE_SynCom.html b/docs/communities/At_RSPHERE_SynCom.html
index b7388403..c3cd8ab7 100644
--- a/docs/communities/At_RSPHERE_SynCom.html
+++ b/docs/communities/At_RSPHERE_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>At-RSPHERE SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000003</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000003</code>
                     </span>
                 </div>
 
@@ -1001,12 +1003,6 @@ <h3>Organic Matter Degradation and Nutrient Cycling</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
-                    </li>
-                    
                     <li>
                         plant-bacterium mutualism
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0044403"
@@ -1264,7 +1260,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Low-nutrient medium used for isolation and maintenance of soil and rhizosphere bacteria from Arabidopsis roots. R2A supports slow-growing oligotrophic bacteria common in soil environments.
 
                 </p>
@@ -1381,7 +1377,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Gnotobiotic plant growth system with 0.5× MS medium supplemented with 1% sucrose and 0.8% agar. Seeds surface-sterilized prior to inoculation. Plates oriented vertically to allow root observation and bacterial colonization tracking.
 
                 </p>
@@ -1674,8 +1670,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("organic substance metabolic process");
-            
             processes.push("plant-bacterium mutualism");
             
             
diff --git a/docs/communities/Australian_Lead_Zinc_Polymetallic.html b/docs/communities/Australian_Lead_Zinc_Polymetallic.html
index 34bde90b..14a2956c 100644
--- a/docs/communities/Australian_Lead_Zinc_Polymetallic.html
+++ b/docs/communities/Australian_Lead_Zinc_Polymetallic.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Australian Lead Zinc Polymetallic Tailings Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000004</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000004</code>
                     </span>
                 </div>
 
@@ -834,12 +836,12 @@ <h3>Lead and Zinc Mobilization from Sulfide Minerals</h3>
                 <p><strong>Metabolites:</strong>
                     
                     galena
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=82328"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:82328</a>), 
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=46718"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:46718</a>), 
                     
                     sphalerite
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=82332"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:82332</a>), 
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=46718"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:46718</a>), 
                     
                     Fe(III)
                     (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=29034"
@@ -864,12 +866,6 @@ <h3>Lead and Zinc Mobilization from Sulfide Minerals</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -966,12 +962,6 @@ <h3>Stratified Iron Redox Cycling</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1159,12 +1149,6 @@ <h3>Copper Mobilization and Toxicity Interactions</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0046688</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1240,12 +1224,6 @@ <h3>Thermophilic Bioleaching in Solar-Heated Microniches</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1324,23 +1302,6 @@ <h3>Heterotrophic Carbon Scavenging and Iron Reduction</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1854,8 +1815,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("response to metal ion");
@@ -1904,8 +1863,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("dissimilatory iron reduction");
@@ -2002,8 +1959,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("response to copper ion");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
@@ -2043,8 +1998,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -2090,12 +2043,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.html b/docs/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.html
index 4e42c661..bc748707 100644
--- a/docs/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.html
+++ b/docs/communities/Avena_Rhizosphere_CrossKingdom_SIP_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Avena Rhizosphere Cross-Kingdom 13C-SIP Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000236</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000236</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.html b/docs/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.html
index 45964af1..81b81095 100644
--- a/docs/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.html
+++ b/docs/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds</
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000245</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000245</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.html b/docs/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.html
new file mode 100644
index 00000000..1998e55d
--- /dev/null
+++ b/docs/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.html
@@ -0,0 +1,1150 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia) - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
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+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia)</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000284</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        black soldier fly larvae gut (gnotobiotic host)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001033"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001033
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A tripartite synthetic microbial community (SynCom) engineered from the core gut microbiota of black soldier fly larvae (BSFL) to enhance protein bioconversion from organic wastes. The SynCom combines the bacteria Bacillus and Lactobacillus with the yeast Issatchenkia and was assembled and tested in germ-free (gnotobiotic) larval hosts using multi-omics. Bacillus provides direct proteolytic activity, whereas Lactobacillus and Issatchenkia are associated with improved protein-conversion performance and amino-acid metabolic responses. The tripartite SynCom showed the highest protein conversion performance and distinct spatiotemporal distribution along the gut pH gradient, increasing final larval protein content by 63%.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1386"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1386
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42167379/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42167379</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"Bacillus showed direct proteolytic activity, whereas Lactobacillus and Issatchenkia were associated with improved protein conversion performance in the tested SynCom."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Lactobacillus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1578"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1578
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42167379/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42167379</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"We identified the bacteria Bacillus and Lactobacillus and the yeast Issatchenkia functionally relevant taxa associated with improved host protein conversion and amino-acid metabolic responses under the tested gnotobiotic conditions."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Issatchenkia (yeast)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4919"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4919
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42167379/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42167379</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"We identified the bacteria Bacillus and Lactobacillus and the yeast Issatchenkia functionally relevant taxa associated with improved host protein conversion and amino-acid metabolic responses under the tested gnotobiotic conditions."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia)</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Spatiotemporal niche partitioning along the gut pH gradient</h3>
+                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42167379/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42167379</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"a tripartite SynCom comprising these taxa showed the highest protein conversion performance and was associated with distinct spatiotemporal distribution patterns along the gut pH gradient, increasing final larval protein content by 63%."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Proteolysis-driven division of labor for protein conversion</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42167379/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42167379</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"Bacillus showed direct proteolytic activity, whereas Lactobacillus and Issatchenkia were associated with improved protein conversion performance in the tested SynCom."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Gnotobiotic BSFL host reared on organic-waste feedstock
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>chicken manure</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>kitchen waste</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> In-vivo cultivation of the SynCom in germ-free (gnotobiotic) black soldier fly larvae under controlled conditions; the larvae were reared on organic-waste feedstocks (chicken manure and kitchen waste). No defined medium composition, temperature, pH value, atmosphere, incubation time, or shaking is reported in the accessible source (full text paywalled in Bioresource Technology; abstract only). The larval gut presents a spatial pH gradient along which the SynCom members show distinct spatiotemporal distribution.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42167379"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42167379
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"employed multi-omics and synthetic microbial communities (SynCom) in germ-free models to examine microbiota-associated protein conversion under controlled conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42167379"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42167379
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"when applied to chicken manure and kitchen waste, the SynCom-BSFL system showed improvements in selected performance metrics"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42167379"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42167379
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"distinct spatiotemporal distribution patterns along the gut pH gradient"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Bacillus"] = {
+            id: "NCBITaxon:1386",
+            label: "Bacillus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Lactobacillus"] = {
+            id: "NCBITaxon:1578",
+            label: "Lactobacillus",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+        taxonData["Issatchenkia (yeast)"] = {
+            id: "NCBITaxon:4919",
+            label: "Issatchenkia (yeast)",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "NICHE_PARTITIONING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Spatiotemporal niche partitioning along the gut pH gradient",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Proteolysis-driven division of labor for protein conversion",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.html b/docs/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.html
index 77cd7eac..6bb9ef80 100644
--- a/docs/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.html
+++ b/docs/communities/Bacillus_Bradyrhizobium_Straw_Humification_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Bacillus-Bradyrhizobium Straw Humification SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000120</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000120</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.html b/docs/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.html
index 42156c98..401b9588 100644
--- a/docs/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.html
+++ b/docs/communities/Bacteroides_Eubacterium_Gnotobiotic_Gut_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Bacteroides-Eubacterium Gnotobiotic Gut Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000158</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000158</code>
                     </span>
                 </div>
 
@@ -955,6 +957,56 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    gnotobiotic mouse gut (standard chow diet rich in complex plant polysaccharides)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Germ-free mice were colonized by gavage with single strains (monoassociation) or both strains (biassociation) and fed a standard chow diet rich in complex plant polysaccharides; ceca were sampled 10 to 14 days after inoculation, when both species had colonized to high levels. Detailed in-vitro bacterial culture conditions are reported only in the paper&#39;s SI Methods.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/19321416"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:19321416
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Ten to fourteen days after inoculation by gavage, both species colonized the ceca of recipient mice, fed a standard chow diet rich in complex plant polysaccharides, to high levels"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.html b/docs/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.html
index 76c7e85f..46622864 100644
--- a/docs/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.html
+++ b/docs/communities/Bacteroides_Methanobrevibacter_Gnotobiotic_Mouse_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Bacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000142</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000142</code>
                     </span>
                 </div>
 
@@ -893,6 +895,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    gnotobiotic mouse gut (autoclaved polysaccharide-rich chow diet)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> NMRI/KI germ-free mice were housed in gnotobiotic isolators on a strict 12-h light cycle and fed a standard autoclaved polysaccharide-rich chow diet ad libitum; each mouse was colonized by a single gavage of 10^8 microbes per strain, with B. thetaiotaomicron harvested from overnight stationary-phase cultures, D. piger from 4-day cultures and M. smithii from serum bottles after a 5-day incubation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/16782812"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:16782812
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"they were maintained on a strict 12-h light cycle (lights on at 0600 h) and fed a standard autoclaved polysaccharide-rich chow diet"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/16782812"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:16782812
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each mouse was inoculated with a single gavage with 10"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Banana_Fusarium_Biocontrol_SynCom12.html b/docs/communities/Banana_Fusarium_Biocontrol_SynCom12.html
index bf8b1935..8f4efba0 100644
--- a/docs/communities/Banana_Fusarium_Biocontrol_SynCom12.html
+++ b/docs/communities/Banana_Fusarium_Biocontrol_SynCom12.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Banana Fusarium Wilt Biocontrol SynCom1.2</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000097</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000097</code>
                     </span>
                 </div>
 
@@ -702,6 +704,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    LB broth (Luria-Bertani)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">27 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Bacterial SynCom members (Pseudomonas chlororaphis subsp. piscium PS5 and Bacillus velezensis BN8.2) were grown in LB broth, then centrifuged and washed with sterile distilled water before use. Isolates were originally recovered on genus-selective agar media (King&#39;s B for Pseudomonas, nutrient agar for Bacillus, starch-casein-KNO3 agar for Streptomyces, and Trichoderma harzianum-selective medium for Trichoderma) with 7 days incubation at 27°C. The three SynCom 1.2 members were applied to soil non-simultaneously to reduce cross-inhibition.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35992653"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35992653
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Pseudomonas spp. and Bacillus spp. isolates were grown in 50 mL tubes containing 20 mL LB broth and incubated at 27°C at 250 rpm for 3 days."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35992653"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35992653
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"After 7 days of incubation at 27°C"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Bay_Area_Sewage_SARS_CoV2_Surveillance_Community.html b/docs/communities/Bay_Area_Sewage_SARS_CoV2_Surveillance_Community.html
index 962f7246..8778c013 100644
--- a/docs/communities/Bay_Area_Sewage_SARS_CoV2_Surveillance_Community.html
+++ b/docs/communities/Bay_Area_Sewage_SARS_CoV2_Surveillance_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>San Francisco Bay Area Sewage SARS-CoV-2 Metagenomic Surveillance Community<
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000249</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000249</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Bayan_Obo_REE_Tailings_Consortium.html b/docs/communities/Bayan_Obo_REE_Tailings_Consortium.html
index 718c0341..afab3a57 100644
--- a/docs/communities/Bayan_Obo_REE_Tailings_Consortium.html
+++ b/docs/communities/Bayan_Obo_REE_Tailings_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Bayan Obo REE Tailings Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000005</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000005</code>
                     </span>
                 </div>
 
@@ -475,7 +477,7 @@ <h2>Taxonomy</h2>
                                     <a href="https://doi.org/10.1016/j.cej.2024.153492"
                                        class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.cej.2024.153492</a>
                                     
-                                    - WRONG_STATEMENT (IN_VITRO)
+                                    - SUPPORT (IN_VITRO)
                                     
                                     <div class="snippet">"acid bioleaching functional bacteria consortium"</div>
                                     
@@ -652,12 +654,6 @@ <h3>Sulfuric Acid Generation and pH Reduction</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -875,7 +871,7 @@ <h4>Evidence</h4>
                             <a href="https://doi.org/10.1016/j.cej.2024.153492"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.cej.2024.153492</a>
                             
-                            - WRONG_STATEMENT (IN_VITRO)
+                            - SUPPORT (IN_VITRO)
                         </div>
                         
                         <div class="snippet">"rare earth elements in Bayan Obo RERT could be high-efficiently bioleached by acid bioleaching functional bacteria consortium"</div>
@@ -1300,8 +1296,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
diff --git a/docs/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.html b/docs/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.html
index 5c3792d3..db6f0a52 100644
--- a/docs/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.html
+++ b/docs/communities/Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Bifidobacterium-Ruminococcus Infant HMO Cross-Feeding Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000220</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000220</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis.html b/docs/communities/BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis.html
index 5f947555..73dc1cd2 100644
--- a/docs/communities/BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis.html
+++ b/docs/communities/BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL1806250003 Spittlebug Sulcia-Sodalis Symbiosis</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000006</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000006</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia.html b/docs/communities/BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia.html
index c86b9155..92c5ec02 100644
--- a/docs/communities/BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia.html
+++ b/docs/communities/BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL1806250004 Sharpshooter Sulcia-Baumannia Symbiosis</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000007</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000007</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia.html b/docs/communities/BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia.html
index e0c9d567..c2e88597 100644
--- a/docs/communities/BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia.html
+++ b/docs/communities/BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL1806250005 Cicada Sulcia-Hodgkinia Symbiosis</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000008</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000008</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BioModels_MODEL2204300001_Kefir_Community_Model.html b/docs/communities/BioModels_MODEL2204300001_Kefir_Community_Model.html
index 0a36d7b9..141db9b9 100644
--- a/docs/communities/BioModels_MODEL2204300001_Kefir_Community_Model.html
+++ b/docs/communities/BioModels_MODEL2204300001_Kefir_Community_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL2204300001 Kefir Community Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000009</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000009</code>
                     </span>
                 </div>
 
@@ -1108,6 +1110,74 @@ <h2>External Resources</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    UHT-pasteurized cow milk (3.5% fat)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> All kefir milk fermentations used Ultra High Temperature pasteurized cow milk with 3.5% fat content; fermentation was initiated by adding 60 g kefir grains per liter milk and carried out static (without shaking) at 25 °C for 48 h (90 h for extended time-course runs), mimicking traditional home fermentation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/33398099"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:33398099
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All kefir milk fermentations were carried out using Ultra High Temperature pasteurized cow milk with 3.5 % fat content"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/33398099"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:33398099
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Fermentation was initiated by adding 60 g of kefir grains for one liter milk (or scaled accordingly for lower volumes). The process was carried at the 25 ˚C and without shaking for 48 h"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.html b/docs/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.html
index 4fd16623..dedbfe38 100644
--- a/docs/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.html
+++ b/docs/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL2209060002 D pigrum - S aureus Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000010</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000010</code>
                     </span>
                 </div>
 
@@ -718,6 +720,158 @@ <h2>External Resources</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    SNM3 (synthetic nasal medium, in silico)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>oxygen</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>iron</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> In silico constraint-based (FBA/FVA) medium, not a bench culture. Main medium is SNM3, a defined synthetic medium developed to mimic the human nose environment; exchange-reaction lower bounds for metabolites present in SNM3 were set to -10 mmol/(gDW*h), except -20 (oxygen) and -0.1 (iron); all other exchanges set to 0. Two additional derived media were also used - a rich medium (COMPM) and a poor medium (COOPM). No temperature, pH, or physical cultivation parameters are reported because the study is purely computational.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The main medium applied herein is SNM3"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"a unique SNM3 has been developed"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"to mimic the human nose environment"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"except oxygen and iron"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"provides both aerobic and anaerobic living conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fcimb.2022.925215"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fcimb.2022.925215
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"one medium as rich in the nutrients of the human nose and the other one as poor in the nutrients"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/BioModels_MODEL2310020001_Mouse_Metaorganism_Model.html b/docs/communities/BioModels_MODEL2310020001_Mouse_Metaorganism_Model.html
index 99c9e698..3109e11c 100644
--- a/docs/communities/BioModels_MODEL2310020001_Mouse_Metaorganism_Model.html
+++ b/docs/communities/BioModels_MODEL2310020001_Mouse_Metaorganism_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL2310020001 Mouse Metaorganism Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000011</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000011</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.html b/docs/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.html
index 783c54fd..0eb5e9c1 100644
--- a/docs/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.html
+++ b/docs/communities/BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL2405300001 Infant Gut HMO SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000012</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000012</code>
                     </span>
                 </div>
 
@@ -1109,6 +1111,97 @@ <h2>External Resources</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    anoxic minimal medium with human milk oligosaccharides as sole carbon source
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Minimal/basal medium (1 g/L yeast extract, Na2S excluded) with 0.4% w/v four- or five-HMO mix as sole carbon source; anoxic (redox constantly below -300 mV); 80% N2:20% CO2 sparged at 6 sl/h; each strain inoculated at 1% v/v of an OD:1-normalized culture; batch start then switched to continuous feed at 12.5 mL/h.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1093/ismejo/wrae209"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1093/ismejo/wrae209
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The working volume was 300 ml and the temperature was set to 37°C. The pH was monitored and maintained at 6"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1093/ismejo/wrae209"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1093/ismejo/wrae209
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A mixed gas of 80% N2 : 20% CO2 was introduced at a 6 sl/h rate."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1093/ismejo/wrae209"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1093/ismejo/wrae209
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Anoxic conditions were monitored based on the redox potential that was constantly below −300 mV."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/BioModels_MODEL2407300002_Sponge_Holobiont_Network.html b/docs/communities/BioModels_MODEL2407300002_Sponge_Holobiont_Network.html
index 48e1a58d..e8a4cf8d 100644
--- a/docs/communities/BioModels_MODEL2407300002_Sponge_Holobiont_Network.html
+++ b/docs/communities/BioModels_MODEL2407300002_Sponge_Holobiont_Network.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>BioModels MODEL2407300002 Sponge Holobiont Network</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000013</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000013</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.html b/docs/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.html
index c091fb1c..294f4237 100644
--- a/docs/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.html
+++ b/docs/communities/Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Brachypodium Young Root Rhizosphere EcoFAB Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000225</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000225</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.html b/docs/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.html
index d1074544..85c3410b 100644
--- a/docs/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.html
+++ b/docs/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Buchnera-Serratia Cinara cedri Endosymbiont Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000148</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000148</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.html b/docs/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.html
new file mode 100644
index 00000000..08a7861f
--- /dev/null
+++ b/docs/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.html
@@ -0,0 +1,1053 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
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+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000275</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        bovine rumen microbial strains grown in in vitro cocultures
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001405"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001405
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A synthetic lignocellulolytic bacterial consortium designed from six bovine rumen microbial strains to enhance lignocellulose degradation for biofuel and enzyme production. Genome-scale community metabolic models were used with flux-based parameters (pairwise metabolic assistance, PMA; growth support index, PGSI) to predict compatible, mutualistic pairs, which were validated in experimentally grown cocultures. The strongest pairwise enzymatic synergism was observed for Butyrivibrio fibrisolvens with Selenomonas ruminantium (a 41% increase in endoglucanase activity), and a three-membered community of B. fibrisolvens, S. ruminantium, and Ruminococcus albus showed synergistic activity across all lignocellulosic substrates, indicating strong metabolic interplay among compatible species.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Butyrivibrio fibrisolvens</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=831"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:831
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42343824/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42343824</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The highest degree of enzymatic synergism has been achieved through the pairwise coculture of Butyrivibrio fibrisolvens and Selenomonas ruminantium, resulting in a 41% increase in the endoglucanase activity."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Selenomonas ruminantium</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=971"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:971
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42343824/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42343824</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The highest degree of enzymatic synergism has been achieved through the pairwise coculture of Butyrivibrio fibrisolvens and Selenomonas ruminantium, resulting in a 41% increase in the endoglucanase activity."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Ruminococcus albus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1264"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1264
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42343824/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42343824</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"a combination of B. fibrisolvens, S. ruminantium, and Ruminococcus albus exhibited synergistic activity across all lignocellulosic substrates"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Enzymatic synergism in the B. fibrisolvens + S. ruminantium coculture</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Butyrivibrio fibrisolvens</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Selenomonas ruminantium</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42343824/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42343824</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"The highest degree of enzymatic synergism has been achieved through the pairwise coculture of Butyrivibrio fibrisolvens and Selenomonas ruminantium, resulting in a 41% increase in the endoglucanase activity."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Three-membered lignocellulolytic synergy</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42343824/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42343824</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"a combination of B. fibrisolvens, S. ruminantium, and Ruminococcus albus exhibited synergistic activity across all lignocellulosic substrates, suggesting the strong metabolic interplay between compatible species"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Butyrivibrio fibrisolvens"] = {
+            id: "NCBITaxon:831",
+            label: "Butyrivibrio fibrisolvens",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Selenomonas ruminantium"] = {
+            id: "NCBITaxon:971",
+            label: "Selenomonas ruminantium",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER", "CROSS_FEEDER"]
+        };
+        
+        taxonData["Ruminococcus albus"] = {
+            id: "NCBITaxon:1264",
+            label: "Ruminococcus albus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Enzymatic synergism in the B. fibrisolvens + S. ruminantium coculture",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Butyrivibrio fibrisolvens";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Selenomonas ruminantium";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Three-membered lignocellulolytic synergy",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/CRC_Fusobacterium_Control_SynCom.html b/docs/communities/CRC_Fusobacterium_Control_SynCom.html
index b15045a1..ee4e22d5 100644
--- a/docs/communities/CRC_Fusobacterium_Control_SynCom.html
+++ b/docs/communities/CRC_Fusobacterium_Control_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>CRC Fusobacterium Control SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000128</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000128</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    GAM medium (Gifu Anaerobic Medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Seven-species SynCom and F. nucleatum cultured in GAM under anaerobic conditions; modified GAM (mGAM, GAM supplemented with arginine and tryptophan) and 1% arginine/tryptophan-supplemented GAM used across multiple transfer generations to test pH-dependent F. nucleatum suppression.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40433987"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40433987
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The nine species were first cultured in vitro under anaerobic condition"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40433987"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40433987
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"growth curves of SynCom in GAM medium"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html b/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html
index 06f482d5..2006850a 100644
--- a/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html
+++ b/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cable Bacteria beneath Photosynthetic Biofilm Sediment Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000145</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000145</code>
                     </span>
                 </div>
 
@@ -649,12 +651,6 @@ <h3>Photosynthesis Stimulates Cable-Bacteria Electron Harvesting</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -719,12 +715,6 @@ <h3>Electrogenic Sulfide Oxidation across Sediment Redox Zones</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019420</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -953,6 +943,87 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    aerated filtered natural seawater over intact salt-marsh sediment cores
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">16 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Sediment cores incubated in a temperature-controlled room (16 ± 1°C) under recirculating aerated filtered Oosterschelde seawater; an oxygenic photosynthetic surface biofilm overlies the suboxic/anoxic cable-bacteria zones on an imposed 12-h light/dark cycle.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/25416774"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:25416774
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"temperature-controlled room (16 ± ∼1°C)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/25416774"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:25416774
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"aerated filtered seawater from the Oosterschelde (salinity 28‰ ± 1‰)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/25416774"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:25416774
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Light was provided by cool white fluorescent lighting (∼300 μmol of photons m−2 s−1)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1038,8 +1109,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("photosynthesis");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
@@ -1084,8 +1153,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("sulfate reduction");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.html b/docs/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.html
index a39c6021..3aee3b9f 100644
--- a/docs/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.html
+++ b/docs/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Caldibacillus-Clostridium Aerotolerant Cellulose Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000179</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000179</code>
                     </span>
                 </div>
 
@@ -985,7 +987,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports cellulose-fed aerotolerant coculture assays; exact medium formulation and temperature details are not asserted in this record.
                 </p>
                 
diff --git a/docs/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.html b/docs/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.html
index bb4d8dce..c6db0347 100644
--- a/docs/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.html
+++ b/docs/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Caldicellulosiruptor Two-Species Hydrogen Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000185</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000185</code>
                     </span>
                 </div>
 
@@ -1120,7 +1122,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports glucose and xylose feed in a continuous-flow stirred tank reactor; detailed medium salts are not asserted here.
 
                 </p>
diff --git a/docs/communities/California_Grassland_Precipitation_Legacy_Soil_Community.html b/docs/communities/California_Grassland_Precipitation_Legacy_Soil_Community.html
index 6f6ee73e..661b84ee 100644
--- a/docs/communities/California_Grassland_Precipitation_Legacy_Soil_Community.html
+++ b/docs/communities/California_Grassland_Precipitation_Legacy_Soil_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>California Grassland Precipitation Legacy Soil Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000215</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000215</code>
                     </span>
                 </div>
 
@@ -557,12 +559,6 @@ <h3>Necromass Cross-Feeding at High Community Growth Efficiency</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                     <li>
                         amino acid biosynthetic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0008652"
@@ -976,8 +972,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("aromatic compound catabolic process");
-            
             processes.push("amino acid biosynthetic process");
             
             processes.push("peptidoglycan biosynthetic process");
diff --git a/docs/communities/Candida_Parapsilosis_Hospitalized_Infant_Microbiome.html b/docs/communities/Candida_Parapsilosis_Hospitalized_Infant_Microbiome.html
index 8f6d542f..22482174 100644
--- a/docs/communities/Candida_Parapsilosis_Hospitalized_Infant_Microbiome.html
+++ b/docs/communities/Candida_Parapsilosis_Hospitalized_Infant_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Candida parapsilosis Hospitalized Infant Gut Microbiome Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000248</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000248</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/CeMbio_Caenorhabditis_Elegans_Microbiome.html b/docs/communities/CeMbio_Caenorhabditis_Elegans_Microbiome.html
index a2b651aa..6e2c8c75 100644
--- a/docs/communities/CeMbio_Caenorhabditis_Elegans_Microbiome.html
+++ b/docs/communities/CeMbio_Caenorhabditis_Elegans_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>CeMbio Caenorhabditis elegans Microbiome</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000159</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000159</code>
                     </span>
                 </div>
 
@@ -598,8 +600,8 @@ <h3>Multi-Strain C. elegans Gut Colonization</h3>
                     
                     <li>
                         multi-organism process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0051704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0051704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
                     
                     <li>
@@ -1064,7 +1066,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> CeMbio strains are cryopreserved in glycerol/LB and can be grown in LB or on LB agar before mixing into inocula for C. elegans plate assays.
                 </p>
                 
@@ -1119,7 +1121,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Synchronized C. elegans L1 larvae were raised on NGM or peptone-free NGM seeded with CeMbio bacterial inoculum.
                 </p>
                 
diff --git a/docs/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.html b/docs/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.html
index 47a7d7d2..77e6b5e6 100644
--- a/docs/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.html
+++ b/docs/communities/Cellulomonas_Rhodobacter_Cellulose_Photohydrogen_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cellulomonas-Rhodobacter Cellulose Photohydrogen Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000265</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000265</code>
                     </span>
                 </div>
 
@@ -1012,7 +1014,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Detailed medium salts and illumination parameters are not asserted from the abstract. The curated medium context is anaerobic coculture with cellulose as the sole carbon source.
 
                 </p>
diff --git a/docs/communities/Cellulose_Methane_Quad_Culture_SynCom.html b/docs/communities/Cellulose_Methane_Quad_Culture_SynCom.html
index 978f3d56..77917951 100644
--- a/docs/communities/Cellulose_Methane_Quad_Culture_SynCom.html
+++ b/docs/communities/Cellulose_Methane_Quad_Culture_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cellulose-to-Methane Quad-Culture SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000089</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000089</code>
                     </span>
                 </div>
 
@@ -744,6 +746,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    modified VM medium (10 g/L cellulose as sole carbon source)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">34 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> All cultures grown anaerobically in triplicate on cellulose as the sole carbon source; about 5 × 10^7 cells inoculated per species; sulfate-perturbation treatment received additional sulfate versus the control condition.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36847519"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36847519
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All fermentation experiments were carried out in 160 mL serum bottles with 20 mL of modified VM medium containing 10 g/L cellulose; the chamber gas contained 3% H2 and 97% N2."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36847519"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36847519
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All cultures were incubated at 34°C with shaking at 200 rpm for 7 days and sampled each day."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36847519"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36847519
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All cultures were grown anaerobically in triplicate using the same medium with cellulose as the sole carbon source."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Cheese_Rind_InSitu_InVitro_Model_Community.html b/docs/communities/Cheese_Rind_InSitu_InVitro_Model_Community.html
index 11955901..f3ba21a9 100644
--- a/docs/communities/Cheese_Rind_InSitu_InVitro_Model_Community.html
+++ b/docs/communities/Cheese_Rind_InSitu_InVitro_Model_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cheese Rind In Situ-In Vitro Model Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000153</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000153</code>
                     </span>
                 </div>
 
@@ -940,7 +942,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Simplified rind communities were inoculated onto cheese curd agar and subjected to bloomy, washed, natural, or unmanipulated control treatments.
                 </p>
                 
diff --git a/docs/communities/Chlamydomonas_Bacterial_H2_Consortium.html b/docs/communities/Chlamydomonas_Bacterial_H2_Consortium.html
index d0f33fa6..becf6269 100644
--- a/docs/communities/Chlamydomonas_Bacterial_H2_Consortium.html
+++ b/docs/communities/Chlamydomonas_Bacterial_H2_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlamydomonas-Bacterial Hydrogen Production Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000014</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000014</code>
                     </span>
                 </div>
 
@@ -564,9 +566,9 @@ <h2>Taxonomy</h2>
                             <strong>Stenotrophomonas goyi</strong>
                         </td>
                         <td>
-                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3050471"
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40323"
                                class="term-link" target="_blank" rel="noopener noreferrer">
-                                NCBITaxon:3050471
+                                NCBITaxon:40323
                             </a>
                         </td>
                         <td>
@@ -1029,9 +1031,9 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                             <td>percent (w/v)</td>
                             <td>
                                 
-                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=89981"
+                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=60004"
                                    class="term-link" target="_blank" rel="noopener">
-                                    CHEBI:89981
+                                    CHEBI:60004
                                 </a>
                                 
                             </td>
@@ -1109,7 +1111,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium prepared for sustained algal-bacterial hydrogen production. Mannitol and yeast extract are added to support bacterial growth and enhance H2 production. Cultures start under aerobic conditions and transition to anaerobic conditions for hydrogen production. Sulfur deprivation may be used to induce anaerobiosis and activate hydrogenase in Chlamydomonas. High-cell density cultures (76.7 μg/mL chlorophyll) produce 313 mL H2/L over 17 days, while low-cell density cultures (10 μg/mL chlorophyll) produce 163.5 mL H2/L over 25 days.
 
                 </p>
@@ -1187,7 +1189,7 @@ <h4 style="color: var(--text);">Evidence</h4>
         };
         
         taxonData["Stenotrophomonas goyi"] = {
-            id: "NCBITaxon:3050471",
+            id: "NCBITaxon:40323",
             label: "Stenotrophomonas goyi",
             abundance: "COMMON",
             roles: ["SYNTROPHIC_PARTNER"]
diff --git a/docs/communities/Chlamydomonas_Methylobacterium_Mutualism.html b/docs/communities/Chlamydomonas_Methylobacterium_Mutualism.html
index 242871fb..c77d9a90 100644
--- a/docs/communities/Chlamydomonas_Methylobacterium_Mutualism.html
+++ b/docs/communities/Chlamydomonas_Methylobacterium_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlamydomonas-Methylobacterium Mutualistic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000015</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000015</code>
                     </span>
                 </div>
 
@@ -1053,7 +1055,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> TAP medium is the standard maintenance medium for Chlamydomonas reinhardtii. For nitrogen stress experiments, cultures are grown in nitrogen-depleted TAP medium to induce the mutualistic interaction with Methylobacterium. The medium contains Tris buffer for pH stability and acetate as a carbon source. Ammonium serves as the nitrogen source under normal conditions, but is omitted or depleted to create nitrogen stress.
 
                 </p>
diff --git a/docs/communities/Chlorella_Azospirillum_Synthetic_Mutualism.html b/docs/communities/Chlorella_Azospirillum_Synthetic_Mutualism.html
index 7a74e01b..7f3f43ae 100644
--- a/docs/communities/Chlorella_Azospirillum_Synthetic_Mutualism.html
+++ b/docs/communities/Chlorella_Azospirillum_Synthetic_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlorella-Azospirillum Synthetic Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000191</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000191</code>
                     </span>
                 </div>
 
@@ -1304,7 +1306,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Publications support alginate bead immobilization and nutrient-perturbation assays for the C. sorokiniana UTEX 2714 and A. brasilense Cd pair. Detailed medium composition is not asserted here beyond the reported nutrient-rich, nitrogen-free, and carbon-free condition classes.
 
                 </p>
diff --git a/docs/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.html b/docs/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.html
index 0c1aa305..5b4041ad 100644
--- a/docs/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.html
+++ b/docs/communities/Chlorella_Ecoli_Mixotrophic_Biofuel_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlorella-Ecoli Mixotrophic Biofuel Precursor Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000269</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000269</code>
                     </span>
                 </div>
 
@@ -1057,7 +1059,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports airlift reactor cocultures tested under mixotrophic glucose, glycerol, and acetate conditions; exact mineral medium formulation is not asserted here.
 
                 </p>
diff --git a/docs/communities/Chlorella_Rhizobium_Bioflocculation.html b/docs/communities/Chlorella_Rhizobium_Bioflocculation.html
index 8ede116d..2568cb3b 100644
--- a/docs/communities/Chlorella_Rhizobium_Bioflocculation.html
+++ b/docs/communities/Chlorella_Rhizobium_Bioflocculation.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlorella-Rhizobium Bioflocculation</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000016</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000016</code>
                     </span>
                 </div>
 
@@ -896,6 +898,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    synthetic wastewater
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Chlorella vulgaris co-cultured with bioflocculant-producing Rhizobium radiobacter F2 in synthetic wastewater; conditions optimized by response surface methodology (bacteria:microalgae inoculation ratio 0.20-0.25, initial glucose concentration &lt;1.5 kg/m3, co-culture time 9-14 days); illumination required for algal photosynthesis.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1111/jbm.12334"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1111/jbm.12334
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the co-culture conditions of C. vulgaris and bioflocculant-producing bacteria in synthetic wastewater"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1111/jbm.12334"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1111/jbm.12334
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"inoculation ratio of bacteria and microalgae of 0·20-0·25, initial glucose concentration of &lt;1·5 kg m(-3) and co-culture time of 9-14 days"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Chlorochromatium_Aggregatum_Phototrophic_Consortium.html b/docs/communities/Chlorochromatium_Aggregatum_Phototrophic_Consortium.html
index 738c4a12..d1bf6ebb 100644
--- a/docs/communities/Chlorochromatium_Aggregatum_Phototrophic_Consortium.html
+++ b/docs/communities/Chlorochromatium_Aggregatum_Phototrophic_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chlorochromatium aggregatum Phototrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000141</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000141</code>
                     </span>
                 </div>
 
@@ -916,7 +918,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The consortium was enriched from eutrophic freshwater lake sediment and maintained in anoxic sulfide-reduced medium.
                 </p>
                 
diff --git a/docs/communities/Chromium_Sulfur_Reduction_Enrichment.html b/docs/communities/Chromium_Sulfur_Reduction_Enrichment.html
index d8ead6a2..f7b48008 100644
--- a/docs/communities/Chromium_Sulfur_Reduction_Enrichment.html
+++ b/docs/communities/Chromium_Sulfur_Reduction_Enrichment.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Chromium Sulfur Reduction Enrichment</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000017</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000017</code>
                     </span>
                 </div>
 
@@ -684,8 +686,8 @@ <h3>Cr(VI) Reduction by Intrasporangiaceae</h3>
                         class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:49544</a>), 
                     
                     chromium hydroxide
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=33104"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:33104</a>)
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=49544"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:49544</a>)
                     
                 </p>
                 
@@ -694,12 +696,6 @@ <h3>Cr(VI) Reduction by Intrasporangiaceae</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         cellular detoxification
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:1990748"
@@ -708,8 +704,8 @@ <h3>Cr(VI) Reduction by Intrasporangiaceae</h3>
                     
                     <li>
                         chromate transport
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0015103"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0015103</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008509"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008509</a>)
                     </li>
                     
                 </ul>
@@ -803,12 +799,6 @@ <h3>Sulfur Oxidation Coupled to Cr(VI) Reduction</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019417</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -868,8 +858,8 @@ <h3>Chromium Immobilization via Cr(III) Precipitation</h3>
                         class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:49544</a>), 
                     
                     chromium hydroxide
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=33104"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:33104</a>)
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=49544"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:49544</a>)
                     
                 </p>
                 
@@ -880,8 +870,8 @@ <h3>Chromium Immobilization via Cr(III) Precipitation</h3>
                     
                     <li>
                         metal ion sequestration
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0051238"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0051238</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0140487"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0140487</a>)
                     </li>
                     
                     <li>
@@ -969,8 +959,8 @@ <h3>Biosorption and EPS-Mediated Metal Binding</h3>
                     
                     <li>
                         biosorption
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0051238"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0051238</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0140487"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0140487</a>)
                     </li>
                     
                 </ul>
@@ -1248,6 +1238,134 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Aerobic acetate mineral medium for chromate reduction (dominant Intrasporangium strain characterization conditions)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">8.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>acetate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>chromate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Aerobic Cr(VI) reduction by the dominant Intrasporangiaceae/Intrasporangium strain, optimal at pH 8.0 and 37°C with acetate (1 mmol/L) as the most efficient carbon source; strain tolerates Cr(VI) to an MIC of 17 mmol/L. Conditions are drawn from the characterization of the closely related dominant strain Intrasporangium sp. Q5-1; the enrichment community source (BioProject PRJNA1272773) reports no explicit medium recipe.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1007/s11274-009-0047-x"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1007/s11274-009-0047-x
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The best condition of Cr(VI) reduction for Q5-1 is pH 8.0 at 37°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1007/s11274-009-0047-x"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1007/s11274-009-0047-x
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"is able to reduce Cr(VI) aerobically"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1007/s11274-009-0047-x"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1007/s11274-009-0047-x
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the most efficient carbon source for stimulating Cr(VI) reduction"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1335,8 +1453,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("cellular detoxification");
             
             processes.push("chromate transport");
@@ -1388,8 +1504,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("thiosulfate oxidation");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/Cinnamate_Degradation_Consortium.html b/docs/communities/Cinnamate_Degradation_Consortium.html
index 75d36f62..ac1b9512 100644
--- a/docs/communities/Cinnamate_Degradation_Consortium.html
+++ b/docs/communities/Cinnamate_Degradation_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cinnamate β-Oxidation Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000018</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000018</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Cinnamate β-Oxidation Consortium</h1>
                     <span class="metadata-value">
                         anaerobic environment
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002229"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001825"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:00002229
+                            ENVO:01001825
                         </a>
                     </span>
                 </div>
@@ -647,12 +649,6 @@ <h3>Cinnamate β-Oxidation to Benzoate</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0006635</a>)
                     </li>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -883,6 +879,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    basal medium (cinnamate as sole carbon and energy source)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Cinnamate provided as the carbon and energy source; consortium grown under methanogenic conditions; 2-bromoethanesulfonic acid (BESA) used to inhibit methanogenesis.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/12432464"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:12432464
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A syntrophic consortium was enriched in a basal medium containing cinnamate as the carbon and energy source"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/12432464"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:12432464
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"under methanogenic conditions without BESA, cinnamate was first transformed to benzoate via beta-oxidation"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -970,8 +1034,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("fatty acid beta-oxidation");
             
-            processes.push("aromatic compound catabolic process");
-            
             
             var evidenceCount = 1;
 
diff --git a/docs/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.html b/docs/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.html
index b4f17fbb..7177f2fe 100644
--- a/docs/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.html
+++ b/docs/communities/Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium autoethanogenum-Clostridium kluyveri Syngas Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000172</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000172</code>
                     </span>
                 </div>
 
@@ -1153,7 +1155,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> PubMed-indexed abstracts support CO/syngas gas substrate, acetate supplementation, and pH effects; exact mineral medium recipes are not curated here.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.html b/docs/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.html
index 88918362..2774c9a0 100644
--- a/docs/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.html
+++ b/docs/communities/Clostridium_Caldicellulosiruptor_Minimal_Medium_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium-Caldicellulosiruptor Minimal Medium Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000193</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000193</code>
                     </span>
                 </div>
 
@@ -1141,7 +1143,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed abstract supports a low-ionic-strength defined minimal nutrient medium with decreased nitrogen, sulfur, phosphate, and vitamin supplements; it reports cocultures with cellulose and xylan but does not provide the full salts and vitamin recipe.
 
                 </p>
diff --git a/docs/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.html b/docs/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.html
index 105dede4..7435c6a1 100644
--- a/docs/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.html
+++ b/docs/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium carboxidivorans-Clostridium kluyveri CO Chain-Elongation Cocultu
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000266</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000266</code>
                     </span>
                 </div>
 
@@ -1126,7 +1128,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The curated culture context is anaerobic stirred-tank bioreactor cocultivation with continuous CO/CO2 gassing; exact mineral salts are not asserted here.
 
                 </p>
diff --git a/docs/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.html b/docs/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.html
index 1c835420..5aaf46a1 100644
--- a/docs/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.html
+++ b/docs/communities/Clostridium_Cellulolyticum_Geobacter_Cellulose_MFC_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium cellulolyticum-Geobacter sulfurreducens Cellulose MFC Coculture<
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000175</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000175</code>
                     </span>
                 </div>
 
@@ -1097,7 +1099,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Two-chamber microbial fuel cell anode culture with cellulose-derived substrates; the abstract reports ferricyanide as catholyte but does not provide a full medium recipe.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.html b/docs/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.html
index ed57b808..c11b8841 100644
--- a/docs/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.html
+++ b/docs/communities/Clostridium_Cellulovorans_Methanosarcina_Cellulose_Methane_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000174</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000174</code>
                     </span>
                 </div>
 
@@ -1097,7 +1099,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The record curates the abstract-supported cellulose-to-methane culture context; detailed mineral medium recipe parameters are not represented here.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.html b/docs/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.html
index 8ede8744..f051510b 100644
--- a/docs/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.html
+++ b/docs/communities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium cellulovorans-Rhodopseudomonas palustris Cellulose Biohydrogen C
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000264</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000264</code>
                     </span>
                 </div>
 
@@ -1013,7 +1015,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Detailed medium formulation is not asserted here because the validator-visible source text is abstract-only. The record curates cellulose and representative volatile-fatty-acid exchange supported by the abstract.
 
                 </p>
diff --git a/docs/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.html b/docs/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.html
index 6e3acb1a..be8f6c10 100644
--- a/docs/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.html
+++ b/docs/communities/Clostridium_Ljungdahlii_Kluyveri_Syngas_Alcohol_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium ljungdahlii-Clostridium kluyveri Syngas Alcohol Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000202</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000202</code>
                     </span>
                 </div>
 
@@ -1202,7 +1204,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> PubMed-indexed text supports continuous syngas feeding, gas stripping, and product condensation; the complete mineral nutrient recipe is not asserted here.
 
                 </p>
diff --git a/docs/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.html b/docs/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.html
index 1d6af629..3d79e685 100644
--- a/docs/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.html
+++ b/docs/communities/Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium phytofermentans-E. coli Cellobiose Biofilm Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000196</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000196</code>
                     </span>
                 </div>
 
@@ -1205,7 +1207,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The published medium recipe also included phosphate buffer salts, magnesium chloride, calcium chloride, ferrous sulfate, resazurin, and a trace metal solution. Biofilms were transferred to fresh medium plates every 2 days.
 
                 </p>
diff --git a/docs/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.html b/docs/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.html
index 0fd24084..76b3d7d2 100644
--- a/docs/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.html
+++ b/docs/communities/Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium-Saccharomyces Cellulose Ethanol Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000206</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000206</code>
                     </span>
                 </div>
 
@@ -1118,7 +1120,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The coculture used alpha-cellulose as the feedstock and controlled diffusive oxygen delivery. The abstract supports the core substrate, oxygen-transfer, scale-up, and ethanol production conditions; detailed GS2 medium composition is left to the full-text resource.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.html b/docs/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.html
index 3d8287e7..3726af54 100644
--- a/docs/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.html
+++ b/docs/communities/Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium-Thermoanaerobacter Cellulosic Bioethanol Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000168</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000168</code>
                     </span>
                 </div>
 
@@ -1074,7 +1076,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Semicontinuous cyclic fed-batch fermentor configuration using cellulose as the recalcitrant substrate; the PubMed abstract reports cellulose loading and controlled pH but not a full medium recipe.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.html b/docs/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.html
index eca4e0c0..532a9b29 100644
--- a/docs/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.html
+++ b/docs/communities/Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium-Thermoanaerobacterium JN4-GD17 Cellulosic Biofuel Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000180</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000180</code>
                     </span>
                 </div>
 
@@ -1067,7 +1069,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The record captures the substrate conditions supported by the abstract and does not assert complete salts, vitamins, or trace-element composition.
                 </p>
                 
diff --git a/docs/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.html b/docs/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.html
index 3fe6677e..0e8e2118 100644
--- a/docs/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.html
+++ b/docs/communities/Clostridium_Thermocellum_Saccharoperbutylacetonicum_Cellulosic_Butanol_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Clostridium Thermocellum-Saccharoperbutylacetonicum Cellulosic Butanol Cocul
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000208</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000208</code>
                     </span>
                 </div>
 
@@ -1193,7 +1195,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The primary record supports a staged process in which C. thermocellum was incubated on Avicel cellulose before N1-4 addition; it does not curate the full salts or reducing-agent composition.
 
                 </p>
diff --git a/docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html b/docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html
index e565eb42..513d5227 100644
--- a/docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html
+++ b/docs/communities/Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Coastal Forested Wetland Seawater-Ion Microcosm Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000258</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000258</code>
                     </span>
                 </div>
 
@@ -683,8 +685,8 @@ <h3>Non-Sulfate Seawater Ions Drive Community And Emission Responses</h3>
                     
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
                     </li>
                     
                 </ul>
@@ -829,8 +831,8 @@ <h3>Artificial Seawater Alters Carbon Nitrogen And Phosphorus Gene Response</h3>
                     
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
                     </li>
                     
                 </ul>
diff --git a/docs/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html b/docs/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html
new file mode 100644
index 00000000..a72d62bc
--- /dev/null
+++ b/docs/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html
@@ -0,0 +1,977 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Five-member bacterial-fungal composting SynCom for lignocellulose degradation - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
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+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Five-member bacterial-fungal composting SynCom for lignocellulose degradation</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000277</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        co-composting of cattle manure and mulberry branches
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002170"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002170
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A rationally designed five-member bacterial-fungal synthetic microbial community (SynCom) used to bioaugment the co-composting of cattle manure and mulberry branches. Inoculation acts as an ecological engineer that elevates pile temperatures, shortens the maturation period by roughly 7 days, and enhances degradation of lignin, cellulose, and hemicellulose while boosting humus content. Metagenomics shows the SynCom restructures the native microbiome, enriching key lignocellulose-degrading functional genera such as Thermobifida and Actinomadura and increasing the abundance of carbohydrate-active enzymes (cellulases, hemicellulases, and lignin-modifying auxiliary-activity enzymes).</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Thermobifida</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=83677"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:83677
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41297400/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41297400</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"enriching for key functional genera such as Thermobifida and Actinomadura"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Actinomadura</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1988"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1988
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41297400/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41297400</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"enriching for key functional genera such as Thermobifida and Actinomadura"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Five-member bacterial-fungal composting SynCom for lignocellulose degradation</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom-driven restructuring and enrichment of native degraders</h3>
+                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41297400/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41297400</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    co-composting substrate (cattle manure and mulberry branches)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Thermophilic solid-state co-composting; SynCom bioaugmentation significantly elevated pile temperatures and shortened the maturation period by ~7 days.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41297400"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41297400
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"significantly elevating pile temperatures and shortening the maturation period"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Thermobifida"] = {
+            id: "NCBITaxon:83677",
+            label: "Thermobifida",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Actinomadura"] = {
+            id: "NCBITaxon:1988",
+            label: "Actinomadura",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COLONIZATION_FACILITATION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "SynCom-driven restructuring and enrichment of native degraders",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
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+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
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+                    .style("fill", "var(--net-label, #475569)")
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+
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+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
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+        // Tooltip
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+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
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+</html>
\ No newline at end of file
diff --git a/docs/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.html b/docs/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.html
index 4be82966..29efab21 100644
--- a/docs/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.html
+++ b/docs/communities/Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Coniochaeta-Sphingobacterium-Citrobacter Wheat Straw Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000195</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000195</code>
                     </span>
                 </div>
 
@@ -1307,7 +1309,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The curated publications support wheat straw-driven cultures and shaking-speed perturbations; this record does not assert the full salts or trace-component medium recipe.
 
                 </p>
diff --git a/docs/communities/Copper_Biomining_Heap_Leach.html b/docs/communities/Copper_Biomining_Heap_Leach.html
index 3f12a717..8436d6a6 100644
--- a/docs/communities/Copper_Biomining_Heap_Leach.html
+++ b/docs/communities/Copper_Biomining_Heap_Leach.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Copper Biomining Heap Leach Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000019</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000019</code>
                     </span>
                 </div>
 
@@ -775,12 +777,6 @@ <h3>Ferrous Iron Oxidation in Early Heaps</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -873,12 +869,6 @@ <h3>Ferrous Iron Oxidation in Aged Heaps</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -963,12 +953,6 @@ <h3>Sulfur Oxidation to Sulfuric Acid</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1051,17 +1035,6 @@ <h3>Copper Sulfide Dissolution</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1126,17 +1099,6 @@ <h3>Thermophilic Iron and Sulfur Oxidation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1568,7 +1530,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Classic 9K medium (Silverman &amp; Lundgren 1959) used for laboratory cultivation of individual consortium members. pH adjusted with H2SO4. For iron oxidizers (At. ferrooxidans, Leptospirillum spp.), use FeSO4 as energy source. For sulfur oxidizers (At. thiooxidans), elemental sulfur S0 is primary substrate. Temperature varies by organism: mesophiles (At. ferrooxidans, At. thiooxidans) at 28-30°C, moderate thermophiles (Sulfobacillus spp.) at 45-55°C. Modifications: For Leptospirillum (obligate autotroph), omit yeast extract. For Ferroplasma (mixotroph), add 0.02-0.1% yeast extract. For Sulfobacillus (facultative autotroph), add 0.02% yeast extract. For nitrogen fixation studies with L. ferrodiazotrophum, omit (NH4)2SO4. Industrial heap operations use in situ bioleaching rather than defined media - ore heaps are irrigated with acidic process solution containing indigenous microorganisms.
                 </p>
                 
@@ -1708,8 +1670,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -1751,8 +1711,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1797,8 +1755,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1841,10 +1797,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1887,10 +1839,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html b/docs/communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html
new file mode 100644
index 00000000..13ab6b0f
--- /dev/null
+++ b/docs/communities/Corynebacterium_glutamicum_Shewanella_oneidensis_Succinic_Acid_Coculture.html
@@ -0,0 +1,1036 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
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+            color: var(--text);
+            line-height: 1.6;
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+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
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+        h1 {
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+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
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+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
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+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
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+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
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+
+        .metadata-item {
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+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
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+        .metadata-value {
+            color: var(--text);
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+
+        .badge {
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+            padding: 0.25rem 0.75rem;
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+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
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+
+        table {
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+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
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+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
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+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
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+
+        tr:not(:last-child) td {
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+        .term-link {
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+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
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+
+        .term-link:hover {
+            text-decoration: underline;
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+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
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+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
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+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
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+
+        .empty-state p {
+            margin: 0.5rem 0;
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+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
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+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
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+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
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+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
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+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
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+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
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+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
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+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
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+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
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+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
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+
+        .legend-circle {
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+
+        .network-tooltip {
+            position: absolute;
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+            line-height: 1.4;
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+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
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+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000294</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        anaerobic bioreactor (succinic acid fermentation)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Engineered two-member co-culture pairing the succinic-acid producer Corynebacterium glutamicum (including an ldhA-deleted, lactate-deficient strain K1) with the electroactive bacterium Shewanella oneidensis to enhance anaerobic succinic acid biosynthesis through interspecies interactions. Co-cultivation raised succinic acid yield markedly over monoculture without altering glucose consumption, and supplementation with riboflavin (the most effective of five screened redox-active additives) further improved production. Transcriptomics showed co-culture reprogrammed C. glutamicum metabolism, reinforcing its electron transport system and redistributing carbon flux toward the reductive TCA pathway.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Corynebacterium glutamicum (ldhA-deleted strain K1)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1718"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1718
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42203120/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42203120</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an engineered co-culture system was developed by pairing C. glutamicum with the electroactive bacterium Shewanella oneidensis to enhance succinic acid biosynthesis through interspecies interactions"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Shewanella oneidensis</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=70863"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:70863
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42203120/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42203120</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an engineered co-culture system was developed by pairing C. glutamicum with the electroactive bacterium Shewanella oneidensis to enhance succinic acid biosynthesis through interspecies interactions"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Riboflavin-mediated interspecies electron transfer enhancing succinic acid production</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Shewanella oneidensis</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Corynebacterium glutamicum (ldhA-deleted strain K1)</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    riboflavin
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17015"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17015</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42203120/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42203120</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Screening of five redox-active compounds identified riboflavin as the most effective additive, and supplementation with 0.1 mM riboflavin further improved production performance."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42203120/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42203120</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Transcriptomic analysis revealed that co-culture induced global metabolic reprogramming in C. glutamicum, including reinforcement of the electron transport system, redistribution of carbon flux toward the reductive TCA pathway"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified (glucose-based anaerobic succinic acid fermentation medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Anaerobic succinic acid fermentation with glucose as carbon source; the optimized co-culture was supplemented with 0.1 mM riboflavin as a redox-active additive. Only the reference abstract was accessible (full text subscription-required); medium name, temperature, pH, and vessel details were not reported in the accessible source.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42203120"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42203120
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Anaerobic production of succinic acid in Corynebacterium glutamicum is often constrained by metabolic imbalances and by-product formation."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42203120"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42203120
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"supplementation with 0.1 mM riboflavin further improved production performance"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Corynebacterium glutamicum (ldhA-deleted strain K1)"] = {
+            id: "NCBITaxon:1718",
+            label: "Corynebacterium glutamicum (ldhA-deleted strain K1)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER"]
+        };
+        
+        taxonData["Shewanella oneidensis"] = {
+            id: "NCBITaxon:70863",
+            label: "Shewanella oneidensis",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROGEN", "ELECTRON_DONOR"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("riboflavin");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Riboflavin-mediated interspecies electron transfer enhancing succinic acid production",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Shewanella oneidensis";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Corynebacterium glutamicum (ldhA-deleted strain K1)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Coscinodiscus_Synthetic_Community.html b/docs/communities/Coscinodiscus_Synthetic_Community.html
index 9051f554..25833ebb 100644
--- a/docs/communities/Coscinodiscus_Synthetic_Community.html
+++ b/docs/communities/Coscinodiscus_Synthetic_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Coscinodiscus Synthetic Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000020</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000020</code>
                     </span>
                 </div>
 
@@ -1002,8 +1004,8 @@ <h3>Community-Level Emergent Effects</h3>
                     
                     <li>
                         microbial community structure
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0140352"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0140352</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0043903"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0043903</a>)
                     </li>
                     
                 </ul>
@@ -1256,9 +1258,9 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                             <td>mg/L</td>
                             <td>
                                 
-                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=86154"
+                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=60720"
                                    class="term-link" target="_blank" rel="noopener">
-                                    CHEBI:86154
+                                    CHEBI:60720
                                 </a>
                                 
                             </td>
@@ -1420,7 +1422,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> f/2 medium (Guillard and Ryther 1962, Guillard 1975) is the standard growth medium for marine diatoms and phytoplankton. The medium is prepared with filtered natural seawater or artificial seawater (30 ppt salinity) enriched with f/2 nutrients, trace metals, and vitamins. Silicate (sodium metasilicate) is essential for diatom growth as it is required to build the biomineralized silica frustule cell wall. Autoclaved f/2 medium may produce silica precipitate. The medium supports both photosynthetic diatom growth and heterotrophic bacterial growth on diatom-derived organic compounds.
 
                 </p>
diff --git a/docs/communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.html b/docs/communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.html
new file mode 100644
index 00000000..94876cdc
--- /dev/null
+++ b/docs/communities/Crucian_Carp_Gut_Disease_Resistance_SynCom.html
@@ -0,0 +1,1033 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Crucian Carp Gut Disease-resistance SynCom - CommunityMech</title>
+    <style>
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+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
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+  :root:not([data-theme="light"]) th{background:#232a3d}
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Crucian Carp Gut Disease-resistance SynCom</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000293</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        crucian carp (Carassius auratus) intestine
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_2100002"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:2100002
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A simplified synthetic microbial community of three gut genera (Cetobacterium, Paraclostridium, and Pseudomonas) assembled from the intestinal microbiota of crucian carp (Carassius auratus). These genera were enriched in fish that displayed mild symptoms after Aeromonas hydrophila infection, and fecal microbiota transplantation from mild-symptom fish conferred enhanced resistance to the pathogen. The reconstituted SynCom significantly reduced A. hydrophila abundance by activating intestinal immune responses and reinforcing the gut barrier, supporting microbiome-based disease prevention in aquaculture.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Cetobacterium</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=180162"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:180162
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41280275/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41280275</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"Further microbial analysis identified Cetobacterium (p = 0.013), Paraclostridium"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Paraclostridium</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1849822"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1849822
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41280275/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41280275</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"Further microbial analysis identified Cetobacterium (p = 0.013), Paraclostridium"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=286"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:286
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41280275/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41280275</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"Paraclostridium (p Pseudomonas (p A. hydrophila (p &lt; 0.05) by activating intestinal immune responses and reinforcing the gut barrier."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Crucian Carp Gut Disease-resistance SynCom</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom-mediated suppression of Aeromonas hydrophila</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+                <p><strong>Target Taxon:</strong> Aeromonas hydrophila</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41280275/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41280275</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"Paraclostridium (p Pseudomonas (p A. hydrophila (p &lt; 0.05) by activating intestinal immune responses and reinforcing the gut barrier."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    BHI and LB (brain heart infusion and Luria-Bertani)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom strains isolated on BHI and LB agar (48 h, anaerobic at 28 C and aerobic), then expanded in 5 mL BHI/LB broth with overnight shaking to OD600 1.0 before combining.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41280275"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41280275
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Plates were incubated for 48 h under both anaerobic conditions at 28 °C and aerobic conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41280275"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41280275
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"inoculated into 5 mL of BHI and LB broth for expansion"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Cetobacterium"] = {
+            id: "NCBITaxon:180162",
+            label: "Cetobacterium",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Paraclostridium"] = {
+            id: "NCBITaxon:1849822",
+            label: "Paraclostridium",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Pseudomonas"] = {
+            id: "NCBITaxon:286",
+            label: "Pseudomonas",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "SynCom-mediated suppression of Aeromonas hydrophila",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+            var tgtKey = "Aeromonas hydrophila";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html b/docs/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html
index 5d83ea22..3348de3e 100644
--- a/docs/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html
+++ b/docs/communities/Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Crystal Geyser CO2-Rich Aquifer Autotrophic CPR Lysolipid Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000252</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000252</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.html b/docs/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.html
index 30696cab..b97151f0 100644
--- a/docs/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.html
+++ b/docs/communities/Cyprus_Copper_Sulphide_Bioleaching_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Cyprus Copper Sulphide Bioleaching Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000217</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000217</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html b/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html
new file mode 100644
index 00000000..31851b00
--- /dev/null
+++ b/docs/communities/DIETsimp_Lignocellulose_to_Methane_DIET_Consortia.html
@@ -0,0 +1,1246 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp) - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
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+        }
+
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+        .network-legend {
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+            position: absolute;
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+            line-height: 1.4;
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+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
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+  :root:not([data-theme="light"]) th{background:#232a3d}
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+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000297</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        anaerobic digestion of lignocellulose (cow manure + paddy soil/marine sediment inocula)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00003965"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00003965
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two simplified methanogenic consortia (DIETsimp) constructed by top-down selection from cow manure combined with paddy soil or marine sediment inocula for high-efficiency conversion of lignocellulose to methane via direct interspecies electron transfer (DIET). Metagenomic analysis identified Methanosarcina mazei, capable of accepting electrons via DIET, as the dominant archaeon, and the electroactive bacteria Sphaerochaeta globosa and Clostridium aceticum as the dominant bacteria. The proposed DIET-based methanogenic pathway has S. globosa and C. aceticum metabolizing intermediates (xylose, glucose, pyruvate, acetate) and transferring electrons to M. mazei for reduction of CO2 to methane. Both consortia shortened methanogenesis periods and increased methane production rates relative to conventional anaerobic digestion.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Methanosarcina mazei</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2209"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:2209
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42229598/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42229598</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Sphaerochaeta globosa</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1131703"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1131703
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42229598/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42229598</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Clostridium aceticum</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=84022"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:84022
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42229598/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42229598</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>DIET syntrophy from S. globosa to M. mazei</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Sphaerochaeta globosa</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Methanosarcina mazei</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    xylose
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18222"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18222</a>), 
+                    
+                    D-glucose
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17634"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17634</a>), 
+                    
+                    pyruvate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15361"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15361</a>), 
+                    
+                    acetate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30089"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30089</a>), 
+                    
+                    carbon dioxide
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>), 
+                    
+                    methane
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16183"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16183</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42229598/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42229598</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>DIET syntrophy from C. aceticum to M. mazei</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Clostridium aceticum</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Methanosarcina mazei</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    xylose
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18222"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18222</a>), 
+                    
+                    D-glucose
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17634"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17634</a>), 
+                    
+                    pyruvate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15361"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15361</a>), 
+                    
+                    acetate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30089"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30089</a>), 
+                    
+                    carbon dioxide
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>), 
+                    
+                    methane
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16183"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16183</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42229598/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42229598</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified anaerobic digestion medium (lignocellulose substrate)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Two simplified consortia (DIETsimp) enriched by &#39;top-down&#39; selection; culture conditions (inoculum ratio, C/N, and period) were optimized via single-factor experiments combined with response surface methodology. No incubation temperature, medium composition, headspace gas, pH value, or vessel/reactor type is reported in the accessible (subscription-only) source abstract.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42229598"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42229598
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a &#39;top-down&#39; selection"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42229598"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42229598
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42229598"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42229598
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Methanosarcina mazei"] = {
+            id: "NCBITaxon:2209",
+            label: "Methanosarcina mazei",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_ACCEPTOR", "ELECTROTROPH"]
+        };
+        
+        taxonData["Sphaerochaeta globosa"] = {
+            id: "NCBITaxon:1131703",
+            label: "Sphaerochaeta globosa",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "ELECTRON_DONOR", "ELECTROGEN", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Clostridium aceticum"] = {
+            id: "NCBITaxon:84022",
+            label: "Clostridium aceticum",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "ELECTRON_DONOR", "ELECTROGEN", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("xylose");
+            
+            metabolites.push("D-glucose");
+            
+            metabolites.push("pyruvate");
+            
+            metabolites.push("acetate");
+            
+            metabolites.push("carbon dioxide");
+            
+            metabolites.push("methane");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "DIET syntrophy from S. globosa to M. mazei",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Sphaerochaeta globosa";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Methanosarcina mazei";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("xylose");
+            
+            metabolites.push("D-glucose");
+            
+            metabolites.push("pyruvate");
+            
+            metabolites.push("acetate");
+            
+            metabolites.push("carbon dioxide");
+            
+            metabolites.push("methane");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "DIET syntrophy from C. aceticum to M. mazei",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Clostridium aceticum";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Methanosarcina mazei";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/DVM_Triculture.html b/docs/communities/DVM_Triculture.html
index 9d4a6149..c48402d0 100644
--- a/docs/communities/DVM_Triculture.html
+++ b/docs/communities/DVM_Triculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>DVM Tri-culture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000021</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000021</code>
                     </span>
                 </div>
 
@@ -1087,6 +1089,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    defined anaerobic medium (lactate 30 mM as sole organic carbon source)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Chemically defined anaerobic medium (basal salt, trace metal and vitamin stocks) reduced with Na2S; lactate (30 mM) sole organic carbon source; cultures incubated at 37 C in triplicate and sub-cultured every three weeks (5% v/v dilution).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1098/rsif.2019.0129"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1098/rsif.2019.0129
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A defined anaerobic medium, adapted from previous studies"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1098/rsif.2019.0129"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1098/rsif.2019.0129
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The cultivations were performed in triplicate, with each set incubated at 37°C for three weeks. The dilution level for sub-culturing was 5% (v/v)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1098/rsif.2019.0129"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1098/rsif.2019.0129
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"chemically defined media with lactate (30 mM), as the sole organic carbon source"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Dangl_SynComm_35.html b/docs/communities/Dangl_SynComm_35.html
index 21ba20c0..90117539 100644
--- a/docs/communities/Dangl_SynComm_35.html
+++ b/docs/communities/Dangl_SynComm_35.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Jeff Dangl&#39;s SynComm 35</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000022</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000022</code>
                     </span>
                 </div>
 
@@ -1446,7 +1448,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> General-purpose rich medium used for growing individual bacterial strains from Brassicaceae roots. Cultures grown to stationary phase, washed, and resuspended in sterile water or MgCl2 solution for inoculation into gnotobiotic plant systems.
 
                 </p>
@@ -1563,7 +1565,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Gnotobiotic Arabidopsis growth system with 0.5× MS medium, 1% sucrose, 0.8% agar. Seven-day-old seedlings inoculated with SynComm 35 bacterial suspension (OD600 0.001 per strain). Colonization monitored for 12-14 days post-inoculation.
 
                 </p>
diff --git a/docs/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.html b/docs/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.html
index f3598fa9..f23c95fe 100644
--- a/docs/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.html
+++ b/docs/communities/Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Deepwater Horizon Deep-Sea Oil Plume Succession</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000166</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000166</code>
                     </span>
                 </div>
 
@@ -1232,6 +1234,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    deep Gulf of Mexico seawater enrichment (Macondo MC252 oil + COREXIT 9500 dispersant)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">5 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Indigenous hydrocarbon-degrading bacteria enriched from deep uncontaminated Gulf water with MC252 oil and COREXIT 9500 dispersant; some enrichments amended with FeCl2.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/22616650"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:22616650
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"During 20 days of incubation at 5°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/22616650"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:22616650
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"enriched and isolated indigenous hydrocarbon-degrading bacteria from deep, uncontaminated waters from the Gulf with oil (Macondo MC252) and dispersant used during the spill (COREXIT 9500)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Defined_Multispecies_Enamel_Caries_Model.html b/docs/communities/Defined_Multispecies_Enamel_Caries_Model.html
index 678d5c37..a9163a03 100644
--- a/docs/communities/Defined_Multispecies_Enamel_Caries_Model.html
+++ b/docs/communities/Defined_Multispecies_Enamel_Caries_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Defined Multispecies Enamel Caries Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000082</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000082</code>
                     </span>
                 </div>
 
@@ -696,6 +698,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    defined-multispecies biofilm growth medium (unspecified)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Four-species biofilms grown on salivary-pellicle-coated enamel slabs with daily medium replacement; medium sucrose 0.5-1.0%, fluoride 0.4-1.0 ppm, calcium 1.0-2.0 mM.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/23446436"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:23446436
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were grown on the surface of salivary-pellicle-coated enamel slabs, with known baseline surface hardness; growth medium was changed daily"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/23446436"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:23446436
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"after 4 days of biofilm formation under the tested conditions"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.html b/docs/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.html
index 1f337ddf..3b515ef2 100644
--- a/docs/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.html
+++ b/docs/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Dehalococcoides-Desulfovibrio Lactate-Fed TCE Dechlorination Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000199</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000199</code>
                     </span>
                 </div>
 
@@ -1249,7 +1251,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The curated sources support lactate-fed anaerobic TCE-dechlorinating coculture conditions; this record does not assert the full defined-medium salts, vitamins, or transfer protocol.
 
                 </p>
diff --git a/docs/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.html b/docs/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.html
index 0fb7bbf9..bf281844 100644
--- a/docs/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.html
+++ b/docs/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Dehalococcoides-Desulfovibrio-Pelosinus Corrinoid Triculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000200</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000200</code>
                     </span>
                 </div>
 
@@ -1215,7 +1217,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The primary source supports cobalamin-free, TCE- and lactate-amended defined consortium conditions with DMB; this record does not assert the complete salts, vitamins, or transfer protocol.
 
                 </p>
diff --git a/docs/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.html b/docs/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.html
index 88225b44..45147ad3 100644
--- a/docs/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.html
+++ b/docs/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Dehalococcoides-Methanosarcina DMB-Guided Cobalamin Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000209</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000209</code>
                     </span>
                 </div>
 
@@ -1140,7 +1142,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed abstract supports H2/CO2-grown M. barkeri, chlorinated ethenes as Dehalococcoides electron acceptors, and 10 microM DMB amendment; this record does not assert the full defined medium recipe.
 
                 </p>
diff --git a/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html b/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
index a035d5cd..48fe43ae 100644
--- a/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
+++ b/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Dehalococcoides-Pelobacter Acetylene TCE Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000184</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000184</code>
                     </span>
                 </div>
 
@@ -1111,7 +1113,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports acetylene-fed anaerobic cocultures with TCE or cis-DCE as electron acceptor; detailed medium salts are not asserted here.
                 </p>
                 
diff --git a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
index 63c6d877..bd482439 100644
--- a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
+++ b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000183</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000183</code>
                     </span>
                 </div>
 
@@ -1163,7 +1165,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed abstract supports butyrate as electron donor/carbon source and TCE as electron acceptor. Full-text methods report the exact serum-bottle formulation, but those details are not asserted here because local reference validation only cached the abstract.
                 </p>
                 
diff --git a/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html b/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
new file mode 100644
index 00000000..a8eacb4d
--- /dev/null
+++ b/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
@@ -0,0 +1,949 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Dehalococcoides mccartyi CWV2 Dechlorinating Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Dehalococcoides mccartyi CWV2 Dechlorinating Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000301</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-natural">
+                            STABLE
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        TCE-contaminated groundwater (biochar-amended enrichment)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001004"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001004
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A native groundwater microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2, a strain capable of completely dechlorinating vinyl chloride (VC) to non-toxic ethene. The consortium remediates trichloroethene (TCE)-contaminated groundwater; amendment with biochar (BC600) derived from Zizania latifolia husks enhances microbial colonization and activity, accelerating TCE degradation and reducing VC accumulation. Community analysis indicates biochar promotes syntrophic hydrogen producers and electroactive bacteria that supply reducing equivalents and ensure long-term dechlorination stability.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Dehalococcoides mccartyi strain CWV2</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=61435"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:61435
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41442978/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41442978</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"a native microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2, a strain capable of completely dechlorinating VC to non-toxic ethene"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Dehalococcoides mccartyi CWV2 Dechlorinating Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Syntrophic hydrogen supply supporting reductive dechlorination</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+
+                
+                <p><strong>Target Taxon:</strong> Dehalococcoides mccartyi strain CWV2</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    hydrogen
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18276"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18276</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41442978/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41442978</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Microbial community analysis further indicated that biochar promoted syntrophic hydrogen producers and electroactive bacteria, ensuring long-term dechlorination stability."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    biochar-amended TCE groundwater enrichment (unspecified medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Native groundwater consortium enriched with BC600 biochar derived from Zizania latifolia (water bamboo) husks; performs reductive dechlorination of TCE and VC to ethene.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41442978"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41442978
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"integrates biochar derived from Zizania latifolia (water bamboo) husks with a native microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Dehalococcoides mccartyi strain CWV2"] = {
+            id: "NCBITaxon:61435",
+            label: "Dehalococcoides mccartyi strain CWV2",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("hydrogen");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Syntrophic hydrogen supply supporting reductive dechlorination",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+            var tgtKey = "Dehalococcoides mccartyi strain CWV2";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 2;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Desert_Tomato_Salt_Stress_SynCom5.html b/docs/communities/Desert_Tomato_Salt_Stress_SynCom5.html
index 105eb3f4..d3e811a6 100644
--- a/docs/communities/Desert_Tomato_Salt_Stress_SynCom5.html
+++ b/docs/communities/Desert_Tomato_Salt_Stress_SynCom5.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Desert-Derived Tomato Salt Stress SynCom5</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000096</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000096</code>
                     </span>
                 </div>
 
@@ -618,6 +620,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    tryptic soy broth (TSB)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom strains cultured in TSB at 28 °C; fast-growing strains in 1/10th TSB for 1 day and slow-growing strains in ½-strength TSB for 5 days; rhizobial strains in yeast extract mannitol (YEM) for 3-4 days; cells washed three times in 0.9% NaCl and combined into an equimolar SynCom at 5 × 10^8 CFU/mL.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35444261"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35444261
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Bacterial strains were cultured in tryptic soy broth medium (TSB) at 28 °C. Fast growing strains were cultivated in 1/10th TSB for 1 day and slow growing strains were cultivated in ½ strength TSB for 5 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Desulfovibrio_Methanococcus_Syntrophy.html b/docs/communities/Desulfovibrio_Methanococcus_Syntrophy.html
index fdd0d08c..55f5e5b1 100644
--- a/docs/communities/Desulfovibrio_Methanococcus_Syntrophy.html
+++ b/docs/communities/Desulfovibrio_Methanococcus_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Desulfovibrio-Methanococcus Syntrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000023</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000023</code>
                     </span>
                 </div>
 
@@ -1248,7 +1250,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium prepared under strict anaerobic conditions using modified Hungate technique. Boiled and cooled under N2/CO2, dispensed anaerobically into serum bottles, sealed with butyl rubber stoppers, and autoclaved. Reducing agents added from sterile anaerobic stock solutions after autoclaving. Final pH adjusted to 7.0. Resazurin indicator used to monitor anaerobiosis (colorless when reduced).
 
                 </p>
diff --git a/docs/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.html b/docs/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.html
index 98a0ae30..2d0cbed5 100644
--- a/docs/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.html
+++ b/docs/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Desulfovibrio-Methanosarcina Lactate Syntrophy</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000150</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000150</code>
                     </span>
                 </div>
 
@@ -907,7 +909,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Sulfate-free anaerobic medium with rumen fluid and vitamins used for methanogenic growth experiments.
                 </p>
                 
diff --git a/docs/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.html b/docs/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.html
index a71c3c6a..bfad0414 100644
--- a/docs/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.html
+++ b/docs/communities/Drosophila_FiveSpecies_Gnotobiotic_Gut_Microbiota.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Drosophila Five-Species Gnotobiotic Gut Microbiota</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000160</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000160</code>
                     </span>
                 </div>
 
@@ -996,7 +998,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Acetobacter members were maintained aerobically, while Lactobacillus plates were kept under carbon dioxide-enriched conditions.
                 </p>
                 
diff --git a/docs/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.html b/docs/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.html
index f821ef69..3e4fed69 100644
--- a/docs/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.html
+++ b/docs/communities/Drought_Rhizosphere_Iron_Actinobacteria_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Drought-Induced Rhizosphere Iron-Enriched Actinobacteria Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000235</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000235</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.html b/docs/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.html
new file mode 100644
index 00000000..fbeab2b6
--- /dev/null
+++ b/docs/communities/Dual_Bacillus_coagulans_Pseudomonas_putida_Lactic_Acid_Coculture.html
@@ -0,0 +1,1256 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000286</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        bioreactor fermentation of undetoxified lignocellulosic (corncob) hydrolysate
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Engineered artificial microbial consortium for L-lactic acid (LA) fermentation directly from undetoxified lignocellulosic (corncob) hydrolysates. A dual Bacillus coagulans (Heyndrickxia coagulans) system pairs a phenolic acid decarboxylase (PAD)-overexpressing biodetoxifying strain, DSM1-25280, with a high-yield LA producer, CC17B-1, and reaches 124.72 g/L LA from undetoxified hydrolysate via a sequential-inoculation division of labor. Multidimensional analysis supports a niche-succession model transitioning from biodetoxification-mediated commensalism to competitive exclusion. A sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL added as a heterologous aromatic scavenger reinforces the system, raising the LA titer to 146.00 g/L at 98.9% yield.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus coagulans DSM1-25280 (PAD-overexpressing)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1398"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1398
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"a phenolic acid decarboxylase (PAD)-overexpressing engineered strain, DSM1-25280"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus coagulans CC17B-1</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1398"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1398
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"a high-yield L-lactic acid (LA) producer, CC17B-1"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas putida KT2440 ZL</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=303"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:303
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"incorporating a sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL as a heterologous aromatic scavenger"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Biodetoxification-mediated commensalism (DSM1-25280 to CC17B-1)</h3>
+                    <span class="interaction-type">COMMENSALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Bacillus coagulans DSM1-25280 (PAD-overexpressing)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bacillus coagulans CC17B-1</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    vanillin
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18346"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18346</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"a strongly supported model of niche succession process within the system, transitioning from biodetoxification-mediated commensalism to competitive exclusion"</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"overexpression of PAD in the engineered strain DSM1-25280 not only enhanced tolerance to phenolic acids but also significantly accelerated vanillin degradation"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Competitive exclusion in the dual Bacillus coagulans consortium</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Bacillus coagulans DSM1-25280 (PAD-overexpressing)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bacillus coagulans CC17B-1</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"transitioning from biodetoxification-mediated commensalism to competitive exclusion"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Aromatic scavenging by P. putida KT2440 ZL reinforces LA fermentation</h3>
+                    <span class="interaction-type">COMMENSALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas putida KT2440 ZL</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bacillus coagulans CC17B-1</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"an enhanced three-strain co-culture system by incorporating a sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL as a heterologous aromatic scavenger"</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42098792/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42098792</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"This system further elevated the LA titer to 146.00 g/L with a yield of 98.9%"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    hydrolysate fermentation medium (100% v/v undetoxified corncob hydrolysate; YE 7.3, CSLP 18.25, NH4Cl 7.3, MgSO4 0.2, KH2PO4 0.22 g/L)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">7.2</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">50 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Dual Bacillus coagulans co-culture fermented under anaerobic conditions at 50 °C and 150 rpm in 150 mL shake flasks containing 50 mL of hydrolysate fermentation medium; 0.5 g CaCO3/g sugar added to regulate pH; strains introduced by a sequential inoculation strategy. The engineered Pseudomonas putida KT2440 ZL was initially cultivated at 30 °C and 200 rpm.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42098792"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42098792
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Fermentation was conducted under anaerobic conditions at 50°C and 150 rpm."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42098792"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42098792
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The strains were inoculated at 4 g/L (wet weight) into 150 mL shake flasks containing 50 mL of hydrolysate fermentation medium, supplemented with 0.5 g CaCO3/g sugar to regulate the pH during fermentation."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
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+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Bacillus coagulans DSM1-25280 (PAD-overexpressing)"] = {
+            id: "NCBITaxon:1398",
+            label: "Bacillus coagulans DSM1-25280 (PAD-overexpressing)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Bacillus coagulans CC17B-1"] = {
+            id: "NCBITaxon:1398",
+            label: "Bacillus coagulans CC17B-1",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Pseudomonas putida KT2440 ZL"] = {
+            id: "NCBITaxon:303",
+            label: "Pseudomonas putida KT2440 ZL",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COMMENSALISM";
+            var metabolites = [];
+            
+            
+            metabolites.push("vanillin");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Biodetoxification-mediated commensalism (DSM1-25280 to CC17B-1)",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Bacillus coagulans DSM1-25280 (PAD-overexpressing)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bacillus coagulans CC17B-1";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Competitive exclusion in the dual Bacillus coagulans consortium",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Bacillus coagulans DSM1-25280 (PAD-overexpressing)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bacillus coagulans CC17B-1";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "COMMENSALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Aromatic scavenging by P. putida KT2440 ZL reinforces LA fermentation",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas putida KT2440 ZL";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bacillus coagulans CC17B-1";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
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+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/ENIGMA_Denitrifying_SynCom.html b/docs/communities/ENIGMA_Denitrifying_SynCom.html
index 25079017..67ee79b5 100644
--- a/docs/communities/ENIGMA_Denitrifying_SynCom.html
+++ b/docs/communities/ENIGMA_Denitrifying_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>ENIGMA Denitrifying SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000024</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000024</code>
                     </span>
                 </div>
 
@@ -895,6 +897,84 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    defined anaerobic minimal medium (20 mM sodium acetate, 10 mM sodium nitrate, 0.1 g/L yeast extract)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">7.2</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> NO3- reduction growth studies were run in a defined minimal medium with 20 mM sodium acetate and 10 mM sodium NO3- plus 0.1 g/L yeast extract to support growth of 3H11 and R12; media were prepared in serum bottles and aliquoted into N2-CO2-flushed, pressurized Balch tubes. Starter cultures were grown in R2A liquid medium at 30 °C with shaking at 100 rpm.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40349173"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40349173
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"NO3- reduction growth studies were performed in Balch tubes (10-ml culture volume) at 30°C in a defined minimal medium as described previously containing 20 mM sodium acetate and 10 mM sodium NO3- at pH 7.2 with a 80:20 N2-CO2 headspace"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40349173"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40349173
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Liquid R2A cultures were incubated at 30°C with shaking at 100 rpm."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Early_Dental_Biofilm_FiveSpecies.html b/docs/communities/Early_Dental_Biofilm_FiveSpecies.html
index b702162c..8728a884 100644
--- a/docs/communities/Early_Dental_Biofilm_FiveSpecies.html
+++ b/docs/communities/Early_Dental_Biofilm_FiveSpecies.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Early Dental Biofilm Five-Species Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000081</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000081</code>
                     </span>
                 </div>
 
@@ -706,6 +708,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Todd-Hewitt broth (THB); flow-cell biofilm fed with sterile saliva
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains were cultivated aerobically on blood agar and transferred to Todd-Hewitt broth (THB) at 35 °C to mid-to-late exponential phase; the five species were inoculated sequentially into a flow-cell system and biofilms grown for 26 h at 35 °C; living biofilms were then stimulated with sterile salivary solutions containing glucose.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/21966490"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:21966490
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were inoculated sequentially into a flow cell system that permitted direct microscopic examination, and biofilms were grown for 26 h at 35°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/21966490"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:21966490
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Organisms were cultivated aerobically on blood agar (SSI, Copenhagen, Denmark) and transferred to THB (Roth, Karlsruhe, Germany) at 35°C until mid to late exponential phase prior to experimental use"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/East_River_Floodplain_Core_Microbiome.html b/docs/communities/East_River_Floodplain_Core_Microbiome.html
index 63310afd..050fed3b 100644
--- a/docs/communities/East_River_Floodplain_Core_Microbiome.html
+++ b/docs/communities/East_River_Floodplain_Core_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>East River Floodplain Core Microbiome</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000137</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000137</code>
                     </span>
                 </div>
 
@@ -697,12 +699,6 @@ <h3>Core Floodplain Aerobic and Sulfur Oxidation Capacity</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0009060</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -777,12 +773,6 @@ <h3>Low-Organic-Carbon Chemolithotrophic Activity</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015977</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1044,8 +1034,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("aerobic respiration");
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1089,8 +1077,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("carbon fixation");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/East_River_Hillslope_Riparian_Transect_Community.html b/docs/communities/East_River_Hillslope_Riparian_Transect_Community.html
index 0ec69671..f68a02af 100644
--- a/docs/communities/East_River_Hillslope_Riparian_Transect_Community.html
+++ b/docs/communities/East_River_Hillslope_Riparian_Transect_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>East River Hillslope Riparian Transect Microbial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000233</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000233</code>
                     </span>
                 </div>
 
@@ -881,17 +883,6 @@ <h3>Weathered Shale and Saturated Sediment Selenium Reduction</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1358,10 +1349,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/EcoFAB_Ring_Trial_SynCom17.html b/docs/communities/EcoFAB_Ring_Trial_SynCom17.html
index 695b4ccc..7e577f7d 100644
--- a/docs/communities/EcoFAB_Ring_Trial_SynCom17.html
+++ b/docs/communities/EcoFAB_Ring_Trial_SynCom17.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>EcoFAB 2.0 Root Microbiome Ring Trial SynCom17</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000025</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000025</code>
                     </span>
                 </div>
 
@@ -2073,6 +2075,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A (bacterial preculture); half-strength Murashige-Skoog (MS) basal salts for the EcoFAB 2.0 plant system
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">27 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom strains were grown from single colonies in R2A liquid at 27 °C (the Paraburkholderia RFP strain grown overnight in R2A shaken at 200 rpm at 27 °C), washed in ½ MS basal salts, and used to inoculate 3-day-old B. distachyon seedlings in EcoFAB 2.0 devices; plants were grown in a chamber at 26 °C (light) / 20 °C (dark) with 110-140 µmol/m²/s PPFD and 70% humidity.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40920748"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40920748
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The Paraburkholderia sp. OAS925 expressing RFP was grown overnight in 7 mL of R2A medium with Kan 20 mg/L, shaken at 200 rpm at 27 °C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40920748"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40920748
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The plates were then moved to the growth chamber with a 14 h photoperiod (16 h for lab C) at 26 °C and 10 h dark at 20 °C with photosynthetic photon flux density (PPFD) at 110 – 140 µmol/m 2 /s and 70% humidity if tunable."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html b/docs/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html
new file mode 100644
index 00000000..fecad466
--- /dev/null
+++ b/docs/communities/Ecoli_Bifidobacterium_bifidum_Infant_gut_HMO_Mutualism_Coculture.html
@@ -0,0 +1,1141 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000296</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        infant gut (in vitro co-culture)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_2100002"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:2100002
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-member infant-gut co-culture of Escherichia coli and Bifidobacterium bifidum. In healthy, term-born, breastfed infants these genera co-exist despite differing ecological strategies and share evolutionary adaptations for lactose acquisition. In vitro co-culture demonstrates a mutualistic cross-feeding interaction in which E. coli supplies cysteine to its auxotrophic partner B. bifidum, facilitating cooperative degradation of 2&#39;-fucosyllactose (the predominant human milk oligosaccharide), and the liberated monosaccharides in turn sustain E. coli growth, potentially helping regulate E. coli abundance in the infant gut.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Escherichia coli</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:562
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bifidobacterium bifidum</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1681"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1681
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Cysteine provision enabling cooperative 2&#39;-fucosyllactose degradation</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Escherichia coli</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bifidobacterium bifidum</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    cysteine
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15356"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15356</a>), 
+                    
+                    2&#39;-fucosyllactose
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=147155"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:147155</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2&#39;-fucosyllactose, the predominant human milk oligosaccharide"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Monosaccharide return sustaining E. coli growth</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Bifidobacterium bifidum</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Escherichia coli</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    monosaccharide
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=35381"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:35381</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42020426/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42020426</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    modified M9 medium (m-M9) with 0.1% (w/v) 2&#39;-fucosyllactose as the primary carbon source
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6.3</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> B. bifidum was grown on 0.1% 2&#39;FL (w/v) as the sole carbon source in modified M9 medium (m-M9) at 37 °C under anoxic conditions; E. coli grew in B. bifidum spent medium only when pH was adjusted to its initial value of 6.3. Strains were initially isolated on modified MRS agar with cysteine (0.1% w/v) and mupirocin (m-MRS), incubated at 37 °C under anaerobic conditions for 48 h.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42020426"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42020426
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"assessed its growth on 0.1% 2&#39;FL (w/v) as the primary carbon source in modified M9-medium (m-M9)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42020426"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42020426
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"B. bifidum was able to grow at 37 °C under anoxic conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42020426"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42020426
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"growth only when the pH was adjusted to its initial value of 6.3"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Escherichia coli"] = {
+            id: "NCBITaxon:562",
+            label: "Escherichia coli",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Bifidobacterium bifidum"] = {
+            id: "NCBITaxon:1681",
+            label: "Bifidobacterium bifidum",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "CROSS_FEEDER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            
+            metabolites.push("cysteine");
+            
+            metabolites.push("2\u0027-fucosyllactose");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Cysteine provision enabling cooperative 2\u0027-fucosyllactose degradation",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Escherichia coli";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bifidobacterium bifidum";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            
+            metabolites.push("monosaccharide");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Monosaccharide return sustaining E. coli growth",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Bifidobacterium bifidum";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Escherichia coli";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.html b/docs/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.html
new file mode 100644
index 00000000..c8d3d4c0
--- /dev/null
+++ b/docs/communities/Electrostimulated_Mixotrophic_VFA_Producing_Enrichment_Consortium.html
@@ -0,0 +1,1021 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Electrostimulated Mixotrophic VFA-producing Enrichment Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
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+            font-size: 0.8rem;
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+            align-items: center;
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+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
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+            border-radius: 50%;
+        }
+
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+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
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+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
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+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
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+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Electrostimulated Mixotrophic VFA-producing Enrichment Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000287</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        continuous electrostimulated bioreactor (bioelectrochemical CO2 conversion)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A specialized mixotrophic microbial consortium enriched in a continuous electrostimulated bioreactor operated at a constant potential of 300 mV for CO2 conversion into volatile fatty acids. Decreasing hydraulic retention time (HRT) selected for a spatially organized community in which Enterococcus and Clostridium dominated the planktonic phase while Desulfovibrio and Enterococcus were enriched in the electrode biofilm. This syntrophic organization enhanced biomass-specific inorganic carbon removal and redirected carbon flux toward acetate, a key product of acetogenic pathways, with electrode-associated taxa contributing reducing equivalents that supported autotrophic CO2/HCO3- fixation.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Enterococcus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1350"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1350
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.21203/rs.3.rs-9518331/v1"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.21203/rs.3.rs-9518331/v1</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Enterococcus and Clostridium dominating the planktonic phase and Desulfovibrio and Enterococcus enriched in the electrode biofilm"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Clostridium</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1485"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1485
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.21203/rs.3.rs-9518331/v1"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.21203/rs.3.rs-9518331/v1</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Enterococcus and Clostridium dominating the planktonic phase and Desulfovibrio and Enterococcus enriched in the electrode biofilm"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Desulfovibrio</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=872"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:872
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.21203/rs.3.rs-9518331/v1"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.21203/rs.3.rs-9518331/v1</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Desulfovibrio and Enterococcus enriched in the electrode biofilm"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Electrostimulated Mixotrophic VFA-producing Enrichment Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Spatially organized syntrophy enhancing inorganic carbon removal</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Desulfovibrio</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Enterococcus</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    acetate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30089"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30089</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.21203/rs.3.rs-9518331/v1"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.21203/rs.3.rs-9518331/v1</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"This syntrophic organization enhanced biomass-specific IC removal by 2.6-fold"</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.21203/rs.3.rs-9518331/v1"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.21203/rs.3.rs-9518331/v1</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"redirected carbon flux toward acetate, a key product of acetogenic pathways"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Enterococcus"] = {
+            id: "NCBITaxon:1350",
+            label: "Enterococcus",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Clostridium"] = {
+            id: "NCBITaxon:1485",
+            label: "Clostridium",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Desulfovibrio"] = {
+            id: "NCBITaxon:872",
+            label: "Desulfovibrio",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROTROPH", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("acetate");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Spatially organized syntrophy enhancing inorganic carbon removal",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Desulfovibrio";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Enterococcus";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
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+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
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+            });
+        });
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+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
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+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html b/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
new file mode 100644
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--- /dev/null
+++ b/docs/communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
@@ -0,0 +1,1178 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate - CommunityMech</title>
+    <style>
+        :root {
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+        .interaction-header {
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+        .interaction-type {
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+            font-size: 0.875rem;
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+        .flow-arrow {
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+        .evidence-list {
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+            margin: 0.5rem 0;
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+            color: var(--text);
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+            margin: 0.5rem 0;
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+        .role-badge {
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+        .network-tooltip strong {
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+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
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+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
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+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
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+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000298</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        microbial electrosynthesis reactor (CO2-to-acetate bioreactor)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Defined synthetic microbial electrosynthesis (MES) consortia constructed by pairing the model bidirectional electroactive bacterium Shewanella oneidensis MR-1 with either the electroactive acetogen Clostridium aceticum or the nonelectroactive acetogen Acetobacterium woodii, mimicking functional guilds of natural MES communities. Co-cultivation boosts CO2-to-acetate production by up to 88%. The two pairings use distinct interspecies electron transfer (IET) modes, namely direct interspecies electron transfer (DIET) via cytochrome c and riboflavin at the biofilm-electrode interface in the S. oneidensis-C. aceticum consortium, versus H2/formate-mediated IET in the planktonic phase for the S. oneidensis-A. woodii consortium. This metabolic stratification lets S. oneidensis act as an &#34;ecosystem engineer&#34; orchestrating electron flow across biofilm and suspension niches.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Shewanella oneidensis MR-1</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=70863"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:70863
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"defined synthetic consortia are constructed by pairing Shewanella oneidensis MR-1, a model bidirectional electroactive bacterium"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Clostridium aceticum (electroactive acetogen)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=84022"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:84022
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"with Clostridium aceticum (electroactive acetogen) or Acetobacterium woodii (nonelectroactive acetogen)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Acetobacterium woodii (nonelectroactive acetogen)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=33952"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:33952
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"with Clostridium aceticum (electroactive acetogen) or Acetobacterium woodii (nonelectroactive acetogen)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>DIET from S. oneidensis to C. aceticum</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Shewanella oneidensis MR-1</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Clostridium aceticum (electroactive acetogen)</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    riboflavin
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17015"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17015</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"DIET via cytochrome c and riboflavin dominates at the biofilm-electrode interface in S. oneidensis-C. aceticum consortia"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>H2/formate-mediated IET from S. oneidensis to A. woodii</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Shewanella oneidensis MR-1</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Acetobacterium woodii (nonelectroactive acetogen)</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    dihydrogen
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18276"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18276</a>), 
+                    
+                    formate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15740"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15740</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"whereas S. oneidensis-A. woodii consortia prefer H2/formate-mediated IET in the planktonic phase"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    DSMZ-Medium 135 base medium (optimized, cathode chamber)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Cathode chamber filled with the culture medium; operated in sequential 7-day cycles with fresh medium added after each cycle.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41236292"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41236292
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The reaction was conducted in a thermostatic chamber (37 °C) with a headspace atmosphere of N2/CO2 (80:20)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41236292"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41236292
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The culture medium for these bacteria is an optimized DSMZ-Medium135 base medium"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Shewanella oneidensis MR-1"] = {
+            id: "NCBITaxon:70863",
+            label: "Shewanella oneidensis MR-1",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROGEN", "ELECTRON_DONOR", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Clostridium aceticum (electroactive acetogen)"] = {
+            id: "NCBITaxon:84022",
+            label: "Clostridium aceticum (electroactive acetogen)",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROTROPH", "ELECTRON_ACCEPTOR", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Acetobacterium woodii (nonelectroactive acetogen)"] = {
+            id: "NCBITaxon:33952",
+            label: "Acetobacterium woodii (nonelectroactive acetogen)",
+            abundance: "UNKNOWN",
+            roles: ["ELECTRON_ACCEPTOR", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("riboflavin");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "DIET from S. oneidensis to C. aceticum",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Shewanella oneidensis MR-1";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Clostridium aceticum (electroactive acetogen)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("dihydrogen");
+            
+            metabolites.push("formate");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "H2/formate-mediated IET from S. oneidensis to A. woodii",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Shewanella oneidensis MR-1";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Acetobacterium woodii (nonelectroactive acetogen)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html b/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
index a4996046..efe430d2 100644
--- a/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
+++ b/docs/communities/Emiliania_Phaeobacter_Dynamic_Interaction.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000143</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000143</code>
                     </span>
                 </div>
 
@@ -884,7 +886,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> E. huxleyi CCMP3266 was grown in L1 medium without sodium silicate; P. inhibens DSM 17395 was added to algal cultures after four days.
                 </p>
                 
diff --git a/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html b/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
index fa26b370..f8c73fb3 100644
--- a/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
+++ b/docs/communities/Engineered_Gut_Amino_Acid_CrossFeeding_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Engineered Gut Amino Acid Cross-Feeding Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000151</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000151</code>
                     </span>
                 </div>
 
@@ -984,7 +986,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Modified M9 minimal medium with glucose and starch carbon sources; cross-fed amino acids were omitted or supplemented depending on the assay.
                 </p>
                 
diff --git a/docs/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html b/docs/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html
new file mode 100644
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--- /dev/null
+++ b/docs/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html
@@ -0,0 +1,1111 @@
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+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000299</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        plastic-contaminated agricultural soil
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002116"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002116
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Synthetic bacterial consortium for polyethylene (PE) biodegradation, built from three strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-isolated from plastic-contaminated agricultural soils. A dual-strain consortium of YF2 and Y2 degraded PE more efficiently than individual strains or the full three-strain combination, using PE as the sole carbon source and inducing oxidative modifications and physical erosion of the polymer. Genomic analysis showed a complementary enzymatic division of labor - YF2 (oxidases LadA, AlkB, CYP450) performs backbone cleavage as the primary degrader, while Y2 (esterases and lipases) carries out intermediate metabolism through cross-feeding.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Ensifer sp. YF2</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=106591"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:106591
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Three bacterial strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-were isolated from plastic-contaminated soils."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Sphingobacterium sp. Y2</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=28453"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:28453
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Three bacterial strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-were isolated from plastic-contaminated soils."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Chryseobacterium sp. MF1</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=59732"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:59732
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Three bacterial strains-Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1-were isolated from plastic-contaminated soils."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Metabolic division of labor in polyethylene degradation</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Ensifer sp. YF2</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Sphingobacterium sp. Y2</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"YF2, encoding key oxidases (LadA, AlkB, CYP450), served as the primary degrader for backbone cleavage, while Y2, enriched with esterases and lipases, facilitated intermediate metabolism through cross-feeding."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Synergistic enhancement of PE degradation in the dual-strain consortium</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Ensifer sp. YF2</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Sphingobacterium sp. Y2</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"A dual-strain consortium (YF2 +Y2) demonstrated enhanced degradation compared to individual strains and the three-strain combination, indicating that functional compatibility rather than taxonomic richness drives consortium performance."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    polyethylene as sole carbon source (medium composition not specified in abstract)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Consortium cultivated with polyethylene (PE) provided as the sole carbon source; full medium, temperature and pH are not reported in the open-access abstract (article paywalled).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41996795"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41996795
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The consortium utilized PE as the sole carbon source, inducing oxidative modifications and physical erosion of the polymer surface."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Ensifer sp. YF2"] = {
+            id: "NCBITaxon:106591",
+            label: "Ensifer sp. YF2",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Sphingobacterium sp. Y2"] = {
+            id: "NCBITaxon:28453",
+            label: "Sphingobacterium sp. Y2",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER", "CROSS_FEEDER"]
+        };
+        
+        taxonData["Chryseobacterium sp. MF1"] = {
+            id: "NCBITaxon:59732",
+            label: "Chryseobacterium sp. MF1",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Metabolic division of labor in polyethylene degradation",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Ensifer sp. YF2";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Sphingobacterium sp. Y2";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Synergistic enhancement of PE degradation in the dual-strain consortium",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Ensifer sp. YF2";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Sphingobacterium sp. Y2";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html b/docs/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html
index 1bf052b1..457c82d7 100644
--- a/docs/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html
+++ b/docs/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000237</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000237</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Ewaste_Bioleaching_Consortium.html b/docs/communities/Ewaste_Bioleaching_Consortium.html
index 59effa52..6df7b871 100644
--- a/docs/communities/Ewaste_Bioleaching_Consortium.html
+++ b/docs/communities/Ewaste_Bioleaching_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>E-waste Bioleaching Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000026</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000026</code>
                     </span>
                 </div>
 
@@ -768,12 +770,6 @@ <h3>Ferrous Iron Oxidation for Metal Dissolution</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -875,17 +871,6 @@ <h3>Base and Precious Metal Solubilization</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -953,12 +938,6 @@ <h3>Sulfuric Acid Generation for pH Maintenance</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1113,12 +1092,6 @@ <h3>Two-Step Iron and Sulfur Oxidation Partnership</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         nitrogen fixation
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0009399"
@@ -1332,6 +1305,84 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    0Cm mineral salts medium (acidophilic iron-oxidizing culture)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">1.2</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> 0Cm basal salts medium derived from 0Km with reduced (NH4)2SO4; pH maintained at 1.2 with H2SO4.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2021.669738"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2021.669738
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The temperature of the reactor was maintained at 35°C with a thermostatic bath (Lauda), and the pH was daily adjusted to 1.2 with H2SO4"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2021.669738"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2021.669738
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"mixing of gas, liquid, and solids with a stirring speed of 650 rpm"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1433,8 +1484,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -1481,10 +1530,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1526,8 +1571,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1611,8 +1654,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("nitrogen fixation");
             
             
diff --git a/docs/communities/Ferroplasma_Leptospirillum_Syntrophy.html b/docs/communities/Ferroplasma_Leptospirillum_Syntrophy.html
index fa45606e..446a66fe 100644
--- a/docs/communities/Ferroplasma_Leptospirillum_Syntrophy.html
+++ b/docs/communities/Ferroplasma_Leptospirillum_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Ferroplasma-Leptospirillum Iron-Cycling Syntrophy</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000027</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000027</code>
                     </span>
                 </div>
 
@@ -631,12 +633,6 @@ <h3>Iron Oxidation by Leptospirillum</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -726,23 +722,6 @@ <h3>Organic Matter Consumption by Ferroplasma</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -819,12 +798,6 @@ <h3>Iron Oxidation by Ferroplasma</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -907,17 +880,6 @@ <h3>Enhanced Chalcopyrite Bioleaching</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1419,7 +1381,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium adjusted to initial pH ~1.7 with H2SO4. For syntrophy experiments, yeast extract concentration is critical: 0.04% wt/vol (0.4 g/L) is optimal for F. acidiphilum growth. Higher concentrations (0.5 g/L) create organic matter stress that demonstrates the syntrophic benefit of co-culture. Co-culture achieves 31.5% higher copper extraction and 31.7% higher Fe3+ generation compared to monocultures under organic stress conditions. Leptospirillum is an obligate aerobe requiring oxygen, while Ferroplasma is microaerophilic and tolerates lower O2. Cultures maintained with aeration but not vigorous sparging to accommodate both organisms.
                 </p>
                 
@@ -1540,8 +1502,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -1582,12 +1542,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1629,8 +1583,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1673,10 +1625,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/GLBRC_Exometabolite_Transwell_SynCom.html b/docs/communities/GLBRC_Exometabolite_Transwell_SynCom.html
index 9b1ba441..1e699e68 100644
--- a/docs/communities/GLBRC_Exometabolite_Transwell_SynCom.html
+++ b/docs/communities/GLBRC_Exometabolite_Transwell_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>GLBRC Exometabolite Transwell SynCom System</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000091</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000091</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    tryptic soy agar/broth (TSA50) - representative Transwell assay
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">29 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Physically separated populations share a common medium reservoir; plates incubated with gentle shaking to homogenize member access to media and exometabolites.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29152587"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29152587
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"cultures in test tubes were incubated at 29°C at 200 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29152587"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29152587
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"each well has a 0.22-μm-pore filter bottom and the plate fits into a shared medium reservoir"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/GLBRC_Populus_Variovorax_SynCom28.html b/docs/communities/GLBRC_Populus_Variovorax_SynCom28.html
index 368e5b6e..2ddb6027 100644
--- a/docs/communities/GLBRC_Populus_Variovorax_SynCom28.html
+++ b/docs/communities/GLBRC_Populus_Variovorax_SynCom28.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>GLBRC Populus Variovorax SynCom28</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000028</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000028</code>
                     </span>
                 </div>
 
@@ -2042,6 +2044,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A (strain propagation) with in planta Populus microcosm colonization
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains grown from R2A plates in liquid R2A at 30°C/200 rpm, then inoculated into sterile Populus microcosms; colonization assessed after 3 weeks.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41543249"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41543249
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Microcosms were sealed and maintained under controlled growth chamber conditions (16 h photoperiod, 21°C/17°C day/night, 60% RH) for 3 weeks"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41543249"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41543249
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A single colony from each plate was used to inoculate 5 mL of R2A and incubated overnight at 30°C and 200 rpm by continually shaking"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/GLBRC_UFMP_Fermentation_Community.html b/docs/communities/GLBRC_UFMP_Fermentation_Community.html
index e71eb7da..ec995b27 100644
--- a/docs/communities/GLBRC_UFMP_Fermentation_Community.html
+++ b/docs/communities/GLBRC_UFMP_Fermentation_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>GLBRC Ultra-Filtered Milk Permeate Fermentation Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000029</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000029</code>
                     </span>
                 </div>
 
@@ -1183,6 +1185,84 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Ultra-filtered milk permeate (UFMP) feed, supplemented with 400 mg N/L as NH4Cl
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">5.5</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> pH maintained at 5.5 by automated addition of 5M NaOH; temperature controlled at 35°C; 6-day hydraulic/solids retention time.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37324413"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37324413
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Temperature and pH were maintained constant at 35°C and 5.5, respectively"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37324413"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37324413
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The pH was monitored and maintained at 5.5 with a pH probe, a pH controller, and automated addition of 5M NaOH"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/GOM_Oil_Degrading_Consortium.html b/docs/communities/GOM_Oil_Degrading_Consortium.html
index 3a71ce70..99855db3 100644
--- a/docs/communities/GOM_Oil_Degrading_Consortium.html
+++ b/docs/communities/GOM_Oil_Degrading_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Gulf of Mexico Oil-Degrading Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000030</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000030</code>
                     </span>
                 </div>
 
@@ -763,17 +765,6 @@ <h3>Polyaromatic Hydrocarbon Degradation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -855,6 +846,66 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    marine medium (filtered-sterilized seawater) with API 35 crude oil as sole carbon source
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> 0.5 g/L sterile API 35 GoM crude oil supplied as the sole carbon source; N and P added at a 100:10:1 C:N:P ratio.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmars.2022.962071"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmars.2022.962071
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Glass flasks containing 20 mL of marine medium were inoculated with each consortium and incubated for 75 days at 30°C, 180 RPM."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -994,10 +1045,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("aromatic compound catabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Garlic_Pseudomonas_SynCom6.html b/docs/communities/Garlic_Pseudomonas_SynCom6.html
index bbc50ceb..27c2db32 100644
--- a/docs/communities/Garlic_Pseudomonas_SynCom6.html
+++ b/docs/communities/Garlic_Pseudomonas_SynCom6.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Garlic Rhizosphere Pseudomonas SynCom6</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000095</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000095</code>
                     </span>
                 </div>
 
@@ -618,6 +620,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Luria-Bertani medium (LB)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Six Pseudomonas strains grown at 28°C (strain B8-7 at 37°C) in 10 ml LB.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32762153"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32762153
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Bacterial strains were cultured (28°C for six Pseudomonas strains, 37°C for B8-7, 18 mm × 180 mm glass tubes, shaking at 200 r.p.m.) in 10 ml LB for 2 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Geobacter_Clostridium_DIET.html b/docs/communities/Geobacter_Clostridium_DIET.html
index 66b4bf85..90316633 100644
--- a/docs/communities/Geobacter_Clostridium_DIET.html
+++ b/docs/communities/Geobacter_Clostridium_DIET.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Geobacter-Clostridium DIET Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000031</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000031</code>
                     </span>
                 </div>
 
@@ -1123,7 +1125,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium supplemented with 10 mL vitamin solution (DSMZ medium 141), 10 mL trace element solution (DSMZ medium 141), and 0.5 mL trace element solution SL-10 (DSMZ medium 320) per liter. Cultures maintained at 35°C with constant agitation under strict anaerobic conditions using Hungate technique. Physical contact between bacteria enables electron exchange either directly via interspecies wiring or indirectly using soluble electron mediators like L-cysteine present in medium.
                 </p>
                 
diff --git a/docs/communities/Geobacter_Methanosaeta_DIET.html b/docs/communities/Geobacter_Methanosaeta_DIET.html
index 5f121f60..55618088 100644
--- a/docs/communities/Geobacter_Methanosaeta_DIET.html
+++ b/docs/communities/Geobacter_Methanosaeta_DIET.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Geobacter-Methanosaeta DIET Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000032</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000032</code>
                     </span>
                 </div>
 
@@ -922,7 +924,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Modified freshwater medium boiled to reduce oxygen solubility, then cooled under N2/CO2 (80:20) gas mixture. Ethanol (20 mM) and other additives added from anaerobic sterile stocks: 1 mM cysteine and 0.5 mM Na2S·9H2O as reducing agents. Bicarbonate/CO2 serves as sole electron acceptor. Vitamins included per standard formulation. Cultures grown in 10 mL anaerobic pressure tubes or serum bottles; larger studies used 50 mL medium in 160 mL serum bottles. Sampling performed with N2/CO2 (80:20) degassed hypodermic syringes. Digesters operated at 37°C mesophilic conditions.
                 </p>
                 
diff --git a/docs/communities/Geobacter_Methanosarcina_DIET.html b/docs/communities/Geobacter_Methanosarcina_DIET.html
index 435f6558..e93b4b27 100644
--- a/docs/communities/Geobacter_Methanosarcina_DIET.html
+++ b/docs/communities/Geobacter_Methanosarcina_DIET.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Geobacter-Methanosarcina DIET Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000033</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000033</code>
                     </span>
                 </div>
 
@@ -1034,7 +1036,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Modified DSM 120 medium with no yeast extract, Casitone, or resazurin. Specific composition: 0.5 mM sulfide, 1 mM cysteine, 0.002 g/L CaCl2·2H2O, 1 g/L NaCl, 2 g/L NaHCO3. Medium boiled to reduce oxygen, cooled under N2/CO2 gas mixture. Sulfide and cysteine essential for long-term M. barkeri cultivation. Initial cocultures: 0.5 ml each organism in 9 ml medium; later transfers: 10% inocula in 45 ml medium.
                 </p>
                 
diff --git a/docs/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.html b/docs/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.html
index 0cd00054..d7f452fc 100644
--- a/docs/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.html
+++ b/docs/communities/Geobacter_Pseudomonas_Formate_Fumarate_Electroactive_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Geobacter-Pseudomonas Formate-Fumarate Electroactive Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000201</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000201</code>
                     </span>
                 </div>
 
@@ -1116,7 +1118,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The source supports restricted medium with formate and fumarate for coculture growth; this record does not assert the complete salts, atmosphere, temperature, or transfer recipe.
 
                 </p>
diff --git a/docs/communities/Grassland_Soil_WetUp_Virus_Host_Community.html b/docs/communities/Grassland_Soil_WetUp_Virus_Host_Community.html
index 2cab0ae3..737b8816 100644
--- a/docs/communities/Grassland_Soil_WetUp_Virus_Host_Community.html
+++ b/docs/communities/Grassland_Soil_WetUp_Virus_Host_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Grassland Soil Wet-Up Virus-Host Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000224</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000224</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.html b/docs/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.html
index 8aaab875..e8560fe0 100644
--- a/docs/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.html
+++ b/docs/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Groundwater Elusimicrobia Diverse Metabolisms Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000242</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000242</code>
                     </span>
                 </div>
 
@@ -602,17 +604,6 @@ <h3>Versatile Heterotrophic/Autotrophic Respiration</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -952,10 +943,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Hanford_300_Area_Unconfined_Aquifer_Community.html b/docs/communities/Hanford_300_Area_Unconfined_Aquifer_Community.html
index 6e35a9ab..e7c48164 100644
--- a/docs/communities/Hanford_300_Area_Unconfined_Aquifer_Community.html
+++ b/docs/communities/Hanford_300_Area_Unconfined_Aquifer_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Hanford 300 Area Unconfined Aquifer Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000138</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000138</code>
                     </span>
                 </div>
 
@@ -679,17 +681,6 @@ <h3>Columbia River Intrusion Community Turnover</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -765,12 +756,6 @@ <h3>Depth-Structured Redox Guilds</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019329</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1006,10 +991,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1053,8 +1034,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("nitrification");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.html b/docs/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.html
index a4607a88..40dbac06 100644
--- a/docs/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.html
+++ b/docs/communities/High_Solids_Switchgrass_Methanogenic_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>High-Solids Switchgrass Methanogenic Microbiome</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000194</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000194</code>
                     </span>
                 </div>
 
@@ -1295,7 +1297,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The paper reports semi-continuous operation on mid-season switchgrass with solids loading increased from 30 to 75, 120, and 150 g/L; full mineral medium details are not asserted here.
 
                 </p>
diff --git a/docs/communities/Honeybee_Core20_Defined_Microbiota.html b/docs/communities/Honeybee_Core20_Defined_Microbiota.html
index 7936c896..eafbf629 100644
--- a/docs/communities/Honeybee_Core20_Defined_Microbiota.html
+++ b/docs/communities/Honeybee_Core20_Defined_Microbiota.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Honeybee Core-20 Defined Microbiota</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000124</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000124</code>
                     </span>
                 </div>
 
@@ -618,6 +620,66 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    heart infusion agar (with 5% sheep blood), MRS agar, or TPY agar
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">CAPNOPHILIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Core-20 strains were revived from -80°C glycerol stocks on rich non-selective agar media before community assembly and honeybee colonization.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36532452"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36532452
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The glycerol stocks were plated on heart infusion agar supplemented with 5% (vol/vol) defibrinated sheep’s blood (Solarbio, Beijing, China), MRS agar (Solarbio, Beijing, China) or TPY agar (Solarbio, Beijing, China) incubated at 35°C in 5% CO2 for 2–3 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.html b/docs/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.html
index 36c53a1e..ed33d430 100644
--- a/docs/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.html
+++ b/docs/communities/Horonobe_Mizunami_URL_Subsurface_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Horonobe and Mizunami Underground Research Laboratory Subsurface Microbiome<
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000218</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000218</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Iberian_Pit_Lake_Stratified_Community.html b/docs/communities/Iberian_Pit_Lake_Stratified_Community.html
index 4b5cad63..83ec6bc6 100644
--- a/docs/communities/Iberian_Pit_Lake_Stratified_Community.html
+++ b/docs/communities/Iberian_Pit_Lake_Stratified_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Iberian Pit Lake Stratified Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000034</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000034</code>
                     </span>
                 </div>
 
@@ -938,12 +940,6 @@ <h3>Stratified Iron Redox Cycling</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1199,12 +1195,6 @@ <h3>Subsurface Heterotrophic Carbon Scavenging</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         tricarboxylic acid cycle
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006099"
@@ -1687,8 +1677,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1823,8 +1811,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("tricarboxylic acid cycle");
             
             
diff --git a/docs/communities/Industrial_Bioreactor_Consortium.html b/docs/communities/Industrial_Bioreactor_Consortium.html
index 26944c7a..f0cf9f97 100644
--- a/docs/communities/Industrial_Bioreactor_Consortium.html
+++ b/docs/communities/Industrial_Bioreactor_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Industrial Bioleaching Reactor Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000035</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000035</code>
                     </span>
                 </div>
 
@@ -929,12 +931,6 @@ <h3>Thermophilic Ferrous Iron Oxidation in Early Reactor Stages</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1025,12 +1021,6 @@ <h3>Thermophilic Sulfur Oxidation to Sulfuric Acid</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1094,23 +1084,6 @@ <h3>Mid-Stage Mixotrophic Iron Oxidation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                    <li>
-                        organic substance metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1167,12 +1140,6 @@ <h3>Late-Stage Extreme Acidophile Iron Oxidation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1251,17 +1218,6 @@ <h3>Chalcopyrite Dissolution by Ferric Iron</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1338,12 +1294,6 @@ <h3>Organic Matter Scavenging by Cuniculiplasma</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance metabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
-                    </li>
-                    
                     <li>
                         heterotrophic metabolism
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0019319"
@@ -1405,17 +1355,6 @@ <h3>Early-Stage Iron Oxidation with Leptospirillum</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1465,17 +1404,6 @@ <h3>Ferroplasma Species Complementarity</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1517,17 +1445,6 @@ <h3>Thermoplasmatales Archaeal Community Structure</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1855,6 +1772,110 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    basal salts solution (moderately thermophilic acidophile medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">2.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">45 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Basal salts solution ((NH4)2SO4 3 g/L, KCl 0.1 g/L, K2HPO4 0.5 g/L, MgSO4·7H2O 0.5 g/L, Ca(NO3)2 0.01 g/L), pH adjusted to 2.0 with 9 M sulfuric acid; ferrous sulfate, elemental sulfur, and chalcopyrite supplied as energy sources; reactor aerated at 200 ml/h/L; culture adapted to 20% (wt/vol) chalcopyrite pulp density by serial subculturing over &gt;2 years.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24242252"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24242252
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All four media consisted of a basal salts solution containing (NH4)2SO4 (3 g/liter), KCl (0.1 g/liter), K2HPO4 (0.5 g/liter), MgSO4·7H2O (0.5 g/liter), and Ca(NO3)2 (0.01 g/liter)."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24242252"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24242252
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The pH of the solution was adjusted to 2.0 with 9 M sulfuric acid."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24242252"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24242252
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"work volume, 8 liters; pulp density, 20% (wt/vol); agitation rate, 200 rpm; temperature, 45°C; airflow, 200 ml/h/liter; inoculum size, 80 ml."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24242252"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24242252
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Depending on the pulp density, the duration of incubation of each subculture ranged from 5 to 28 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1975,8 +1996,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -2018,8 +2037,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -2060,12 +2077,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            processes.push("organic substance metabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -2102,8 +2113,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -2151,10 +2160,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -2196,8 +2201,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("organic substance metabolic process");
-            
             processes.push("heterotrophic metabolism");
             
             
@@ -2236,10 +2239,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -2278,10 +2277,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -2316,10 +2311,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.html b/docs/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.html
index 43c319d0..fa7dbb72 100644
--- a/docs/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.html
+++ b/docs/communities/Industrial_Milk_Line_FourSpecies_Model_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Industrial Milk-Line Four-Species Model Biofilm</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000152</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000152</code>
                     </span>
                 </div>
 
@@ -1031,7 +1033,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Strains were routinely cultivated on tryptic soy agar plates or in liquid tryptic soy broth with agitation.
                 </p>
                 
diff --git a/docs/communities/Infant_Gut_DNA_Phage_Succession_Community.html b/docs/communities/Infant_Gut_DNA_Phage_Succession_Community.html
index 42ae176b..388ecb41 100644
--- a/docs/communities/Infant_Gut_DNA_Phage_Succession_Community.html
+++ b/docs/communities/Infant_Gut_DNA_Phage_Succession_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Infant Gut DNA Phageome Succession Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000223</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000223</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Infant_Gut_Prebiotic_Response_SynCom.html b/docs/communities/Infant_Gut_Prebiotic_Response_SynCom.html
new file mode 100644
index 00000000..285e4738
--- /dev/null
+++ b/docs/communities/Infant_Gut_Prebiotic_Response_SynCom.html
@@ -0,0 +1,1281 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Infant-gut Prebiotic-response SynCom - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
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+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
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+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
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+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
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+            position: absolute;
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+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
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+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Infant-gut Prebiotic-response SynCom</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000281</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        early-life (infant) gut; donor-derived faecal fermentations
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_2100002"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:2100002
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A defined synthetic microbial community (SynCom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. Human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promote bifidobacterial expansion, while Bacteroides/Phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. The SynCom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with Phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters Escherichia coli metabolic activity. Competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk pH.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Bifidobacterium spp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1678"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1678
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.64898/2026.05.29.728681"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"both human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promoted bifidobacterial expansion"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacteroides/Phocaeicola spp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=816"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:816
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.64898/2026.05.29.728681"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Bacteroides/Phocaeicola species varied according to feeding background and substrate identity"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Phocaeicola vulgatus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=821"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:821
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.64898/2026.05.29.728681"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Phocaeicola vulgatus as a context-dependent ecological hub that disproportionately shaped succinate and propionate production"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Escherichia coli</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=562"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:562
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.64898/2026.05.29.728681"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"altered  Escherichia coli metabolic activity without affecting its abundance"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Infant-gut Prebiotic-response SynCom</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Substrate-dependent cross-feeding network</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.64898/2026.05.29.728681"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Mechanistic dissection using SynCom revealed extensive cross-feeding networks and substrate-dependent interaction rewiring"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Phocaeicola vulgatus hub modulates Escherichia coli metabolism</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Phocaeicola vulgatus</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Escherichia coli</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    succinate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=26806"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:26806</a>), 
+                    
+                    propionate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17272"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17272</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.64898/2026.05.29.728681"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"disproportionately shaped succinate and propionate production and altered  Escherichia coli metabolic activity without affecting its abundance"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Lactate-mediated species-specific inhibition</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    lactate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=24996"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:24996</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.64898/2026.05.29.728681"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.64898/2026.05.29.728681</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"with lactate exerting species-specific inhibitory effects independent of bulk pH changes"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    eGAM (enhanced Gifu Anaerobic Medium); adjusted M9 minimal medium for metabolic labelling
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Enhanced GAM (eGAM) was used for all routine culturing (adjusted M9 minimal medium for metabolic labelling and secondary-metabolite production); exact medium composition is given in the paper&#39;s supplementary Excel sheet. For SynCom assembly, baseline growth rates were measured in eGAM+glucose (1:100 dilution from a two-day culture); strains were abundance-equalised to reach OD 0.2 at 5 h, and each 48 h culture was centrifuged (3000 x g, 10 min, RT) and resuspended in fresh medium before pooling.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.64898/2026.05.29.728681"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.64898/2026.05.29.728681
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All bacteria were grown under anaerobic conditions (5% CO2, 5% H2, balanced with N2) using an anaerobic vinyl chamber (Coy Laboratory Products) at 37°C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.64898/2026.05.29.728681"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.64898/2026.05.29.728681
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"As medium either eGAM (enhanced GAM; for all culturing if not indicated differently) or adjusted M9 minimal medium (for metabolic labelling and secondary metabolite production) was used"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.64898/2026.05.29.728681"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.64898/2026.05.29.728681
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"we constructed a six-member simplified defined microbial community (referred to as SynCom; see Methods) comprising Phocaeicola vulgatus"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Bifidobacterium spp."] = {
+            id: "NCBITaxon:1678",
+            label: "Bifidobacterium spp.",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "CROSS_FEEDER"]
+        };
+        
+        taxonData["Bacteroides/Phocaeicola spp."] = {
+            id: "NCBITaxon:816",
+            label: "Bacteroides/Phocaeicola spp.",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "CROSS_FEEDER"]
+        };
+        
+        taxonData["Phocaeicola vulgatus"] = {
+            id: "NCBITaxon:821",
+            label: "Phocaeicola vulgatus",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+        taxonData["Escherichia coli"] = {
+            id: "NCBITaxon:562",
+            label: "Escherichia coli",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Substrate-dependent cross-feeding network",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            
+            metabolites.push("succinate");
+            
+            metabolites.push("propionate");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Phocaeicola vulgatus hub modulates Escherichia coli metabolism",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Phocaeicola vulgatus";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Escherichia coli";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            
+            metabolites.push("lactate");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Lactate-mediated species-specific inhibition",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 7;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Infant_Gut_Strain_Persistence_Maternal_Community.html b/docs/communities/Infant_Gut_Strain_Persistence_Maternal_Community.html
index c90912cf..b49b0616 100644
--- a/docs/communities/Infant_Gut_Strain_Persistence_Maternal_Community.html
+++ b/docs/communities/Infant_Gut_Strain_Persistence_Maternal_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Infant Gut Strain Persistence and Maternal Seeding Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000240</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000240</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Ion_Adsorption_REE_Indigenous_Community.html b/docs/communities/Ion_Adsorption_REE_Indigenous_Community.html
index d843625d..f830fd03 100644
--- a/docs/communities/Ion_Adsorption_REE_Indigenous_Community.html
+++ b/docs/communities/Ion_Adsorption_REE_Indigenous_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Ion-Adsorption REE Indigenous Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000036</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000036</code>
                     </span>
                 </div>
 
@@ -995,17 +997,6 @@ <h3>Bioweathering and REE Mineral Dissolution</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1160,17 +1151,6 @@ <h3>Fungal Bioweathering and Mineral Dissolution</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1242,17 +1222,6 @@ <h3>Oligotrophic REE Mobilization and Deep Profile Colonization</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1444,6 +1413,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Luria-Bertani (LB) medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Community members (incl. Bacillus and Micrococcus) were isolated on R2A separation medium (incubated at 28°C for 5–7 days), then cultivated in LB (yeast extract 5.0, tryptone 5.0, NaCl 10.0 g/L) for the REE biosorption experiments.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35708325"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35708325
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All the bacteria were cultivated in Luria-Bertani (LB) medium at 25°C for 24 h. LB had the following composition (in g L −1 of ultrapure water): yeast extract, 5.00; tryptone, 5.00; NaCl, 10.00 (pH 6.9 to 7.1)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35708325"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35708325
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"R2A was used as the separation culture medium."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1608,10 +1645,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1693,10 +1726,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1735,10 +1764,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Jala_Maize_PGPB_SynCom.html b/docs/communities/Jala_Maize_PGPB_SynCom.html
index 69f68a04..e910c98b 100644
--- a/docs/communities/Jala_Maize_PGPB_SynCom.html
+++ b/docs/communities/Jala_Maize_PGPB_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Jala Maize PGPB SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000099</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000099</code>
                     </span>
                 </div>
 
@@ -744,6 +746,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Luria Bertani (LB) medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom member strains were revived on solid LB and grown individually in LB liquid medium to exponential phase, then adjusted to defined densities for SynCom assembly.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37275168"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37275168
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were recovered in a solid Luria Bertani (LB) medium and incubated at 28°C for 48 h."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37275168"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37275168
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each bacteria strain was grown individually in LB liquid media to the exponential phase."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html b/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
index b627b3bd..b42ac6c3 100644
--- a/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
+++ b/docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>KB-1 Chlorinated Ethene Dechlorinating Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000132</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000132</code>
                     </span>
                 </div>
 
@@ -908,7 +910,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Vitamin-free mineral medium used to test KB-1 growth and dechlorination dependency on endogenous cobamide-producing populations.
                 </p>
                 
diff --git a/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html b/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
index 4d564910..835981e3 100644
--- a/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
+++ b/docs/communities/KBase_Models_for_Zahmeeth_Original_PLOS.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>KBase Models for Zahmeeth Original PLOS</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000037</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000037</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/KBase_ORT_Workflow_Community_Model.html b/docs/communities/KBase_ORT_Workflow_Community_Model.html
index 0937fa08..7c0517ed 100644
--- a/docs/communities/KBase_ORT_Workflow_Community_Model.html
+++ b/docs/communities/KBase_ORT_Workflow_Community_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>KBase ORT Workflow Community Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000038</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000038</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/KBase_Synthetic_Bacterial_Community_R2A.html b/docs/communities/KBase_Synthetic_Bacterial_Community_R2A.html
index 66075140..968f03ec 100644
--- a/docs/communities/KBase_Synthetic_Bacterial_Community_R2A.html
+++ b/docs/communities/KBase_Synthetic_Bacterial_Community_R2A.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>KBase Synthetic Bacterial Community in R2A Medium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000039</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000039</code>
                     </span>
                 </div>
 
@@ -844,6 +846,79 @@ <h2>External Resources</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A (complex medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> R2A selected as the complex medium (a parallel MOPS-glucose minimal medium was also tested); community mixed at approximately equal OD600 and serially passaged every 48 h at a 1:10 dilution for 15 passages. Member strains are obligate aerobes or facultative anaerobes and shaking ensured aeration.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/33995895"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:33995895
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each strain was inoculated from an agar plate and grown individually in a test tube with 10 mL R2A or MOPS liquid medium and cultivated in a shaking incubator at 30 °C and 200 rpm for 48 h."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/33995895"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:33995895
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Triplicate cultures, for both media, were incubated for 48 h at 30 °C with shaking at 200 rpm and passaged every 48 h at a 1:10 dilution for 15 passages."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Kombucha_KMC_IMBG1_Fermentation_Community.html b/docs/communities/Kombucha_KMC_IMBG1_Fermentation_Community.html
index 99bf3f9a..8f85c073 100644
--- a/docs/communities/Kombucha_KMC_IMBG1_Fermentation_Community.html
+++ b/docs/communities/Kombucha_KMC_IMBG1_Fermentation_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Kombucha KMC-IMBG1 Fermentation Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000154</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000154</code>
                     </span>
                 </div>
 
@@ -988,7 +990,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Filter-sterilized black tea extract with sucrose; KMC-IMBG1 was also maintained in nonsterile sweetened black tea and sterile black tea with honey.
                 </p>
                 
diff --git a/docs/communities/LBNL_Brachypodium_Drought_SynCom15.html b/docs/communities/LBNL_Brachypodium_Drought_SynCom15.html
index a35fc363..a048125c 100644
--- a/docs/communities/LBNL_Brachypodium_Drought_SynCom15.html
+++ b/docs/communities/LBNL_Brachypodium_Drought_SynCom15.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>LBNL Brachypodium Drought SynCom15</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000088</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000088</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A (SynCom member cultivation); 0.2X MS for in-planta drought assay
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">24 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom member isolates grown in R2A to log phase, then combined at equal cell numbers (4x10^7 cells each) and applied to Brachypodium distachyon in 0.2X Murashige and Skoog (MS) medium; plants held in a growth chamber at 24°C, 16-h light, 50% humidity. Strains were originally isolated on 1X R2A and RCH2 minimal media incubated at 30°C in the dark for 7 days.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40862137"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40862137
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Individual SynCom isolates were cultivated in R2A media for 24–72 h until they reached log phase"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40862137"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40862137
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The mixture was incubated in a plant growth chamber with conditions set at 16-h light, 24°C temperature, and 50% humidity."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/LBNL_Human_Gut_Interaction_SynCom.html b/docs/communities/LBNL_Human_Gut_Interaction_SynCom.html
index bcea4e84..4313c51b 100644
--- a/docs/communities/LBNL_Human_Gut_Interaction_SynCom.html
+++ b/docs/communities/LBNL_Human_Gut_Interaction_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>LBNL Human Gut Interaction SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000122</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000122</code>
                     </span>
                 </div>
 
@@ -618,6 +620,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Anaerobic Basal Broth (ABB) (Oxoid)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Cultured in a Coy anaerobic chamber; synthetic assemblages arrayed into 96-well deep-well plates and incubated at 37°C without shaking; communities serially transferred at ~24 h intervals using a 1:20 dilution over 72 h.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29930200"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29930200
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"into 15 ml of Anaerobic Basal Broth (ABB) media (Oxoid) in an anaerobic chamber and incubated at 37°C without shaking."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29930200"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29930200
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Cells were cultured in an anaerobic chamber (Coy Lab Products) using mixed gas tanks containing 85% N 2 , 5% H 2 , and 10% CO 2 ."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/LBNL_Switchgrass_Soil_SynCom16.html b/docs/communities/LBNL_Switchgrass_Soil_SynCom16.html
index 0f3897be..e8d5ead3 100644
--- a/docs/communities/LBNL_Switchgrass_Soil_SynCom16.html
+++ b/docs/communities/LBNL_Switchgrass_Soil_SynCom16.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>LBNL Switchgrass Soil SynCom16</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000087</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000087</code>
                     </span>
                 </div>
 
@@ -618,6 +620,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A (Teknova, 1x)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Communities grown in 200 μL 1x R2A in 96-well plates without shaking; individual isolates grown in 14 mL culture tubes in 1x R2A; higher community alpha-diversity achieved with low-nutrient (diluted 1x, 0.1x) R2A; cryopreserved with 20% glycerol at −80°C; also colonizes Brachypodium distachyon in EcoFAB devices at 24°C under a 16 h light/8 h dark regime.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36472419"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36472419
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Communities were grown in 200 μL of liquid R2A medium in 96-well plates in aerobic conditions at 30°C without shaking."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36472419"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36472419
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Individual isolates were grown in 3 to 5 mL liquid cultures of 1× R2A medium (Teknova, cat number R0005) in 14 mL culture tubes in aerobic conditions at 30°C without shaking."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Lac_Pavin_Stratified_Lake_Community.html b/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
index 6e022786..221be02e 100644
--- a/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
+++ b/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Lac Pavin Permanently Stratified Lake Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000226</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000226</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html b/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
index 2654cea6..0bdf223e 100644
--- a/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
+++ b/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Lake Washington Methane-Oxygen Methylotroph Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000261</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000261</code>
                     </span>
                 </div>
 
@@ -1342,7 +1344,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Lake Washington sediment was incubated in microcosms with methane supplied at a fixed concentration and oxygen supplied across five different tension treatments. Detailed medium chemistry beyond sediment, methane, and oxygen is not asserted here.
 
                 </p>
diff --git a/docs/communities/Lotus_LjSC3.html b/docs/communities/Lotus_LjSC3.html
index 4bb3fc74..200cf496 100644
--- a/docs/communities/Lotus_LjSC3.html
+++ b/docs/communities/Lotus_LjSC3.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Lotus Lj-SC3 Synthetic Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000040</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000040</code>
                     </span>
                 </div>
 
@@ -1113,8 +1115,8 @@ <h3>Plant Growth Promotion</h3>
                     
                     <li>
                         regulation of plant growth
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0080001"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0080001</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1903338"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1903338</a>)
                     </li>
                     
                     <li>
@@ -1600,7 +1602,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> General-purpose medium used for isolation and maintenance of bacteria from Lotus japonicus roots and nodules. Mesorhizobium and other rhizosphere bacteria cultured individually before community assembly.
 
                 </p>
@@ -1734,7 +1736,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Modified Broughton and Dilworth nitrogen-free plant nutrient medium for studying symbiotic nitrogen fixation and nodulation. Gnotobiotic system allowing visualization of root colonization and nodule formation by Mesorhizobium strains. Medium supports both nitrogen-fixing symbionts and non-nodulating commensal bacteria.
 
                 </p>
diff --git a/docs/communities/MAMC_M48_Lignocellulose.html b/docs/communities/MAMC_M48_Lignocellulose.html
index b8853d5d..26440aa4 100644
--- a/docs/communities/MAMC_M48_Lignocellulose.html
+++ b/docs/communities/MAMC_M48_Lignocellulose.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>MAMC-M48 Lignocellulose-Degrading Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000041</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000041</code>
                     </span>
                 </div>
 
@@ -1156,7 +1158,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Mineral salts medium (MSM) supplemented with 1% sugarcane straw as lignocellulose substrate. All five strains are aerobic degraders isolated from soil through enrichment on sugarcane waste. Each strain inoculated at 1x10^5 cells/mL for total inoculum of 5x10^5 cells/mL. The consortium was optimized through reductive screening from 18 candidate strains using molecular phenotyping and metabolic characterization. MAMC-M48 (synthetic community 48) showed highest degradation efficiency (50.6% of all lignocellulose fractions), reaching 96.5% of the degradation rate observed with full 18-species pool.
 
                 </p>
diff --git a/docs/communities/MSC1_Dominant_Core.html b/docs/communities/MSC1_Dominant_Core.html
index 9990d4ca..0df52ac8 100644
--- a/docs/communities/MSC1_Dominant_Core.html
+++ b/docs/communities/MSC1_Dominant_Core.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>MSC-1 Dominant Core</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000042</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000042</code>
                     </span>
                 </div>
 
@@ -1746,6 +1748,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    chitin/soil-extract agar (100 ppm shrimp-shell chitin)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">20 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Enriched from arid grassland soil with chitin as the main carbon and nitrogen source; field soil incubated 7 months at 20°C in the dark with 100 ppm chitin, then serially diluted in PBS and plated on chitin/soil-extract agar and grown ~1 week at 20°C. Pairwise interactions were assayed in M9 minimal liquid medium with 10 mM N-acetylglucosamine, shaken at 24°C for 5 days. Consortia stored as glycerol or lyophilized stocks at −80°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32983014"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32983014
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Samples were collected from an arid grassland soil and microbial communities (consisting mainly of bacterial species) were enriched on agar plates containing chitin as the main carbon source."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32983014"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32983014
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The soil samples were incubated for 7 months at 20°C in the dark, with respiration used to monitor bioactivity once a week"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/MSC2_Model_Soil_Consortium.html b/docs/communities/MSC2_Model_Soil_Consortium.html
index c76b0496..8818f5d5 100644
--- a/docs/communities/MSC2_Model_Soil_Consortium.html
+++ b/docs/communities/MSC2_Model_Soil_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Model Soil Consortium-2 (MSC-2)</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000086</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000086</code>
                     </span>
                 </div>
 
@@ -914,6 +916,74 @@ <h2>External Resources</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    M9 minimal medium (18 mM NH4Cl) with colloidal chitin
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">20 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Each strain precultured on R2A agar for 3 days, washed and resuspended in M9 (18 mM NH4Cl); community grown on colloidal shrimp-shell chitin as the sole carbon source (100 ppm for growth screens, 500 ppm for the community multiomics flasks); five biological-replicate flasks (30 mL M9) incubated at 20°C for 5 days.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36154140"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36154140
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Plates were shaken at 180 rpm during growth, and cultivation was carried out at 20°C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36154140"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36154140
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Five biological replicate flasks, labeled A to E, were started and incubated at 20°C for 5 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.html b/docs/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.html
index 048a5529..36547bc9 100644
--- a/docs/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.html
+++ b/docs/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>MUCC Freshwater Wetland Methane-Cycling Network Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000257</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000257</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.html b/docs/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.html
index 37a647cd..e15faf63 100644
--- a/docs/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.html
+++ b/docs/communities/Maize_Benzoxazinoid_Metabolizing_SynComs.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Maize Benzoxazinoid-Metabolizing SynComs</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000101</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000101</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    50% TSB (tryptic soy broth, 15 g/L)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains routinely grown on 100% TSA plates or in liquid 50% TSB; SynComs grown in 96-well plates in 50% TSB supplemented with 500 µM MBOA for 68 h; precultures grown to stationary phase over 4 days at 28°C, 180 rpm; community-structure assays used Erlenmeyer flasks; parallel minimal-medium assays used MBOA (500 or 2,500 µM) or glucose as the sole carbon source.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40853002"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40853002
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"MRB collection, 8 ) were routinely grown on solid 100% TSA plates (30 g/L tryptic soy broth and 15 g/L of agar, both Sigma-Aldrich) or in liquid 50% TSB medium (15 g/L tryptic soy broth) with 180 rpm shaking at 25–28°C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40853002"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40853002
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Pre-culture plates were covered with a Breathe-Easy membrane (Diversified Biotech, Dedham, USA) and grown until stationary phase for 4 days at 28°C and 180 rpm."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Maize_Drought_Response_SynCom.html b/docs/communities/Maize_Drought_Response_SynCom.html
index 7cc882f3..89afef04 100644
--- a/docs/communities/Maize_Drought_Response_SynCom.html
+++ b/docs/communities/Maize_Drought_Response_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Maize Drought Response SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000103</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000103</code>
                     </span>
                 </div>
 
@@ -618,6 +620,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    greenhouse pot substrate (7:1 sphagnum:perlite)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Maize hybrids grown in a netted greenhouse; drought imposed by switching from full to reduced irrigation; seeds stored at 4 °C prior to sowing.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/34745050"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:34745050
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Plants were grown in 18-L pots filled with a commercial substrate (Biogrow, Brazil) modified to contain a 7:1 sphagnum:perlite"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/34745050"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:34745050
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the photoperiod was extended until 8:00 pm with halogen bulbs PAR38 100 W"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Maize_Root_Simplified_Community.html b/docs/communities/Maize_Root_Simplified_Community.html
index 221bbab0..aa13c28e 100644
--- a/docs/communities/Maize_Root_Simplified_Community.html
+++ b/docs/communities/Maize_Root_Simplified_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Maize Root Simplified Bacterial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000043</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000043</code>
                     </span>
                 </div>
 
@@ -1457,6 +1459,118 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    1/2 Murashige and Skoog (MS) agar gnotobiotic maize-root system (members precultured on 0.1x TSA / tryptic soy broth)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Community members were streaked on 0.1x TSA plates (30 °C, 24-48 h) and precultured in tryptic soy broth (TSB) shaken at 30 °C before inoculation. The simplified synthetic community was assembled on the roots of axenic maize seedlings grown in sterile 1/2 MS agar [0.8% (wt/vol), pH adjusted to 6.0 to simulate soil pH] within double-tube gnotobiotic chambers. Surface-sterilized seeds were germinated at 30 °C in the dark for ~50-55 h. Soil-grown plants were kept in a plant growth chamber at 25 °C with 54% relative humidity under a 16 h light / 8 h dark cycle.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28275097"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28275097
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The bacterial strains for inoculation were streaked on 0.1× TSA plates and incubated at 30 °C for 24–48 h. Then, a single colony of each strain was inoculated in 5 mL of tryptic soy broth (TSB) and shaken at 30 °C overnight."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28275097"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28275097
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the resulting seedlings were grown in sterile 1/2 Murashige and Skoog (MS) agar [0.8% (wt/vol)] (adjusting the pH to 6.0 to simulate the pH of soil"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28275097"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28275097
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A seed inoculated with bacteria was put into a glass test tube (16 × 150 mm) containing 20 mL of 1/2 MS agar"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28275097"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28275097
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"10 seeds, embryo side up, were placed in a Perti dish (9-cm diameter) filled with 7 mL of sterile water and incubated at 30 °C in the dark until the seeds germinated (usually after 50–55 h)."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28275097"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28275097
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the pots were placed in a plant growth chamber under the following conditions: 16 h of light (day) and 8 h of dark (night), 25 °C, and a relative humidity of 54%."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Medicago_Nodule_Biofertilizer_SynCom.html b/docs/communities/Medicago_Nodule_Biofertilizer_SynCom.html
index e4299446..c5f11c59 100644
--- a/docs/communities/Medicago_Nodule_Biofertilizer_SynCom.html
+++ b/docs/communities/Medicago_Nodule_Biofertilizer_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Medicago Nodule Biofertilizer SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000108</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000108</code>
                     </span>
                 </div>
 
@@ -660,6 +662,82 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    TSA and TY (bacterial maintenance media); greenhouse pots (plant assay)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Pseudomonas strains maintained on Tryptic Soy Agar (TSA) and Ensifer strains on Tryptone-Yeast (TY); inoculated M. sativa grown ~60 days in pots under greenhouse conditions, with a 40 °C heat-stress treatment applied for 5 consecutive days in a growth chamber.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37299063"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37299063
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Pseudomonas strains were maintained in TSA (Tryptic Soy Agar; Intron Biotechnology, Seongnam, Republic of Korea) plates and Ensifer strains in TY"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37299063"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37299063
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"M. sativa plants after 60 days in pots under greenhouse conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37299063"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37299063
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"plants were subjected to 40 °C during 5 consecutive days in a growth chamber"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Mediterranean_Grassland_qSIP_Rainfall_Community.html b/docs/communities/Mediterranean_Grassland_qSIP_Rainfall_Community.html
index 906a42e4..a6d585c5 100644
--- a/docs/communities/Mediterranean_Grassland_qSIP_Rainfall_Community.html
+++ b/docs/communities/Mediterranean_Grassland_qSIP_Rainfall_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Mediterranean Grassland qSIP Rainfall-Gradient Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000227</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000227</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Mercury_SFA_EFPC_Sediment_Community.html b/docs/communities/Mercury_SFA_EFPC_Sediment_Community.html
index c8180a66..29d229bb 100644
--- a/docs/communities/Mercury_SFA_EFPC_Sediment_Community.html
+++ b/docs/communities/Mercury_SFA_EFPC_Sediment_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Mercury SFA East Fork Poplar Creek Sediment Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000044</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000044</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Methane_Oxidation_CrVI_Reduction_SynCom.html b/docs/communities/Methane_Oxidation_CrVI_Reduction_SynCom.html
index 228f3c7d..79672bce 100644
--- a/docs/communities/Methane_Oxidation_CrVI_Reduction_SynCom.html
+++ b/docs/communities/Methane_Oxidation_CrVI_Reduction_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methane Oxidation-Cr(VI) Reduction SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000121</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000121</code>
                     </span>
                 </div>
 
@@ -702,6 +704,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified methane-fed medium (SynCom enrichment)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">MICROAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom assembled by controlling methane concentration and chromium load; methane-oxidation-coupled Cr(VI) reduction operated under hypoxic (microaerobic) conditions.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41932525"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41932525
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41932525"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41932525
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.html b/docs/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.html
index e3cd3b9c..c2a59d19 100644
--- a/docs/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.html
+++ b/docs/communities/Methylacidiphilum_Galdieria_Thermoacidophilic_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylacidiphilum-Galdieria Thermoacidophilic Methane Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000171</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000171</code>
                     </span>
                 </div>
 
@@ -1076,7 +1078,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed-indexed abstract supports methane-fed photobioreactor and low-oxygen coculture conditions; detailed medium recipe is not curated here.
                 </p>
                 
diff --git a/docs/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.html b/docs/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.html
index fe5b9e67..c145e144 100644
--- a/docs/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.html
+++ b/docs/communities/Methylocaldum_Cupriavidus_Methane_Acetate_Crossfeeding_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylocaldum-Cupriavidus Methane Acetate Cross-Feeding Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000197</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000197</code>
                     </span>
                 </div>
 
@@ -1015,7 +1017,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The primary article reports an aerobic methanotroph coculture; this record does not assert the full salt, vitamin, or seawater recipe because the locally cached reference text is abstract-only.
 
                 </p>
diff --git a/docs/communities/Methylocaldum_Methyloceanibacter_Methane_Crossfeeding_Coculture.html b/docs/communities/Methylocaldum_Methyloceanibacter_Methane_Crossfeeding_Coculture.html
index 72cd9305..3dd21281 100644
--- a/docs/communities/Methylocaldum_Methyloceanibacter_Methane_Crossfeeding_Coculture.html
+++ b/docs/communities/Methylocaldum_Methyloceanibacter_Methane_Crossfeeding_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylocaldum-Methyloceanibacter Methane Cross-Feeding Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000169</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000169</code>
                     </span>
                 </div>
 
@@ -997,7 +999,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The strains were grown together in 40 mL NMS-SP medium in a 200 mL glass bottle.
                 </p>
                 
diff --git a/docs/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.html b/docs/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.html
index c7f7068e..f94b402f 100644
--- a/docs/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.html
+++ b/docs/communities/Methylocystis_Rhodococcus_Methane_VFA_PHBV_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylocystis-Rhodococcus Methane VFA PHBV Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000204</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000204</code>
                     </span>
                 </div>
 
@@ -1000,7 +1002,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> M. parvus and R. opacus were grown as active inocula, then coculture biomass was transferred to nitrogen-free mineral salt medium supplemented with valeric acid or a mixed VFA cosubstrate for PHBV accumulation; pH was adjusted to 7.
                 </p>
                 
diff --git a/docs/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.html b/docs/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.html
index f2dc1ca0..8d32acd0 100644
--- a/docs/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.html
+++ b/docs/communities/Methylomicrobium_Chlorella_Methane_Sequestration_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylomicrobium-Chlorella Methane Sequestration Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000192</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000192</code>
                     </span>
                 </div>
 
@@ -1178,7 +1180,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The source publication supports saline medium, methane-fed enclosed serum bottle experiments, and coculture conditions for M. alcaliphilum 20Z and Chlorella sp. HS2. Detailed medium composition is not asserted here beyond the verified saline, methane, and carbon dioxide context.
 
                 </p>
diff --git a/docs/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.html b/docs/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.html
index d8c4f193..762e0d85 100644
--- a/docs/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.html
+++ b/docs/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Methylotuvimicrobium-Synechococcus Gas Feedstock Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000170</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000170</code>
                     </span>
                 </div>
 
@@ -1001,7 +1003,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed-indexed abstract supports gas-feed and illumination conditions but does not provide full mineral medium composition.
                 </p>
                 
diff --git a/docs/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.html b/docs/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.html
index b69c1cbc..ee69092c 100644
--- a/docs/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.html
+++ b/docs/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Microcoleus-Massilia Cyanosphere Urea Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000157</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000157</code>
                     </span>
                 </div>
 
@@ -1056,7 +1058,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> M. vaginatus PCC 9802 was maintained in 50% BG11 and shifted into nitrogen-limited BG11-based media; Massilia sp. METH4 was maintained on N-free Burks medium and paired with M. vaginatus under carbon- and nitrogen-free coculture conditions.
                 </p>
                 
diff --git a/docs/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.html b/docs/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.html
index b29afe7e..1e6b266f 100644
--- a/docs/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.html
+++ b/docs/communities/Miscanthus_REE_Tailings_Nitrogen_SynCom10.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Miscanthus REE Tailings Nitrogen SynCom10</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000111</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000111</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Mixed_Gallium_LED_Recovery_Consortium.html b/docs/communities/Mixed_Gallium_LED_Recovery_Consortium.html
index bc8ebaf3..428f6687 100644
--- a/docs/communities/Mixed_Gallium_LED_Recovery_Consortium.html
+++ b/docs/communities/Mixed_Gallium_LED_Recovery_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Mixed Gallium LED Recovery Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000045</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000045</code>
                     </span>
                 </div>
 
@@ -673,12 +675,6 @@ <h3>Biogenic Sulfuric Acid Production for Gallium Leaching</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -764,12 +760,6 @@ <h3>Ferric Iron Generation for Multi-Metal Recovery</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -844,12 +834,6 @@ <h3>Synergistic Lixiviant Production in Mixed Consortium</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -922,17 +906,6 @@ <h3>Non-Contact Bioleaching System Design</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1129,6 +1102,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    biogenic lixiviant (A. thiooxidans/A. ferrooxidans/L. ferrooxidans 1:1:1 mixed culture)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">1.53</span>
+                    </div>
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Cell-free biogenic lixiviant generated by the mixed community and used for non-contact bioleaching of waste LEDs at 15 g/L pulp density; A. thiooxidans oxidizes elemental sulfur to sulfuric acid, lowering the pH to 1.53.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.jece.2025.120403"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.jece.2025.120403
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A. thiooxidans in the mixed bacterial community oxidizes the elemental sulfur to generate sulfuric acid, thereby decreasing the pH to 1.53."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.jece.2025.120403"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.jece.2025.120403
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The biogenic lixiviants achieved a Ga leaching efficiency of 99.5 % in 15 g/L pulp density during 3 days of non-contact bioleaching."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1216,8 +1257,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1261,8 +1300,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -1311,8 +1348,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1356,10 +1391,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html b/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
index ac95113e..a5101fd9 100644
--- a/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
+++ b/docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Model Cyanobacterial Consortia Core Microbiome</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000214</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000214</code>
                     </span>
                 </div>
 
@@ -895,7 +897,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Stable in vitro cocultures of cyanobacteria with freshwater-derived heterotrophs; specific medium composition is not enumerated in the abstract.
                 </p>
                 
diff --git a/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html b/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
index fe22bf7f..61497e70 100644
--- a/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
+++ b/docs/communities/Model_Lignocellulose_Formaldehyde_Crossfeeding_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Model Lignocellulose Formaldehyde Cross-Feeding Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000178</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000178</code>
                     </span>
                 </div>
 
@@ -1137,7 +1139,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Defined minimal Model Lignocellulose medium used for reproducible coculture experiments; exact concentrations are not asserted in this record.
                 </p>
                 
diff --git a/docs/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html b/docs/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html
new file mode 100644
index 00000000..84a5bcee
--- /dev/null
+++ b/docs/communities/Multi_stage_Anaerobic_Digestion_SynCom_YSJ_and_SynCom_J.html
@@ -0,0 +1,989 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
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+        .roles-list {
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+        }
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+        .role-badge {
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000274</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        semi-continuous anaerobic digester treating food waste
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002124"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002124
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two function-driven synthetic microbial communities (SynComs) constructed for bioaugmentation of food-waste anaerobic digestion. SynCom-J is a methanogen-only consortium, whereas SynCom-YSJ is a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members. Both were introduced into semi-continuous reactors already harboring a metabolically complete native microbiome. The multi-stage SynCom-YSJ increased methane yield by 22% (vs 8% for SynCom-J), nearly eliminated the start-up lag phase, reduced propionate accumulation, and reshaped the digester microenvironment (elevated acetate, reduced propionate), upregulating genes for hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Individual member species are not named in the source abstract, so no NCBITaxon-grounded members are asserted here.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Staged metabolic hand-off across hydrolytic, acidogenic and methanogenic members</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41825563/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41825563</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ)"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Interspecies electron transfer supporting methanogenesis</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41825563/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41825563</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Deterministic selection of the resident community by SynCom colonization</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41825563/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41825563</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"thereby imposing deterministic selection on the resident community"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    partially hydrolyzed food-waste feedstock (semi-continuous AD)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Semi-continuous food-waste anaerobic digesters fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41825563"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41825563
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Staged metabolic hand-off across hydrolytic, acidogenic and methanogenic members",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Interspecies electron transfer supporting methanogenesis",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Deterministic selection of the resident community by SynCom colonization",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Multiomics_Corn_Straw_Degradation_SynCom.html b/docs/communities/Multiomics_Corn_Straw_Degradation_SynCom.html
index 4f6d6043..75adfca3 100644
--- a/docs/communities/Multiomics_Corn_Straw_Degradation_SynCom.html
+++ b/docs/communities/Multiomics_Corn_Straw_Degradation_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Multiomics Corn Straw Degradation SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000119</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000119</code>
                     </span>
                 </div>
 
@@ -618,6 +620,56 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified (solid-state corn straw fermentation medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Solid-state fermentation of corn straw; optimum 10% inoculum level (w/v) with a 4% nitrogen source ratio.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37774801"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37774801
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html b/docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html
index c11dfc40..3c4781fe 100644
--- a/docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html
+++ b/docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Mushroom Spring Hot-Spring Phototrophic Mat Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000260</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000260</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/NCycle_Bioflocculation_Model_Consortium.html b/docs/communities/NCycle_Bioflocculation_Model_Consortium.html
index bf5cad82..2816b543 100644
--- a/docs/communities/NCycle_Bioflocculation_Model_Consortium.html
+++ b/docs/communities/NCycle_Bioflocculation_Model_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>N-Cycle Bioflocculation Model Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000126</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000126</code>
                     </span>
                 </div>
 
@@ -618,6 +620,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    HEPES-buffered N-cycle coculture medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Precultures shaken in the dark in phosphate-buffered coculture medium with ammonium and nitrite; carbonate added and yeast extract omitted to promote autotrophic growth; alginate entrapment used as a cell retention system.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40536564"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40536564
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Precultures of AOB and NOB were shaken at 28 °C (in the dark) in a phosphate-buffered coculture medium with ammonium and nitrite"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Naica_Deep_Subsurface_Thermophilic.html b/docs/communities/Naica_Deep_Subsurface_Thermophilic.html
index 3bf491ff..64f6b528 100644
--- a/docs/communities/Naica_Deep_Subsurface_Thermophilic.html
+++ b/docs/communities/Naica_Deep_Subsurface_Thermophilic.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Naica Deep Subsurface Thermophilic Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000046</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000046</code>
                     </span>
                 </div>
 
@@ -823,12 +825,6 @@ <h3>Thermophilic Ammonia Oxidation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015977</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -902,17 +898,6 @@ <h3>Heterotrophic Carbon Scavenging</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1030,23 +1015,6 @@ <h3>Proteobacterial Oligotrophic Metabolism</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1424,8 +1392,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("carbon fixation");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
@@ -1460,10 +1426,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1548,12 +1510,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.html b/docs/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.html
index 568e2ddc..f04d78cf 100644
--- a/docs/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.html
+++ b/docs/communities/Neocallimastix_Methanobrevibacter_Xylan_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Neocallimastix-Methanobrevibacter Xylanolytic Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000156</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000156</code>
                     </span>
                 </div>
 
@@ -936,7 +938,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Anaerobic ruminal fungi were grown axenically or in coculture with M. smithii using xylan as the principal polysaccharide substrate.
                 </p>
                 
diff --git a/docs/communities/Ngawha_Geothermal_Mercury_Cycling_Community.html b/docs/communities/Ngawha_Geothermal_Mercury_Cycling_Community.html
index 0368a99a..c23cc4d6 100644
--- a/docs/communities/Ngawha_Geothermal_Mercury_Cycling_Community.html
+++ b/docs/communities/Ngawha_Geothermal_Mercury_Cycling_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Ngawha Geothermal Acidic Springs Mercury Cycling Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000243</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000243</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.html b/docs/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.html
index 69650130..403488e1 100644
--- a/docs/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.html
+++ b/docs/communities/OMM12_Gnotobiotic_Mouse_Gut_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>OMM12 Gnotobiotic Mouse Gut Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000133</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000133</code>
                     </span>
                 </div>
 
@@ -603,8 +605,8 @@ <h3>Reproducible Multi-Strain Intestinal Colonization</h3>
                     
                     <li>
                         multi-organism process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0051704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0051704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
                     </li>
                     
                 </ul>
@@ -760,6 +762,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified (anaerobic OMM12 cultivation medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Media kept anoxic in an anaerobic chamber for at least 2 days before use; germ-free C57Bl/6J mice colonized with a frozen strain mixture, with a second application of the strains after 72 h to improve community stability.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31998276"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31998276
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Media used for cultivation were kept under anoxic conditions"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.html b/docs/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.html
index 7c996d68..f4faa638 100644
--- a/docs/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.html
+++ b/docs/communities/ORNL_Clostridium_Desulfovibrio_Geobacter_Trophic_Model.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>ORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000176</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000176</code>
                     </span>
                 </div>
 
@@ -821,17 +823,6 @@ <h3>Fumarate-Linked Dependence of G. sulfurreducens</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -886,17 +877,6 @@ <h3>Electron Donor and Acceptor Limitation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1211,7 +1191,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Abstract-supported medium summary; exact recipe concentrations are not curated here.
                 </p>
                 
@@ -1418,10 +1398,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1456,10 +1432,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/ORNL_PMI_Populus_PD10_SynCom.html b/docs/communities/ORNL_PMI_Populus_PD10_SynCom.html
index 1af0cfae..edfebde7 100644
--- a/docs/communities/ORNL_PMI_Populus_PD10_SynCom.html
+++ b/docs/communities/ORNL_PMI_Populus_PD10_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>ORNL PMI Populus PD10 SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000047</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000047</code>
                     </span>
                 </div>
 
@@ -1589,6 +1591,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A or MOPS-glucose liquid medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains grown individually and as a community by serial passaging in either complex R2A or defined MOPS-glucose mineral salts medium; growth followed by OD600.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/33995895"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:33995895
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"grown individually in a test tube with 10 mL R2A or MOPS liquid medium and cultivated in a shaking incubator at 30 °C and 200 rpm for 48 h"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.html b/docs/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.html
index 9e9cc5e9..152b4014 100644
--- a/docs/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.html
+++ b/docs/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Oak Ridge FRC Uranium-Nitrate Groundwater Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000136</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000136</code>
                     </span>
                 </div>
 
@@ -774,12 +776,6 @@ <h3>Mixed Metal and Nitrate Reduction Potential</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         denitrification
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0019333"
@@ -1079,8 +1075,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("denitrification");
             
             
diff --git a/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html b/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
index 8f9352d1..420ef0b6 100644
--- a/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
+++ b/docs/communities/Okeke_Lu_Cellulolytic_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Okeke-Lu Cellulolytic-Xylanolytic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000048</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000048</code>
                     </span>
                 </div>
 
@@ -1180,7 +1182,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Mineral salts medium supplemented with carboxymethyl cellulose (CMC) as cellulose substrate for enrichment and isolation of cellulolytic bacteria from Alabama soil. The consortium was composed from 19 purified monocultures evaluated for cellulolytic-xylanolytic potential, with 5 selected isolates (DB1, DB2, DB7, DB8, DB13) chosen based on high enzyme production. All strains are aerobic or facultatively anaerobic. Isolates DB1 and DB2 displayed the highest filter paper cellulase activity (27.83 and 31.22 U/mg). The defined consortium produces complete enzyme system: filter paper cellulase, beta-glucosidase, xylanase, and beta-xylosidase for comprehensive lignocellulose bioprocessing.
 
                 </p>
diff --git a/docs/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.html b/docs/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.html
index 0318d5e7..2b67ad7c 100644
--- a/docs/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.html
+++ b/docs/communities/Ostreococcus_Dinoroseobacter_BVitamin_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Ostreococcus-Dinoroseobacter B-Vitamin Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000155</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000155</code>
                     </span>
                 </div>
 
@@ -911,7 +913,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> L1 medium was used for axenic O. tauri and cocultures containing O. tauri; vitamin additions were varied according to the experimental treatment.
                 </p>
                 
diff --git a/docs/communities/PET_Artificial_FourSpecies_Degradation_Consortium.html b/docs/communities/PET_Artificial_FourSpecies_Degradation_Consortium.html
index 0eef7c31..66f266b9 100644
--- a/docs/communities/PET_Artificial_FourSpecies_Degradation_Consortium.html
+++ b/docs/communities/PET_Artificial_FourSpecies_Degradation_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>PET Artificial Four-Species Degradation Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000163</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000163</code>
                     </span>
                 </div>
 
@@ -726,17 +728,6 @@ <h3>PETase-MHETase Depolymerization Module</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -802,12 +793,6 @@ <h3>Rhodococcus TPA Detoxification Module</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                     <li>
                         biological process involved in interspecies interaction between organisms
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
@@ -881,12 +866,6 @@ <h3>Pseudomonas EG Detoxification Module</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         biological process involved in interspecies interaction between organisms
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
@@ -1185,7 +1164,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Initial seed cultures were grown in LB; four-member PET degradation assays used washed cells diluted in Wn medium with 2 ug/mL erythromycin and PET film as substrate.
                 </p>
                 
@@ -1253,7 +1232,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Optimized starting ratio was Bs_PETase:Bs_MHETase:R. jostii:P. putida = 3:1:10:10^-5 in Wn medium.
                 </p>
                 
@@ -1370,10 +1349,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1413,8 +1388,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("aromatic compound catabolic process");
-            
             processes.push("biological process involved in interspecies interaction between organisms");
             
             
@@ -1457,8 +1430,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("biological process involved in interspecies interaction between organisms");
             
             
diff --git a/docs/communities/PGM_Spent_Catalyst_Bioleaching.html b/docs/communities/PGM_Spent_Catalyst_Bioleaching.html
index ccf6dfb8..52990f0a 100644
--- a/docs/communities/PGM_Spent_Catalyst_Bioleaching.html
+++ b/docs/communities/PGM_Spent_Catalyst_Bioleaching.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>PGM Spent Catalyst Bioleaching Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000049</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000049</code>
                     </span>
                 </div>
 
@@ -761,12 +763,6 @@ <h3>Complementary Iron and Sulfur Oxidation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -937,12 +933,6 @@ <h3>Alumina Support Matrix Dissolution</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1043,12 +1033,6 @@ <h3>Biogenic Thiosulfate-PGM Complexation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1146,17 +1130,6 @@ <h3>Column Bioreactor PGM Recovery</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1236,12 +1209,6 @@ <h3>Thiosulfate Metabolic Cycling</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0006790</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1532,6 +1499,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    biogenic thiosulfate production medium (biogas biodesulfurization consortium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">MICROAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Thiosulfate-producing sulfur-oxidizing consortium operated under anoxic and microaerobic conditions; optimum biogenic thiosulfate (4.9 g/L) at batch mode, pH 10 and airflow 0.033 vvm.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38138568"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38138568
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Biogenic thiosulfate production was optimized in a gas-lift bioreactor by studying the pH (8-10) and operation modes (batch and continuous) under anoxic and microaerobic conditions for 35 d."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1626,8 +1648,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1724,8 +1744,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1773,8 +1791,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
@@ -1819,10 +1835,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1863,8 +1875,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("sulfur compound metabolic process");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/PMI_Variovorax_Thermotolerance_Collection.html b/docs/communities/PMI_Variovorax_Thermotolerance_Collection.html
index 93d1d893..e0deb715 100644
--- a/docs/communities/PMI_Variovorax_Thermotolerance_Collection.html
+++ b/docs/communities/PMI_Variovorax_Thermotolerance_Collection.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>PMI Variovorax Thermotolerance Collection</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000050</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000050</code>
                     </span>
                 </div>
 
@@ -923,6 +925,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A broth (bacterial culture); liquid MS medium (plant assay)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains streaked on R2A agar (28 °C, 2 d), single colonies grown in R2A broth (28 °C, 250 rpm, overnight), washed and resuspended in liquid MS medium to OD600 0.01; Arabidopsis seedlings floated on liquid MS medium in 6-well plates.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37386471"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37386471
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"A single bacterial colony from the agar plate was inoculated into 3 mL of R2A broth and cultured at 28 °C with shaking at 250 rpm overnight"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/PSY_Transgenic_Rice_Rhizosphere_Methane_Community.html b/docs/communities/PSY_Transgenic_Rice_Rhizosphere_Methane_Community.html
index 98393b42..9dece36b 100644
--- a/docs/communities/PSY_Transgenic_Rice_Rhizosphere_Methane_Community.html
+++ b/docs/communities/PSY_Transgenic_Rice_Rhizosphere_Methane_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>PSY Transgenic Rice Rhizosphere Methane-Mitigating Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000216</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000216</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html b/docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html
index 4e87f87a..7acf90b2 100644
--- a/docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html
+++ b/docs/communities/Panzhihua_Vanadium_Titanium_Tailings.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Panzhihua Vanadium Titanium Tailings Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000051</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000051</code>
                     </span>
                 </div>
 
@@ -1028,12 +1030,6 @@ <h3>Dissimilatory Vanadium Reduction and Immobilization</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         dissimilatory reduction
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0019645"
@@ -1132,12 +1128,6 @@ <h3>Soil Organic Carbon Transformation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015976</a>)
                     </li>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         cellular carbohydrate metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0005975"
@@ -1320,12 +1310,6 @@ <h3>Ochrobactrum Metal Tolerance and Metabolic Flexibility</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         cellular response to metal ion
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0071248"
@@ -1626,6 +1610,87 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    yeast mannitol agar (YMA)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Rhizobia isolated from surface-sterilized P. pinnata root nodules and streaked on Congo red YMA (mannitol/yeast extract, pH 7.0-7.2); heavy-metal tolerance assayed in YMA liquid medium (pH 7.0). Host P. pinnata plants were cultivated in pots of VTM tailings in a greenhouse (day 25°C for 16 h, night 17°C for 8 h) until nodulation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2023.1078333"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2023.1078333
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"after incubation in an orbital shaker (28°C, 150 rpm) for seven days"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2023.1078333"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2023.1078333
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Congo red-containing yeast mannitol agar (YMA, 10.0 g/L mannitol, 1.0 g/L yeast extract"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2023.1078333"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2023.1078333
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The pots were kept in a greenhouse with a day temperature of 25°C for 16 h and a night temperature of 17°C for 8 h"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1830,8 +1895,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("dissimilatory reduction");
             
             processes.push("cellular detoxification");
@@ -1875,8 +1938,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("carbon utilization");
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("cellular carbohydrate metabolic process");
             
             
@@ -1967,8 +2028,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("cellular response to metal ion");
             
             
diff --git a/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html b/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
new file mode 100644
index 00000000..fd36ab7f
--- /dev/null
+++ b/docs/communities/Parachlorella_Saccharomyces_Mutualistic_Coculture.html
@@ -0,0 +1,1174 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000295</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        co-culture bioreactor for microalgal lipid production
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-member engineered co-culture of the green microalga Parachlorella kessleri and the yeast Saccharomyces cerevisiae, established to enhance microalgal lipid productivity. The partners form a mutualistic relationship based on reciprocal oxygen/carbon dioxide gas exchange. Under co-culture, biomass and lipid production increased 4-fold relative to microalgal monoculture. Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion and promoted lipid accumulation through nutrient competition, while microalgae are inferred to provide metabolic support to the yeast via exopolysaccharide (EPS)-derived molecules. Nanomechanical analyses (AFM, FluidFM) showed increased EPS production and stronger, longer microalga-yeast cell-cell interactions in co-culture.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Parachlorella kessleri</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3074"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:3074
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42217804/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42217804</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"This study examines the physiological and biophysical responses of Parachlorella kessleri when co-cultured with Saccharomyces cerevisiae to enhance lipid productivity"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Saccharomyces cerevisiae</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4932"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4932
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42217804/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42217804</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"This study examines the physiological and biophysical responses of Parachlorella kessleri when co-cultured with Saccharomyces cerevisiae to enhance lipid productivity"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Reciprocal oxygen/carbon dioxide gas exchange</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Parachlorella kessleri</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Saccharomyces cerevisiae</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    oxygen
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15379"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15379</a>), 
+                    
+                    carbon dioxide
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42217804/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42217804</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Microalgae and yeasts can establish a mutualistic relationship based on reciprocal oxygen/carbon dioxide exchange, offering a strategy to overcome productivity limits caused by the slow growth of microalgae."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Yeast support of microalgal growth and lipid accumulation</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Saccharomyces cerevisiae</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Parachlorella kessleri</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42217804/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42217804</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day 6) and promoted lipid accumulation through nutrient competition."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>EPS-mediated metabolic support of yeast by microalgae</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Parachlorella kessleri</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Saccharomyces cerevisiae</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42217804/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42217804</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"yeast viability remained above 68%, indicating possible metabolic support from microalgae via exopolysaccharides (EPS) - derived molecules"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    BBM + NO3 medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Microalga-yeast co-culture; yeast supplied with glucose as initial carbon source, which was depleted by day 6, after which the microalga transitioned to phototrophy; culture experienced ~8 days of nutrient limitation. Microalgal monoculture reference grown in the same BBM + NO3 medium.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42217804"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42217804
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"biomass and lipid production increased 4-fold compared to microalgal monoculture grown in BBM + NO3 medium"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42217804"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42217804
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion (day 6)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Parachlorella kessleri"] = {
+            id: "NCBITaxon:3074",
+            label: "Parachlorella kessleri",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER", "CROSS_FEEDER"]
+        };
+        
+        taxonData["Saccharomyces cerevisiae"] = {
+            id: "NCBITaxon:4932",
+            label: "Saccharomyces cerevisiae",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            
+            metabolites.push("oxygen");
+            
+            metabolites.push("carbon dioxide");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Reciprocal oxygen/carbon dioxide gas exchange",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Parachlorella kessleri";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Saccharomyces cerevisiae";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Yeast support of microalgal growth and lipid accumulation",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Saccharomyces cerevisiae";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Parachlorella kessleri";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "EPS-mediated metabolic support of yeast by microalgae",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Parachlorella kessleri";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Saccharomyces cerevisiae";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
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+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html b/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
index dd56e811..91337d4d 100644
--- a/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
+++ b/docs/communities/Peanut_Seed_Bacterial_CS_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Peanut Seed Bacterial CS SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000102</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000102</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html b/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html
index f51ab26c..02080172 100644
--- a/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html
+++ b/docs/communities/Pelotomaculum_Methanocella_Propionate_RNASeq_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pelotomaculum-Methanocella Propionate RNA-Seq Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000190</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000190</code>
                     </span>
                 </div>
 
@@ -1195,7 +1197,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Abstract-level evidence supports a propionate-oxidizing P. thermopropionicum and hydrogenotrophic M. conradii coculture assayed under anaerobic syntrophic conditions; detailed medium composition is not asserted here.
 
                 </p>
diff --git a/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html b/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
index 64e76e4b..d69be9bf 100644
--- a/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
+++ b/docs/communities/Pelotomaculum_Methanothermobacter_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pelotomaculum-Methanothermobacter Syntrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000052</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000052</code>
                     </span>
                 </div>
 
@@ -1272,7 +1274,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium prepared under strict anaerobic conditions for thermophilic cultivation at 55 degrees C. Medium boiled and cooled under N2/CO2 atmosphere, dispensed anaerobically into serum bottles, sealed with butyl rubber stoppers, and autoclaved. Reducing agents (Na2S, cysteine, and titanium(III) citrate) added from sterile anaerobic stock solutions after autoclaving. Final pH adjusted to 7.0. Resazurin used as redox indicator. The consortium requires coaggregation between P. thermopropionicum and M. thermautotrophicus for efficient interspecies hydrogen transfer at thermophilic temperatures.
 
                 </p>
diff --git a/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html b/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
index c958d1b9..f855c598 100644
--- a/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
+++ b/docs/communities/Pepper_Growth_Rhizosphere_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pepper Growth Rhizosphere SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000104</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000104</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    pepper seedling substrate (artificial climate chamber)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Relative humidity 80%. Seeds germinated on 0.5x MS in the dark at 30°C for 36 h; seedlings pre-grown on 0.5x MS solution at 28°C, 80% humidity, 16 h light/8 h dark. SynCom members pre-cultured before inoculation: bacteria in liquid LB at 37°C, 170 rpm for 24 h; fungi in liquid PDA at 28°C, 170 rpm for 5 days. PPFD reported in source as 300 mmol m2 s−1.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39858916"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39858916
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"They were cultivated for 5 days in an artificial climate chamber with the following conditions: 16 h of light at 28 °C and 8 h of dark at 28 °C, ensuring a photosynthetic photon flux density of 300 mmol m2 s−1 and a constant relative humidity of 80%"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39858916"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39858916
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the newly prepared SynCom was inoculated into soil at a concentration of 1 × 107 CFU/g. Following 45 days of cultivation"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Pepper_Phytophthora_SynCom5.html b/docs/communities/Pepper_Phytophthora_SynCom5.html
index 3748b842..5fbdff95 100644
--- a/docs/communities/Pepper_Phytophthora_SynCom5.html
+++ b/docs/communities/Pepper_Phytophthora_SynCom5.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pepper Phytophthora-Resistance SynCom5</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000105</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000105</code>
                     </span>
                 </div>
 
@@ -744,6 +746,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    tryptic soy broth (TSB)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Rhizosphere strains isolated on tryptic soy agar (TSA); growth of the five SynCom isolates monitored in TSB at 30°C, 180 rpm. Dual-culture antagonism assays against P. capsici incubated at 25°C for 5 days. Pepper plant assay conducted in a controlled growth chamber (day/night 18-23°C and 12-16°C).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40508300"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40508300
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were monitored in tryptic soy broth (TSB) at 30 °C with shaking at 180 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40508300"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40508300
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The experiment was conducted in a controlled growth chamber at Kyungpook National University under day/night temperatures of 18–23 °C and 12–16 °C"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Phenol_Carboxylation_Consortium.html b/docs/communities/Phenol_Carboxylation_Consortium.html
index 4a38fcff..a82c002e 100644
--- a/docs/communities/Phenol_Carboxylation_Consortium.html
+++ b/docs/communities/Phenol_Carboxylation_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Phenol Carboxylation Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000053</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000053</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Phenol Carboxylation Consortium</h1>
                     <span class="metadata-value">
                         anaerobic environment
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002229"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001825"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:00002229
+                            ENVO:01001825
                         </a>
                     </span>
                 </div>
@@ -695,12 +697,6 @@ <h3>Phenol Carboxylation to Benzoate</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0018958</a>)
                     </li>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -837,17 +833,6 @@ <h3>Sulfate Reduction Contribution to Syntrophy</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -922,6 +907,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    methanogenic medium (phenol as sole carbon source)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Obligate syntrophic coculture cultivated under methanogenic (strictly anaerobic) conditions; phenol served as the sole carbon source with an H2-scavenging methanogen partner.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/18281436"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:18281436
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Phenol degradation under methanogenic conditions has long been studied, but the anaerobes responsible for the degradation reaction are still largely unknown"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1018,8 +1058,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("phenol-containing compound catabolic process");
             
-            processes.push("aromatic compound catabolic process");
-            
             
             var evidenceCount = 1;
 
@@ -1104,10 +1142,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Phormidium_Alkaline_Consortium.html b/docs/communities/Phormidium_Alkaline_Consortium.html
index cc6526d2..c11d872a 100644
--- a/docs/communities/Phormidium_Alkaline_Consortium.html
+++ b/docs/communities/Phormidium_Alkaline_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Phormidium Alkaline Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000054</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000054</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Phormidium Alkaline Consortium</h1>
                     <span class="metadata-value">
                         soda lake
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00000274"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002121"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:00000274
+                            ENVO:00002121
                         </a>
                     </span>
                 </div>
@@ -861,17 +863,6 @@ <h3>Carbon Transfer to Heterotrophs</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1391,6 +1382,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    alkaline soda-lake medium (bicarbonate/carbonate-buffered)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Consortium enriched from alkaline soda-lake microbial mats and grown in laboratory photobioreactors. Illumination by full-spectrum LED (6400 K). Sodium bicarbonate and sodium carbonate were mixed to set the initial medium pH; four regimes tested (low-pH ammonium/nitrate pH 8.3, high-pH nitrate/urea pH 10.4). Sustained biomass productivity ~15.2 g/m2/day over 4 years of crash-free growth.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2022.780346"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2022.780346
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All experiments where performed at ∼25°C. Light was provided with full spectrum LED lights (Model T5H0; 6400K, Sunblaster Holdings ULC, Langley, BC, Canada) using a 16 h: 8 h light to dark cycle."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2022.780346"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2022.780346
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Sodium bicarbonate and sodium carbonate concentrations were mixed to adjust the initial pH of the medium"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1543,10 +1607,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.html b/docs/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.html
new file mode 100644
index 00000000..e921edf1
--- /dev/null
+++ b/docs/communities/Phosphitivorax_Methanoculleus_Lithosyntrophy_Phosphite_Coculture.html
@@ -0,0 +1,1038 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture - CommunityMech</title>
+    <style>
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+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000290</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-natural">
+                            STABLE
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        anoxic phosphite-oxidizing methanogenic enrichment culture
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001405"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001405
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>An anoxic, methanogenic enrichment culture defining &#34;lithosyntrophy,&#34; an obligate syntrophic interaction in which the electrons driving hydrogenotrophic methanogenesis originate from an inorganic compound. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (oxidation state +3) to phosphate coupled to hydrogenogenesis, in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase; the methanogen consumes the H2 to keep the reaction thermodynamically favorable, establishing interspecies electron transfer that links the phosphorus and carbon redox cycles in anoxic ecosystems.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Candidatus Phosphitivorax anaerolimi Phox-21</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1918507"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1918507
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41811448/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41811448</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (HPO32-, oxidation state +3) to phosphate coupled to hydrogenogenesis in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Methanoculleus sp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=45989"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:45989
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41811448/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41811448</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Lithosyntrophic interspecies H2 transfer</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Candidatus Phosphitivorax anaerolimi Phox-21</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Methanoculleus sp.</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    hydrogen (H2)
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18276"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18276</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41811448/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41811448</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"we describe &#34;lithosyntrophy,&#34; a mode of syntrophic interaction in which electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41811448/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41811448</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"In this pathway, electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    anoxic phosphite-oxidizing methanogenic enrichment medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Anoxic methanogenic enrichment culture; phosphite serves as the electron donor and Phox-21 grows mixotrophically, assimilating acetate to form biomass.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41811448"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41811448
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"electrons that drive hydrogenotrophic methanogenesis originate from an inorganic compound rather than from the canonical organic substrates"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41811448"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41811448
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Phox-21 is a mixotroph that assimilates acetate to form biomass"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Candidatus Phosphitivorax anaerolimi Phox-21"] = {
+            id: "NCBITaxon:1918507",
+            label: "Candidatus Phosphitivorax anaerolimi Phox-21",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_DONOR"]
+        };
+        
+        taxonData["Methanoculleus sp."] = {
+            id: "NCBITaxon:45989",
+            label: "Methanoculleus sp.",
+            abundance: "UNKNOWN",
+            roles: ["SYNTROPHIC_PARTNER", "ELECTRON_ACCEPTOR"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("hydrogen (H2)");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Lithosyntrophic interspecies H2 transfer",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Candidatus Phosphitivorax anaerolimi Phox-21";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Methanoculleus sp.";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Phylogenetically_Diverse_Denitrifying_SynCom.html b/docs/communities/Phylogenetically_Diverse_Denitrifying_SynCom.html
index 38a7cfb3..610611f9 100644
--- a/docs/communities/Phylogenetically_Diverse_Denitrifying_SynCom.html
+++ b/docs/communities/Phylogenetically_Diverse_Denitrifying_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Phylogenetically Diverse Denitrifying SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000113</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000113</code>
                     </span>
                 </div>
 
@@ -660,6 +662,129 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Modified marine broth 2216 supplemented with 20 mM NaNO3 (nitrate as electron acceptor)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>marine broth 2216 (modified)</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>sodium nitrate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Conditions are drawn from the same group&#39;s closely related, open-access all-Shewanella denitrifying-SynCom study (Wu et al. 2023, Microbiol Spectr), which describes the identical cultivation used to build the Shewanella (closely related, CR) synthetic denitrifying communities of this record; the paywalled primary paper (PMID:37207729) reports no Methods in its abstract. Strains cultured anaerobically in a modified marine broth 2216 (Becton, Dickinson) with 20 mM NaNO3 as electron acceptor, at 25°C in replicate Balch tubes, then serially transferred for experimental evolution.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/spectrum.04528-22"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/spectrum.04528-22
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"cultured anaerobically in three replicate Balch tubes at 25°C in the modified marine broth 2216 (Becton, Dickinson)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/spectrum.04528-22"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/spectrum.04528-22
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"cultivated in a modified 2216 medium"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/spectrum.04528-22"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/spectrum.04528-22
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"as the electron acceptor"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
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+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Pinus armandii Endophytic Biocontrol SynCom</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000280</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        Pinus armandii endosphere (endophytic host tissues)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001001"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001001
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A five-strain synthetic bacterial community (SynCom) assembled from endophytic bacteria isolated from multiple tissues of Pinus armandii to promote seedling growth and prime blister rust-associated defense responses. The optimized, functionally complementary SynCom comprises Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, selected for plant growth-promoting traits (nitrogen fixation, phosphate and potassium solubilization, IAA production) and antagonism of the rust pathogen. In pot experiments the SynCom increased seedling height and biomass and raised defense-related polyphenol oxidase and peroxidase activities relative to the control.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas koreensis RC1</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=198620"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:198620
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The optimized SynCom, comprising Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, significantly increased seedling height and biomass accumulation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Paenibacillus terrae RE7</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=159743"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:159743
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The optimized SynCom, comprising Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, significantly increased seedling height and biomass accumulation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus velezensis OB3</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=492670"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:492670
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The optimized SynCom, comprising Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, significantly increased seedling height and biomass accumulation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus velezensis NA3</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=492670"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:492670
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The optimized SynCom, comprising Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, significantly increased seedling height and biomass accumulation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus subtilis NA11</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1423"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1423
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"The optimized SynCom, comprising Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, significantly increased seedling height and biomass accumulation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Pinus armandii Endophytic Biocontrol SynCom</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Functionally complementary biocontrol SynCom assembly</h3>
+                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"this study screened endophytic bacteria with superior plant growth-promoting (PGP) and antagonistic functions to construct a functionally complementary and stable synthetic microbial community (SynCom)."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Community antagonism of the blister rust pathogen</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42322490/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42322490</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"antagonistic potential using dual-culture assays and inhibition of urediniospore germination."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Pseudomonas koreensis RC1"] = {
+            id: "NCBITaxon:198620",
+            label: "Pseudomonas koreensis RC1",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Paenibacillus terrae RE7"] = {
+            id: "NCBITaxon:159743",
+            label: "Paenibacillus terrae RE7",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Bacillus velezensis OB3"] = {
+            id: "NCBITaxon:492670",
+            label: "Bacillus velezensis OB3",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Bacillus velezensis NA3"] = {
+            id: "NCBITaxon:492670",
+            label: "Bacillus velezensis NA3",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+        taxonData["Bacillus subtilis NA11"] = {
+            id: "NCBITaxon:1423",
+            label: "Bacillus subtilis NA11",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "NICHE_PARTITIONING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Functionally complementary biocontrol SynCom assembly",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Community antagonism of the blister rust pathogen",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 7;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html b/docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html
new file mode 100644
index 00000000..ea9d5ed5
--- /dev/null
+++ b/docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html
@@ -0,0 +1,1099 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Pleuromutilin-degrading Artificial Consortium (5-strain) - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
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+        .term-link {
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+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
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+            margin-bottom: 1rem;
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+
+        .back-link:hover {
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+            border-radius: 8px;
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+            margin: 1rem 0 2rem;
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+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
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+            height: 14px;
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+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Pleuromutilin-degrading Artificial Consortium (5-strain)</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000300</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        pleuromutilin-contaminated environment (enrichment-derived)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01000313"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01000313
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A defined five-strain artificial microbial consortium constructed to degrade the antibiotic pleuromutilin, assembled from bacteria isolated out of a natural consortium (En4) that was itself developed by gradient enrichment and domestication under pleuromutilin stress. The consortium comprises Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis, and achieves a pleuromutilin degradation rate of 91.97%. In the parent natural community, pleuromutilin stress reduced microbial diversity and selected core taxa with functional specialization (notably Proteobacteria, and enriched pollutant-degrading genera such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Cupriavidus), and potential degradation products and metabolic pathways were proposed for the artificial consortium.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Stenotrophomonas pavanii</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=487698"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:487698
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Stenotrophomonas maltophilia</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=40324"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:40324
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Lysinibacillus sphaericus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1421"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1421
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Lysinibacillus mangiferihumi</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1130819"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1130819
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas songnenensis</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1176259"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1176259
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Pleuromutilin-degrading Artificial Consortium (5-strain)</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Cooperative pleuromutilin biodegradation by the artificial consortium</h3>
+                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                </div>
+
+                
+
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    pleuromutilin
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=8269"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:8269</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"an efficient artificial microbial consortium comprising five strains: Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis, was constructed, achieving a degradation rate of 91.97%."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42133144/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42133144</a>
+                            
+                            - SUPPORT (OTHER)
+                        </div>
+                        
+                        <div class="snippet">"core communities with functional specialization were identified across multiple taxa, primarily at the level of Proteobacteria"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Stenotrophomonas pavanii"] = {
+            id: "NCBITaxon:487698",
+            label: "Stenotrophomonas pavanii",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Stenotrophomonas maltophilia"] = {
+            id: "NCBITaxon:40324",
+            label: "Stenotrophomonas maltophilia",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Lysinibacillus sphaericus"] = {
+            id: "NCBITaxon:1421",
+            label: "Lysinibacillus sphaericus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Lysinibacillus mangiferihumi"] = {
+            id: "NCBITaxon:1130819",
+            label: "Lysinibacillus mangiferihumi",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Pseudomonas songnenensis"] = {
+            id: "NCBITaxon:1176259",
+            label: "Pseudomonas songnenensis",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "NICHE_PARTITIONING";
+            var metabolites = [];
+            
+            
+            metabolites.push("pleuromutilin");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Cooperative pleuromutilin biodegradation by the artificial consortium",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 6;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Polaromonas_Vanadium_Reduction_Community.html b/docs/communities/Polaromonas_Vanadium_Reduction_Community.html
index 1a376d30..2e5bc65f 100644
--- a/docs/communities/Polaromonas_Vanadium_Reduction_Community.html
+++ b/docs/communities/Polaromonas_Vanadium_Reduction_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Polaromonas Vanadium Reduction Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000055</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000055</code>
                     </span>
                 </div>
 
@@ -763,12 +765,6 @@ <h3>Dissimilatory V(V) Reduction by Polaromonas</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         dissimilatory reduction
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0019645"
@@ -872,16 +868,10 @@ <h3>Vanadium Immobilization via V(IV) Precipitation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         metal ion sequestration
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0051238"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0051238</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0140487"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0140487</a>)
                     </li>
                     
                 </ul>
@@ -969,12 +959,6 @@ <h3>Sulfide-Mediated Chemical V(V) Reduction</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019420</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1050,12 +1034,6 @@ <h3>Sequential Fe(III) and V(V) Reduction</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1434,8 +1412,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("dissimilatory reduction");
             
             processes.push("cellular detoxification");
@@ -1477,8 +1453,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("metal ion sequestration");
             
             
@@ -1524,8 +1498,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("sulfate reduction");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
@@ -1570,8 +1542,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
diff --git a/docs/communities/Populus_Salt_Tolerant_SynComs.html b/docs/communities/Populus_Salt_Tolerant_SynComs.html
index c53e31ac..da6dc1c1 100644
--- a/docs/communities/Populus_Salt_Tolerant_SynComs.html
+++ b/docs/communities/Populus_Salt_Tolerant_SynComs.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Populus Salt-Tolerant Rhizosphere SynComs</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000090</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000090</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html b/docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html
index b6fc9589..96e2ac96 100644
--- a/docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html
+++ b/docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Prairie Pothole Wetland Sulfur-Carbon Virus-Host Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000256</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000256</code>
                     </span>
                 </div>
 
@@ -741,8 +743,8 @@ <h3>Diverse Sulfate-Reduction Guild</h3>
                     
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
                     </li>
                     
                 </ul>
diff --git a/docs/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.html b/docs/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.html
index 0f6ba4b7..02aa500f 100644
--- a/docs/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.html
+++ b/docs/communities/Premature_Infant_Gut_Escherichia_Diametric_Ratio_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Premature Infant Gut Escherichia In-Situ Physiological-Condition Community</
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000253</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000253</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Prochlorococcus_Alteromonas_Helper_Coculture.html b/docs/communities/Prochlorococcus_Alteromonas_Helper_Coculture.html
index 57d51d38..0fd14f04 100644
--- a/docs/communities/Prochlorococcus_Alteromonas_Helper_Coculture.html
+++ b/docs/communities/Prochlorococcus_Alteromonas_Helper_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Prochlorococcus-Alteromonas Helper Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000131</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000131</code>
                     </span>
                 </div>
 
@@ -852,6 +854,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    PEv medium (artificial seawater amended with Pro99 nutrients at 1/25 standard concentrations)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">21 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Prochlorococcus VOL4 (MIT9312) co-cultured with Alteromonas EZ55; inoculated tubes rotated on a tissue culture rotator in a Percival growth chamber; ambient (400 ppm) versus elevated (800 ppm) CO2 treatments.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1038/ismej.2017.189"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1038/ismej.2017.189
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All cultures were grown in PEv medium (artificial seawater amended with Pro99 nutrients at 1/25 standard concentrations)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1038/ismej.2017.189"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1038/ismej.2017.189
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Inoculated tubes were placed on a tissue culture rotator (Thermo Fisher Scientific, Waltham, MA, USA) in a Percival growth chamber at 21 °C under 150 μmol photons m−2 s−1 on a 14:10 light–dark cycle."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.html b/docs/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.html
index d6732187..9d517e91 100644
--- a/docs/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.html
+++ b/docs/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Propanotrophic Chlorinated Ethene Cometabolism Enrichment Cultures</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000271</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000271</code>
                     </span>
                 </div>
 
@@ -857,12 +859,6 @@ <h3>Propane-Cometabolic TCE Degradation by Rhodococcus</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0071466</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1298,6 +1294,97 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    mineral salts medium (phosphate buffer plus trace-metal stock; K2HPO4/KH2PO4/NH4Cl with MgSO4, FeSO4, MnSO4, ZnSO4, CoCl2)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">7.4</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">room temperature °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Propane supplied as the sole carbon and energy source in the headspace; serial transfers (10 mL culture into 20 mL fresh medium; dilution ratio changed from 1:9 to 1:2).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.jenvman.2026.129957"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.jenvman.2026.129957
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"consisted of 160 mL serum bottles containing 10 g (wet weight) of soil or sediment and 30 mL of liquid media, with the remaining volume serving as the gas headspace"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.jenvman.2026.129957"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.jenvman.2026.129957
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All microcosms were incubated at room temperature on an orbital shaker operated at 120 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.jenvman.2026.129957"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.jenvman.2026.129957
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The solution pH was then adjusted to 7.4 and placed in the autoclave for sterilization"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1420,8 +1507,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("cellular response to xenobiotic stimulus");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.html b/docs/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.html
index 618a83d0..0cd4dcff 100644
--- a/docs/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.html
+++ b/docs/communities/Pseudomonas_Pedobacter_Social_Spreading_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pseudomonas-Pedobacter Social Spreading Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000161</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000161</code>
                     </span>
                 </div>
 
@@ -951,7 +953,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Low-nutrient, high-NaCl TSB-NK medium solidified with 2% agar; mixed Pf0-1 and V48 colonies were incubated on the agar surface to assay spreading.
                 </p>
                 
diff --git a/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html b/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
index 6eadcad6..f229270b 100644
--- a/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
+++ b/docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pseudomonas-Rhodococcus Chloronitrobenzene Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000181</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000181</code>
                     </span>
                 </div>
 
@@ -625,12 +627,6 @@ <h3>Pseudomonas Partial Chloronitrobenzene Transformation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                     <li>
                         interspecies interaction between organisms
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
@@ -696,12 +692,6 @@ <h3>Rhodococcus Intermediate Degradation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                     <li>
                         interspecies interaction between organisms
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
@@ -774,17 +764,6 @@ <h3>Coculture Chloronitrobenzene Mineralization</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1096,7 +1075,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract confirms 3- and 4-CNB mineralization in the presence of an additional carbon source; more specific medium formulation is not asserted here.
                 </p>
                 
@@ -1215,8 +1194,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("aromatic compound catabolic process");
-            
             processes.push("interspecies interaction between organisms");
             
             
@@ -1255,8 +1232,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("aromatic compound catabolic process");
-            
             processes.push("interspecies interaction between organisms");
             
             
@@ -1300,10 +1275,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("aromatic compound catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html b/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
new file mode 100644
index 00000000..6937a3f3
--- /dev/null
+++ b/docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
@@ -0,0 +1,1091 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
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+
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+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
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+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
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+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
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+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
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+        .metadata-item {
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+        .metadata-label {
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+            color: var(--text-muted);
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+            text-transform: uppercase;
+            letter-spacing: 0.05em;
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+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
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+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
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+            border-radius: 8px;
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+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
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+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
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+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
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+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
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+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
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+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
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+
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+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
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+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
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+
+        .legend-circle {
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+        .network-tooltip {
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+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
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+
+        .network-tooltip strong {
+            color: #93c5fd;
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+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
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+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000289</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        TPA-fed coculture fermentation (bioreactor)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-strain synthetic consortium of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) grown with terephthalic acid (TPA), a primary polyethylene terephthalate (PET) monomer, as the sole carbon and energy source. Although both strains utilize TPA at comparable rates in monoculture, Pp-TE consistently outcompetes RDK17 in batch and multitransfer coculture fermentations. Dominance is driven jointly by exploitative competition for TPA and by interference competition through the Pp-TE type VI secretion system, which impairs RDK17 growth via contact-dependent inhibition. Loss of TPA metabolism in Pp-TE abolishes its dominance, illustrating how interspecies interaction and metabolic capability co-determine consortium structure and overall TPA degradation.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas putida strain Pp-TE (engineered)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=303"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:303
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42324694/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42324694</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"we investigated the coculture dynamics of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) in the presence of TPA as the sole carbon and energy source"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Rhodococcus sp. strain RDK17 (native)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1827"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1827
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42324694/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42324694</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"we investigated the coculture dynamics of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) in the presence of TPA as the sole carbon and energy source"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Exploitative competition for terephthalic acid</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas putida strain Pp-TE (engineered)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rhodococcus sp. strain RDK17 (native)</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    terephthalic acid (TPA)
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15702"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15702</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42324694/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42324694</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations, even when RDK17 was inoculated at a significantly higher initial abundance"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Interference competition via type VI secretion system</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas putida strain Pp-TE (engineered)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rhodococcus sp. strain RDK17 (native)</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42324694/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42324694</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"the dominance of Pp-TE was primarily conferred by its type VI secretion system, which impaired the growth of RDK17 via contact-dependent inhibition"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    minimal medium with terephthalic acid (TPA) as the sole carbon and energy source
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Batch and multitransfer (serial-transfer) coculture fermentations of Pseudomonas putida strain Pp-TE with Rhodococcus sp. strain RDK17.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42324694"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42324694
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"in the presence of TPA as the sole carbon and energy source"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42324694"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42324694
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Pseudomonas putida strain Pp-TE (engineered)"] = {
+            id: "NCBITaxon:303",
+            label: "Pseudomonas putida strain Pp-TE (engineered)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Rhodococcus sp. strain RDK17 (native)"] = {
+            id: "NCBITaxon:1827",
+            label: "Rhodococcus sp. strain RDK17 (native)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            
+            metabolites.push("terephthalic acid (TPA)");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Exploitative competition for terephthalic acid",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas putida strain Pp-TE (engineered)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rhodococcus sp. strain RDK17 (native)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Interference competition via type VI secretion system",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas putida strain Pp-TE (engineered)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rhodococcus sp. strain RDK17 (native)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
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+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
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+        // Stabilize after 300 ticks then stop
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+        simulation.stop();
+
+        // Apply final positions
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+            .attr("x2", function(d) { return d.target.x; })
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+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
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+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html b/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
new file mode 100644
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--- /dev/null
+++ b/docs/communities/Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium.html
@@ -0,0 +1,1040 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
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+            --success: #10b981;
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+        }
+
+        * {
+            margin: 0;
+            padding: 0;
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+
+        body {
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+        .container {
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+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
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+
+        h3 {
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+            font-size: 1.25rem;
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+        .metadata {
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+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
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+            letter-spacing: 0.05em;
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+
+        table {
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+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
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+
+        th {
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+            font-size: 0.875rem;
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+
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+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
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+        .empty-state {
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+            padding: 2rem;
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+        .empty-state p {
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+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
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+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
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+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
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+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
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+}
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+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
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+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
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+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000291</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        engineered consortium immobilized on S-N-doped biochar (naphthalene bioremediation reactor)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-member engineered bioremediation consortium in which genetically engineered Pseudomonas stutzeri (overexpressing nahAc and nahB) and a Rhodococcus strain (overexpressing nahH and catA) are co-anchored on S-N-doped biochar to mineralize naphthalene. Pseudomonas stutzeri acts as an oxidative bio-anode that initiates naphthalene degradation and releases electrons, while the conductive biochar matrix mediates direct interspecies electron transfer (DIET) and extracellular electron transfer (EET) to Rhodococcus, which serves as a reductive bio-cathode driving oxygenolytic ring-cleavage catalysis. The resulting bioelectrochemical syntrophic circuit achieved &gt;98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas stutzeri (overexpressing nahAc and nahB)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=316"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:316
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42139785/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42139785</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"co-anchoring engineered Pseudomonas stutzeri (overexpressing nahAc and nahB)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Rhodococcus rhodococcus (overexpressing nahH and catA)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1827"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1827
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42139785/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42139785</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Rhodococcus rhodococcus (overexpressing nahH and catA)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Biochar-bridged direct interspecies electron transfer (DIET)</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas stutzeri (overexpressing nahAc and nahB)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rhodococcus rhodococcus (overexpressing nahH and catA)</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42139785/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42139785</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"facilitating direct interspecies electron transfer (DIET) and enhancing extracellular electron transfer (EET)"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Syntrophic naphthalene mineralization circuit</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas stutzeri (overexpressing nahAc and nahB)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rhodococcus rhodococcus (overexpressing nahH and catA)</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    naphthalene
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16482"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16482</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42139785/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42139785</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Electrochemical and multi-omics analyses confirmed the establishment of this syntrophic circuit, demonstrating elevated electron flux, coordinated upregulation of catabolic genes"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Pseudomonas stutzeri (overexpressing nahAc and nahB)"] = {
+            id: "NCBITaxon:316",
+            label: "Pseudomonas stutzeri (overexpressing nahAc and nahB)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "ELECTRON_DONOR", "ELECTROGEN", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Rhodococcus rhodococcus (overexpressing nahH and catA)"] = {
+            id: "NCBITaxon:1827",
+            label: "Rhodococcus rhodococcus (overexpressing nahH and catA)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER", "ELECTRON_ACCEPTOR", "ELECTROTROPH", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Biochar-bridged direct interspecies electron transfer (DIET)",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas stutzeri (overexpressing nahAc and nahB)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rhodococcus rhodococcus (overexpressing nahH and catA)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            
+            metabolites.push("naphthalene");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Syntrophic naphthalene mineralization circuit",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas stutzeri (overexpressing nahAc and nahB)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rhodococcus rhodococcus (overexpressing nahH and catA)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html b/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
index bc781d2f..ca556c27 100644
--- a/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
+++ b/docs/communities/Pseudonitzschia_Sulfitobacter_Association.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Pseudo-nitzschia-Sulfitobacter Marine Association</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000056</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000056</code>
                     </span>
                 </div>
 
@@ -865,9 +867,9 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                             <td>mg/L</td>
                             <td>
                                 
-                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=86154"
+                                <a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=60720"
                                    class="term-link" target="_blank" rel="noopener">
-                                    CHEBI:86154
+                                    CHEBI:60720
                                 </a>
                                 
                             </td>
@@ -1029,7 +1031,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> f/2 medium (Guillard) is used for marine diatom Pseudo-nitzschia multiseries cultivation. The medium is prepared with natural seawater enriched with f/2 nutrients, metals, and vitamins. Silicate is essential for diatom frustule formation. P. multiseries can grow over a salinity range of 15-40 psu and temperature range of 4-20°C, but optimal conditions are around 19°C and 30 ppt salinity. The diatom-bacteria association is maintained in co-culture with Sulfitobacter sp. SA11, which produces IAA auxin to promote diatom growth.
 
                 </p>
diff --git a/docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html b/docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html
index 7a792f82..c3b5207f 100644
--- a/docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html
+++ b/docs/communities/Rammelsberg_Cobalt_Nickel_Tailings.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rammelsberg Cobalt-Nickel Tailings Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000057</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000057</code>
                     </span>
                 </div>
 
@@ -622,12 +624,6 @@ <h3>Iron Oxidation and Ferric Iron Generation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0006826</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -700,17 +696,6 @@ <h3>Cobalt and Copper Mobilization from Sulfide Minerals</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -795,12 +780,6 @@ <h3>Sulfur Oxidation and Acid Generation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -1218,8 +1197,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("iron ion transport");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
@@ -1260,10 +1237,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1307,8 +1280,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             
diff --git a/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html b/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html
index 4d3351d9..42521224 100644
--- a/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html
+++ b/docs/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rhodopseudomonas-E. coli Cross-Feeding Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000092</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000092</code>
                     </span>
                 </div>
 
@@ -660,6 +662,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    MDC (M9-derived coculture medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Mono- and cocultures grown in 10 ml MDC in tubes made anaerobic under 100% N2 at 30 °C, shaken at 150 rpm beside a 60 W incandescent bulb; serially passaged at 2% v/v of stationary-phase coculture.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32788711"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32788711
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Experimental mono- and cocultures were grown in 10 ml of M9-derived coculture medium (MDC)"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32788711"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32788711
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Tubes were made anaerobic under 100% N2"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32788711"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32788711
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"shaken at 150 rpm beneath a 60 W incandescent bulb (750 lumens)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
index 36fbdd12..fa81c477 100644
--- a/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
+++ b/docs/communities/Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rhodopseudomonas-Geobacter Magnetite Redox Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000268</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000268</code>
                     </span>
                 </div>
 
@@ -631,12 +633,6 @@ <h3>Magnetite-Mediated Electron Sharing</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -718,12 +714,6 @@ <h3>Phototrophic Magnetite Fe(II) Oxidation</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -784,12 +774,6 @@ <h3>Anaerobic Magnetite Fe(III) Reduction</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -843,17 +827,6 @@ <h3>Biogeochemical Battery Function</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1140,7 +1113,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports magnetite nanoparticles and light-dependent phototrophic Fe(II) oxidation in a coculture with anaerobic Fe(III) reduction; exact salts, buffer composition, and electron donor concentrations are not asserted here.
 
                 </p>
@@ -1262,8 +1235,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1310,8 +1281,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             processes.push("photosynthesis");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
@@ -1351,8 +1320,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1389,10 +1356,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html b/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html
index 4a3afae5..f61acf07 100644
--- a/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html
+++ b/docs/communities/Rice_Acid_Soil_Bioinoculant_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rice Acid Soil Bioinoculant SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000109</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000109</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Rice_Duckweed_Bacillus_SynCom.html b/docs/communities/Rice_Duckweed_Bacillus_SynCom.html
index bd9c0c23..73562c24 100644
--- a/docs/communities/Rice_Duckweed_Bacillus_SynCom.html
+++ b/docs/communities/Rice_Duckweed_Bacillus_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rice-Duckweed Bacillus Biocontrol SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000058</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000058</code>
                     </span>
                 </div>
 
@@ -804,6 +806,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    LB (lysogeny broth)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Each of the eight Bacillus isolates cultured independently in LB broth to mid-log phase, harvested by centrifugation (4000 × g, 5 min), and combined into the SynCom before greenhouse application to rice.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41736136"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41736136
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"each of the eight Bacillus isolates was first cultured independently in LB broth at 28 °C with shaking (180 rpm) until reaching mid-log phase"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Rice_P_Uptake_Intercropping_SynCom4.html b/docs/communities/Rice_P_Uptake_Intercropping_SynCom4.html
index 522232ff..d3bd5f7f 100644
--- a/docs/communities/Rice_P_Uptake_Intercropping_SynCom4.html
+++ b/docs/communities/Rice_P_Uptake_Intercropping_SynCom4.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rice Phosphorus Uptake Intercropping SynCom4</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000110</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000110</code>
                     </span>
                 </div>
 
@@ -744,6 +746,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    strain-specific liquid media (SynCom members)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> The four SynCom strains were each cultured in their respective liquid media on a shaker, harvested by centrifugation (5000 x g, 10 min), adjusted to 1 x 10^8 CFU/g, and applied to potted rice 5 days after transplanting.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39684532"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39684532
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"bacteria were cultured in their respective liquid media on a shaker (180 rpm, 28 °C) for two days and harvested by centrifugation"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Richmond_Mine_AMD_Biofilm.html b/docs/communities/Richmond_Mine_AMD_Biofilm.html
index 7cbc47ad..8c2a2395 100644
--- a/docs/communities/Richmond_Mine_AMD_Biofilm.html
+++ b/docs/communities/Richmond_Mine_AMD_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Richmond Mine AMD Biofilm</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000059</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000059</code>
                     </span>
                 </div>
 
@@ -835,12 +837,6 @@ <h3>Ferrous Iron Oxidation by Leptospirillum</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -931,12 +927,6 @@ <h3>Ferrous Iron Oxidation by Ferroplasma</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         carbon fixation
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0015977"
@@ -1024,17 +1014,6 @@ <h3>Pyrite Dissolution</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -1184,12 +1163,6 @@ <h3>Organic Carbon Scavenging by ARMAN</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         tricarboxylic acid cycle
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006099"
@@ -1271,12 +1244,6 @@ <h3>Iron and Sulfur Oxidation at Higher pH Refugia</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1781,7 +1748,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium for cultivation of Ferroplasma acidarmanus isolated from Richmond Mine AMD. F. acidarmanus grows chemomixotrophically on ferrous iron + yeast extract or sugars. This isolate requires much higher levels of organic carbon (0.1% wt/vol yeast extract) compared to F. acidiphilum (0.02-0.04%). Capable of facultative anaerobic growth by coupling chemoorganotrophic growth on yeast extract to reduction of ferric iron. Optimum pH 1.0-1.7, capable of growth at pH 0. Temperature optimum 35-42°C. Microaerophilic, tolerates low oxygen concentrations. Note: This medium supports pure culture growth of isolated F. acidarmanus, but the intact Richmond Mine biofilm community has not been successfully replicated in laboratory culture.
                 </p>
                 
@@ -1934,7 +1901,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Nitrogen-free medium developed for selective isolation of Leptospirillum ferrodiazotrophum (Leptospirillum group III), the nitrogen-fixing member of Richmond Mine biofilm. Richmond Mine AMD biofilm sample naturally abundant in group III was homogenized, filtered, and serially diluted into nitrogen-free liquid medium. Culture grew autotrophically to maximum density ~10^6 cells/ml, oxidizing ferrous iron as sole energy source. Ammonium sulfate deliberately omitted to select for diazotrophic organisms capable of nitrogen fixation. This selective isolation strategy was guided by metagenomic data showing a single nif operon on a Leptospirillum group III genome fragment. Axenic culture confirmed by 16S rRNA-ITS clone library analysis. Note: This medium supports L. ferrodiazotrophum but not the complete biofilm community.
                 </p>
                 
@@ -2094,8 +2061,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -2137,8 +2102,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("carbon fixation");
             
             
@@ -2179,10 +2142,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -2261,8 +2220,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("tricarboxylic acid cycle");
             
             
@@ -2309,8 +2266,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
diff --git a/docs/communities/Rifle_Aquifer_Bioanode_EET_Community.html b/docs/communities/Rifle_Aquifer_Bioanode_EET_Community.html
index b4282afb..a7e3b3af 100644
--- a/docs/communities/Rifle_Aquifer_Bioanode_EET_Community.html
+++ b/docs/communities/Rifle_Aquifer_Bioanode_EET_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rifle Aquifer Bioanode Extracellular Electron Transfer Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000241</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000241</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Rifle_Uranium_Reducing_Community.html b/docs/communities/Rifle_Uranium_Reducing_Community.html
index 8a31aba3..d23cdf51 100644
--- a/docs/communities/Rifle_Uranium_Reducing_Community.html
+++ b/docs/communities/Rifle_Uranium_Reducing_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Rifle Uranium-Reducing Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000060</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000060</code>
                     </span>
                 </div>
 
@@ -774,12 +776,6 @@ <h3>Acetate Oxidation Coupled to Fe(III) and U(VI) Reduction</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         acetate catabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0045733"
@@ -872,17 +868,6 @@ <h3>Uranium Immobilization via Uraninite Formation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -938,17 +923,6 @@ <h3>Hydrogen-Mediated U(VI) Reduction by Anaeromyxobacter</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1019,12 +993,6 @@ <h3>Sulfate Reduction and Chemical U(VI) Reduction</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019420</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1080,17 +1048,6 @@ <h3>Community Succession from Metal to Sulfate Reduction</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1174,12 +1131,6 @@ <h3>Complementary Sulfate Reduction and U(VI) Reduction</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019420</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1426,6 +1377,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    in situ Old Rifle aquifer groundwater (acetate-amended)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Acetate (1-3 mM) injected into the subsurface over a 3-month period via an injection gallery of 20 wells to stimulate in situ activity of indigenous metal-reducing bacteria; U(VI) declined below the 0.18 μM treatment level within 50 days.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/14532040"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:14532040
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Acetate (1 to 3 mM) was injected into the subsurface over a 3-month period via an injection gallery composed of 20 injection wells"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/14532040"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:14532040
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"there was a loss of sulfate from the groundwater and an accumulation of sulfide"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1531,8 +1550,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("acetate catabolic process");
             
             
@@ -1569,10 +1586,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1615,10 +1628,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1661,8 +1670,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("sulfate reduction");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
@@ -1704,10 +1711,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1755,8 +1758,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("sulfate reduction");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/SF356_Cellulose_Degrader.html b/docs/communities/SF356_Cellulose_Degrader.html
index ba9c309d..daa18c06 100644
--- a/docs/communities/SF356_Cellulose_Degrader.html
+++ b/docs/communities/SF356_Cellulose_Degrader.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>SF356 Thermophilic Cellulose-Degrading Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000061</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000061</code>
                     </span>
                 </div>
 
@@ -1169,7 +1171,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> PCS basal medium (peptone-cellulose-salt) supplemented with filter paper as cellulose substrate and calcium carbonate buffer. Medium prepared with loose caps to allow oxygen entry while maintaining high humidity. Static (non-shaking) incubation. The aerobic members (Pseudoxanthomonas, Brevibacillus, Bordetella) consume oxygen to create localized anaerobic microenvironments for the cellulolytic Clostridium species. Inoculum volume: 40 microliters per 4 mL medium. Subculture protocol: 40-700 microliters transferred to fresh medium after 6 days.
 
                 </p>
diff --git a/docs/communities/SIHUMIx_Human_Intestinal_Model_Community.html b/docs/communities/SIHUMIx_Human_Intestinal_Model_Community.html
index b5bb7dac..b2e7c70c 100644
--- a/docs/communities/SIHUMIx_Human_Intestinal_Model_Community.html
+++ b/docs/communities/SIHUMIx_Human_Intestinal_Model_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>SIHUMIx Human Intestinal Model Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000080</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000080</code>
                     </span>
                 </div>
 
@@ -1137,7 +1139,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The eight strains are grown individually before inoculation and the mixed community is maintained anaerobically in complex intestinal medium.
                 </p>
                 
diff --git a/docs/communities/SMutans_CAlbicans_ECC_Biofilm.html b/docs/communities/SMutans_CAlbicans_ECC_Biofilm.html
index f518db59..09276481 100644
--- a/docs/communities/SMutans_CAlbicans_ECC_Biofilm.html
+++ b/docs/communities/SMutans_CAlbicans_ECC_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Streptococcus mutans - Candida albicans ECC Biofilm Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000083</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000083</code>
                     </span>
                 </div>
 
@@ -705,6 +707,79 @@ <h4>Evidence</h4>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    UFYTE (ultrafiltered tryptone-yeast extract) broth with 1% sucrose
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">CAPNOPHILIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Cospecies biofilms of S. mutans UA159 (~2 x 10^6 CFU/mL) and C. albicans SC5314 (~2 x 10^4 CFU/mL) grown in UFYTE broth containing 1% (30 mM) sucrose; grown undisturbed for the first 18 h, then medium changed twice daily until 42 h.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24566629"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24566629
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"tryptone-yeast extract (UFYTE) broth containing 1% (30 mM) sucrose"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/24566629"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:24566629
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"at 37°C under 5% CO2"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/SMutans_SSputigena_ECC_Pathobiont.html b/docs/communities/SMutans_SSputigena_ECC_Pathobiont.html
index 9264ac6e..438ee24f 100644
--- a/docs/communities/SMutans_SSputigena_ECC_Pathobiont.html
+++ b/docs/communities/SMutans_SSputigena_ECC_Pathobiont.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Streptococcus mutans - Selenomonas sputigena ECC Pathobiont Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000084</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000084</code>
                     </span>
                 </div>
 
@@ -651,6 +653,79 @@ <h4>Evidence</h4>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Brain Heart Infusion Supplemented (BHIS) medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> BHI broth supplemented with 5 g/L yeast extract, 5 mg/L hemin, 1 mg/L vitamin K1, and 0.5 g/L L-cysteine; single or mixed biofilms grown on apatitic surfaces in BHIS with 1% sucrose to simulate cariogenic conditions.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37217495"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37217495
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Bacteria were grown in Brain Heart Infusion Supplemented (BHIS) medium (Brain Heart Infusion broth supplemented with 5 g/L yeast extract, 5 mg/L Hemin, 1 mg/L Vitamin K1, and 0.5 g/L L-cysteine) at 37 °C to exponential phase in an anaerobic chamber (Anaerobe Systems)."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37217495"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37217495
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The cultures were incubated in the anaerobic chamber at 37 °C for 48 h."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/SMutans_VParvula_ASC_Biofilm.html b/docs/communities/SMutans_VParvula_ASC_Biofilm.html
index 03d7ec15..6f7fc036 100644
--- a/docs/communities/SMutans_VParvula_ASC_Biofilm.html
+++ b/docs/communities/SMutans_VParvula_ASC_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Streptococcus mutans - Veillonella parvula Adult Severe Caries Model</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000085</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000085</code>
                     </span>
                 </div>
 
@@ -651,6 +653,79 @@ <h4>Evidence</h4>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    brain heart infusion (BHI) broth
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. mutans grown in BHI broth/agar; V. parvula grown in BHI supplemented with 0.6% sodium lactate; 1% sucrose added to BHI broth for biofilm studies.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39345197"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39345197
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"S. mutans was routinely anaerobically (85% N2, 5% CO2, 10% H2) incubated at 37°C in brain heart infusion (BHI) broth (Difco, MD, USA) or on BHI agar plates."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39345197"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39345197
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Mono- and dual-species biofilms were grown on saliva-coated hydroxyapatite slides placed in 24-well plates horizontally with 2.0 mL of microbial suspensions at 37°C for 24 h under facultative anaerobic conditions without disturbance."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/SPRUCE_Peatland_Methane_Cycling_Community.html b/docs/communities/SPRUCE_Peatland_Methane_Cycling_Community.html
index aedd4eb6..ab5b478b 100644
--- a/docs/communities/SPRUCE_Peatland_Methane_Cycling_Community.html
+++ b/docs/communities/SPRUCE_Peatland_Methane_Cycling_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>SPRUCE Peatland Methane-Cycling Microbial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000135</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000135</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.html b/docs/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.html
index 34854f69..92e72149 100644
--- a/docs/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.html
+++ b/docs/communities/Saanich_Inlet_OMZ_Redox_Gradient_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Saanich Inlet Oxygen Minimum Zone Redox-Gradient Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000140</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000140</code>
                     </span>
                 </div>
 
@@ -669,12 +671,6 @@ <h3>SUP05 Nitrite Leakage Supports Anammox</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019333</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -752,12 +748,6 @@ <h3>Complementary Nitrous Oxide Reduction Niche</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019333</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -830,12 +820,6 @@ <h3>Redox-Driven Pathway Partitioning</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0019333</a>)
                     </li>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -1078,8 +1062,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("denitrification");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 2;
 
@@ -1124,8 +1106,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("denitrification");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
@@ -1174,8 +1154,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("denitrification");
             
-            processes.push("oxidation-reduction process");
-            
             
             var evidenceCount = 1;
 
diff --git a/docs/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.html b/docs/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.html
index 4ee1afe7..e2429608 100644
--- a/docs/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.html
+++ b/docs/communities/Saccharomyces_Acinetobacter_Lignocellulose_Detox_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Saccharomyces-Acinetobacter Lignocellulose Hydrolysate Detoxification Cocult
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000263</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000263</code>
                     </span>
                 </div>
 
@@ -753,6 +755,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    synthetic lignocellulosic hydrolysate (SLH) medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SLH mimics 70%-diluted spruce hydrolysate: d-glucose 12.18 g/L, d-xylose 7.91 g/L, d-mannose 10.43 g/L, d-galactose 7.14 g/L, acetic acid 2.66 g/L, ferulic acid 0.5 g/L, p-coumaric acid 0.5 g/L, furfural 0.84 g/L, HMF 0.35 g/L, formic acid 0.28 g/L, yeast extract 5 g/L, urea 2.5 g/L.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38711153"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38711153
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The liquid cultivations were incubated at 30 °C and 300 rpm in an Innova 44 shaker (Eppendorf, Germany), cultivations using LB-agar plates were incubated at 30 °C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38711153"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38711153
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Fermentations were carried out in a 3.5 L bioreactor with 1 L SLH medium in 30 °C and pH was maintained at 6.0 by 2 M HCl and 8% (v/v)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.html b/docs/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.html
index a1fa9364..5d096490 100644
--- a/docs/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.html
+++ b/docs/communities/Saccharomyces_Chlamydomonas_Fungal_Algal_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Saccharomyces-Chlamydomonas Fungal-Algal Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000165</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000165</code>
                     </span>
                 </div>
 
@@ -988,7 +990,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Sealed illuminated cocultures used glucose as the yeast carbon source and oxidized nitrogen sources to impose reciprocal carbon and nitrogen dependencies.
                 </p>
                 
diff --git a/docs/communities/Salar_Atacama_Lithium_Brine_Community.html b/docs/communities/Salar_Atacama_Lithium_Brine_Community.html
index 4cc4f1ba..d5698fb7 100644
--- a/docs/communities/Salar_Atacama_Lithium_Brine_Community.html
+++ b/docs/communities/Salar_Atacama_Lithium_Brine_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Salar de Atacama Lithium Brine Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000062</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000062</code>
                     </span>
                 </div>
 
@@ -876,12 +878,6 @@ <h3>Organic Matter Degradation in Hypersaline Brine</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         aerobic respiration
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0009060"
@@ -1073,12 +1069,6 @@ <h3>Bacterial Heterotrophic Activity and Functional Redundancy</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
                     <li>
                         aerobic respiration
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0009060"
@@ -1296,6 +1286,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Luria Bertani (LB) broth
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Brine enrichments grown in Luria Bertani broth and isolated on Luria Bertani agar; isolates LIBR002/LIBR003 grew over 20-45 °C (optimum 37 °C) and pH 3-9 (optima pH 5-6), tolerating high NaCl and LiCl.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31354691"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31354691
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The enrichment cultures were grown at 37°C (temperature used for the culture of extreme halophiles with salinities of 20 % w/v NaCl or more; Schneegurt, 2012) and agitated at 130 rpm for 4 weeks."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31354691"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31354691
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"However, for both strains, optimum growth was attained at 37°C, and growth was lowest at 20°C."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1448,8 +1506,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("aerobic respiration");
             
             
@@ -1568,8 +1624,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("organic substance catabolic process");
-            
             processes.push("aerobic respiration");
             
             
diff --git a/docs/communities/Shewanella_Denitrifying_Richness_SynComs.html b/docs/communities/Shewanella_Denitrifying_Richness_SynComs.html
index ddcbd8b6..2b06bfaf 100644
--- a/docs/communities/Shewanella_Denitrifying_Richness_SynComs.html
+++ b/docs/communities/Shewanella_Denitrifying_Richness_SynComs.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Shewanella Denitrifying Richness SynComs</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000114</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000114</code>
                     </span>
                 </div>
 
@@ -618,6 +620,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    modified marine broth 2216
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Modified marine broth 2216 (Becton, Dickinson) supplemented with 20 mM NaNO3 as the electron acceptor; SDCs propagated by transferring 3% (300 µL of the 10 mL culture) into fresh medium every 3 days (72 h).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37154752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37154752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The Shewanella species/strains were cultured anaerobically in three replicate Balch tubes at 25°C in the modified marine broth 2216 (Becton, Dickinson) supplemented with 20 mM NaNO3 as the electron acceptor."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/37154752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:37154752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All SDCs were grown and propagated in the modified marine broth 2216 by transferring 3% (300 μL) of the final volume (10 mL) into a fresh medium after 72 h when all Shewanella bacteria reached their saturation stages, and each transfer was 3 days."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.html b/docs/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.html
index 70168315..0e53c141 100644
--- a/docs/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.html
+++ b/docs/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Shewanella-Geobacter Three-Species Exoelectrogenic Biofilm Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000177</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000177</code>
                     </span>
                 </div>
 
@@ -708,17 +710,6 @@ <h3>Positive Mixed-Species Interaction</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -773,17 +764,6 @@ <h3>Accelerated Electron Transfer in Mixed-Species Anode Communities</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1128,10 +1108,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1166,10 +1142,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.html b/docs/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.html
new file mode 100644
index 00000000..acee1a96
--- /dev/null
+++ b/docs/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.html
@@ -0,0 +1,1102 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
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+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
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+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000288</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        anaerobic Fe0-fed denitrification system (water/wastewater treatment)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002124"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002124
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Engineered two-member denitrifying consortium of the electroactive bacterium Shewanella oneidensis and the denitrifier Pseudomonas aeruginosa, operated in anaerobic conditions with metallic iron (Fe0) as the sole electron donor. S. oneidensis acts as a bio-engine, using its membrane-bound CymA-OmcA-MtrC complexes to harvest electrons from Fe0 biocorrosion and transfer them to P. aeruginosa. P. aeruginosa accepts these electrons for nitrate reduction, accomplishing microbial denitrification via a Fe0-S. oneidensis-P. aeruginosa electron-transfer system. This Fe0-dependent electro-syntrophy defines a metabolic window for denitrifier growth relevant to nitrate removal in water/wastewater treatment and the global nitrogen cycle.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Shewanella oneidensis</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=70863"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:70863
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"In a model denitrifying consortium of Shewanella oneidensis and Pseudomonas aeruginosa"</div>
+                                    
+                                </li>
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"using Fe0 as the sole electron donor, S. oneidensis can act as a bio-engine to harvest electrons and conserve energy from Fe0 biocorrosion"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas aeruginosa</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=287"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:287
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"In a model denitrifying consortium of Shewanella oneidensis and Pseudomonas aeruginosa"</div>
+                                    
+                                </li>
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"P. aeruginosa can accept electrons for nitrate reduction via the constructed electron transfer system of Fe0-S. oneidensis-P. aeruginosa"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Fe0-dependent electro-syntrophic electron transfer</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Shewanella oneidensis</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Pseudomonas aeruginosa</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Electrons released by S. oneidensis are utilized by P. aeruginosa for accomplishing microbial denitrification."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/39504696/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39504696</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"the direct electron cross-feeding process facilitates the expression of genes encoding for denitrification enzymes, intracellular electron transfer proteins, and quorum sensing of P. aeruginosa"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Anaerobic Fe0-fed denitrification medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>metallic iron (Fe0)</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                        <tr>
+                            <td><strong>nitrate</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Metallic iron (Fe0) supplied as the sole electron donor; nitrate serves as the terminal electron acceptor for denitrification by P. aeruginosa. No medium composition detail, temperature, pH, or reactor configuration was recoverable — the primary source (Water Research, PMID:39504696) is paywalled and only abstract-level conditions could be extracted.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39504696"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39504696
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"In natural or engineered anaerobic environments"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39504696"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39504696
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"using Fe0 as the sole electron donor"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39504696"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39504696
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"P. aeruginosa can accept electrons for nitrate reduction"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Shewanella oneidensis"] = {
+            id: "NCBITaxon:70863",
+            label: "Shewanella oneidensis",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROGEN", "ELECTRON_DONOR", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Pseudomonas aeruginosa"] = {
+            id: "NCBITaxon:287",
+            label: "Pseudomonas aeruginosa",
+            abundance: "UNKNOWN",
+            roles: ["ELECTROTROPH", "ELECTRON_ACCEPTOR", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Fe0-dependent electro-syntrophic electron transfer",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Shewanella oneidensis";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Pseudomonas aeruginosa";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.html b/docs/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.html
index 24e8a22f..ab498a27 100644
--- a/docs/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.html
+++ b/docs/communities/Shewanella_Streptococcus_Starch_Microbial_Fuel_Cell.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Shewanella-Streptococcus Starch-Fueled Microbial Fuel Cell Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000203</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000203</code>
                     </span>
                 </div>
 
@@ -1084,7 +1086,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> PubMed abstract supports starch as the input substrate and lactic acid as the cross-fed fermentation product; the complete salts and electrode configuration are not asserted here.
 
                 </p>
diff --git a/docs/communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.html b/docs/communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.html
new file mode 100644
index 00000000..c3314cfc
--- /dev/null
+++ b/docs/communities/Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture.html
@@ -0,0 +1,949 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000279</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        engineered electro-syntrophic co-culture
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001405"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001405
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Engineered two-species electro-syntrophic co-culture of Shewanella oneidensis MR-1 (the electron-donating partner) and Rhodopseudomonas palustris (the electron-accepting partner) built to study and enhance artificial interspecies electron transfer (IET). In-situ polydopamine (PDA) nano-encapsulation of the S. oneidensis MR-1 surface created a conductive, adhesive cell-to-cell interface that promoted stable coaggregation of the two partners and shifted the dominant IET mode from H2-mediated MIET toward contact-dependent direct electron transfer involving outer-membrane c-type cytochromes. Nitrogenase-derived CH4, used as a quantitative indicator of IET efficiency, increased by roughly 380% in the engineered community.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Shewanella oneidensis MR-1</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=70863"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:70863
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTRON_DONOR</span>
+                                
+                                <span class="role-badge">ELECTROGEN</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42285537/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42285537</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"in-situ polydopamine (PDA) nano-encapsulation of Shewanella oneidensis MR-1 (SW, electron donating partner) surfaces"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Rhodopseudomonas palustris</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1076"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1076
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">ELECTRON_ACCEPTOR</span>
+                                
+                                <span class="role-badge">ELECTROTROPH</span>
+                                
+                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42285537/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42285537</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"stable and intimate coaggregation of SW with Rhodopseudomonas palustris (RP, electron accepting partner)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Engineered interspecies electron transfer (MIET-to-DIET shift)</h3>
+                    <span class="interaction-type">SYNTROPHY</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Shewanella oneidensis MR-1</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rhodopseudomonas palustris</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42285537/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42285537</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"This cell-to-cell PDA interface promoted a shift in the dominant IET mode from H2-mediated MIET toward contact-dependent electron transfer involving outer membrane C-type cytochromes."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Shewanella oneidensis MR-1"] = {
+            id: "NCBITaxon:70863",
+            label: "Shewanella oneidensis MR-1",
+            abundance: "UNKNOWN",
+            roles: ["ELECTRON_DONOR", "ELECTROGEN", "SYNTROPHIC_PARTNER"]
+        };
+        
+        taxonData["Rhodopseudomonas palustris"] = {
+            id: "NCBITaxon:1076",
+            label: "Rhodopseudomonas palustris",
+            abundance: "UNKNOWN",
+            roles: ["ELECTRON_ACCEPTOR", "ELECTROTROPH", "SYNTROPHIC_PARTNER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "SYNTROPHY";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Engineered interspecies electron transfer (MIET-to-DIET shift)",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Shewanella oneidensis MR-1";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rhodopseudomonas palustris";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SkinCom_Synthetic_Skin_Community.html b/docs/communities/SkinCom_Synthetic_Skin_Community.html
index b006f130..c13059a1 100644
--- a/docs/communities/SkinCom_Synthetic_Skin_Community.html
+++ b/docs/communities/SkinCom_Synthetic_Skin_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>SkinCom Synthetic Skin Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000125</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000125</code>
                     </span>
                 </div>
 
@@ -618,6 +620,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    brain-heart infusion (BHI)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Strains cultured in 1X BHI at 37°C without shaking; obligate anaerobes (e.g. C. acnes) in cysteine-reduced medium in Hungate tubes. Aerobic and anaerobic members grown separately, anaerobic incubation in a vinyl anaerobic chamber (N2/CO2/H2 85%/10%/5%). Oxic and anoxic growth monitored for 144 and 140 h respectively; inoculum diluted to OD600 0.065 and arrayed into 96-well plates.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39111313"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39111313
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Individual strains were cultured in sterile BHI broth at 37°C, without shaking."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/39111313"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:39111313
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Under anaerobic conditions, plates were incubated in a vinyl anaerobic chamber (Coy Lab Products) with an atmosphere of N2/CO2/H2 (85%/10%/5%)."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Soil_BGC_Phylum_Depth_Vegetation_Community.html b/docs/communities/Soil_BGC_Phylum_Depth_Vegetation_Community.html
index 5dca5fb6..a8cafcc9 100644
--- a/docs/communities/Soil_BGC_Phylum_Depth_Vegetation_Community.html
+++ b/docs/communities/Soil_BGC_Phylum_Depth_Vegetation_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Soil Biosynthetic Gene Cluster Phylum-Depth-Vegetation Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000250</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000250</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Soil_CPR_Nanoarchaea_Rare_Biosphere_Community.html b/docs/communities/Soil_CPR_Nanoarchaea_Rare_Biosphere_Community.html
index 58f32e72..7d97b0e9 100644
--- a/docs/communities/Soil_CPR_Nanoarchaea_Rare_Biosphere_Community.html
+++ b/docs/communities/Soil_CPR_Nanoarchaea_Rare_Biosphere_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Soil CPR Bacteria and Nanoarchaea Rare-Biosphere Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000247</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000247</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Soil_Corrinoid_B12_Reservoir_Community.html b/docs/communities/Soil_Corrinoid_B12_Reservoir_Community.html
index 7306e881..f21d792d 100644
--- a/docs/communities/Soil_Corrinoid_B12_Reservoir_Community.html
+++ b/docs/communities/Soil_Corrinoid_B12_Reservoir_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Soil Corrinoid Reservoir Microbial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000221</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000221</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Sorghum_SRC1_Subset.html b/docs/communities/Sorghum_SRC1_Subset.html
index 2c9bc4d2..789a5c58 100644
--- a/docs/communities/Sorghum_SRC1_Subset.html
+++ b/docs/communities/Sorghum_SRC1_Subset.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Sorghum SRC1 Subset Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000063</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000063</code>
                     </span>
                 </div>
 
@@ -1180,6 +1182,56 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    unspecified solid media (in vitro); gnotobiotic in planta
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SRC1 growth was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field; community cohesion was most robust when cultivated with the Sorghum bicolor host under laboratory conditions. No medium composition, temperature, or pH is reported in the accessible abstract.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1093/ismejo/wrae126"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1093/ismejo/wrae126
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/South_Bay_Salt_Pond_Methane_Restoration_Community.html b/docs/communities/South_Bay_Salt_Pond_Methane_Restoration_Community.html
index 61a9d89b..2978dbd4 100644
--- a/docs/communities/South_Bay_Salt_Pond_Methane_Restoration_Community.html
+++ b/docs/communities/South_Bay_Salt_Pond_Methane_Restoration_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>South Bay Salt Pond Methane Restoration Microbial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000246</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000246</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.html b/docs/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.html
index cdcdfeda..911cb688 100644
--- a/docs/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.html
+++ b/docs/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Soybean Chlorophyll-Selected Biofertilizer SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000129</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000129</code>
                     </span>
                 </div>
 
@@ -660,6 +662,82 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    G2MY (rhizosphere propagation); YMA/TSA/SDA (isolate maintenance)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Soil isolates plated on YMA, TSA and SDA and incubated at 28°C and 37°C; the rhizosphere microbiota was propagated in G2MY liquid medium for reinoculation. Soybean plants were grown in a greenhouse with 30-day selection cycles under gnotobiotic conditions.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42007760"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42007760
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"SDA (Oxoid, Dardilly, France) and incubated at 28°C and 37°C"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42007760"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42007760
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"the rhizosphere microbiota was grown in G2MY"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42007760"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42007760
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"After 30 days in the greenhouse, the rhizosphere and nodules were recovered"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Soybean_N_Fixation_sfSynCom.html b/docs/communities/Soybean_N_Fixation_sfSynCom.html
index ae9cf12f..3149c7a5 100644
--- a/docs/communities/Soybean_N_Fixation_sfSynCom.html
+++ b/docs/communities/Soybean_N_Fixation_sfSynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Soybean N-Fixation Simplified SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000064</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000064</code>
                     </span>
                 </div>
 
@@ -1091,7 +1093,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Standard medium for Bradyrhizobium elkanii and other slow-growing rhizobia. Supports growth of nitrogen-fixing symbionts isolated from soybean nodules. Colonies typically appear after 3-5 days incubation.
 
                 </p>
@@ -1235,7 +1237,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Rich medium for cultivation of Pantoea helper strains that produce acyl homoserine lactones (AHL). Faster-growing than Bradyrhizobium, typically reaching stationary phase within 24 hours.
 
                 </p>
@@ -1369,7 +1371,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Nitrogen-free growth medium for soybean to study symbiotic nitrogen fixation. Leonard jar system or vermiculite substrate watered with nitrogen-free nutrient solution. Plants inoculated with sfSynCom (Bradyrhizobium BXYD3 plus Pantoea helper strains) to assess nodulation efficiency and nitrogen fixation capacity.
 
                 </p>
diff --git a/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html b/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
index f4036660..b2e3e459 100644
--- a/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
+++ b/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Sphingobium-Rhodococcus Lignin-Dimer Valorization Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000267</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000267</code>
                     </span>
                 </div>
 
@@ -624,17 +626,6 @@ <h3>Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -697,17 +688,6 @@ <h3>Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1001,7 +981,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The publication supports coculture systems fed lignin-derived dimers; exact mineral medium salts and aeration details are not asserted here.
 
                 </p>
@@ -1120,10 +1100,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("aromatic compound catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
@@ -1164,10 +1140,6 @@ <h4 style="color: var(--text);">Evidence</h4>
             
             var processes = [];
             
-            
-            processes.push("aromatic compound catabolic process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html b/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
index d51c361d..58c255e9 100644
--- a/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
+++ b/docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Stordalen Mire Methylotrophic Methanogenesis Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000254</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000254</code>
                     </span>
                 </div>
 
@@ -777,8 +779,8 @@ <h3>Bacterial Anaerobic Methylotrophy</h3>
                     
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
                     </li>
                     
                 </ul>
diff --git a/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html b/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
index 9a25731f..a6c27729 100644
--- a/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
+++ b/docs/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Subsurface Carboxydocella CO-Oxidation Aquifer Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000251</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000251</code>
                     </span>
                 </div>
 
@@ -540,17 +542,6 @@ <h3>CODH-Mediated Subsurface CO Oxidation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -824,10 +815,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html b/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
index 3e1a5fc8..9c620d24 100644
--- a/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
+++ b/docs/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Sulfide Spring Autotrophic CPR-Hosting Biofilm</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000222</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000222</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html b/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
index 432fdaab..12b4cfed 100644
--- a/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
+++ b/docs/communities/SynComBac10_Chicken_Intestinal_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>SynComBac10 Chicken Intestinal SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000127</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000127</code>
                     </span>
                 </div>
 
@@ -618,6 +620,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    GAM medium (Gifu Anaerobic Medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Each strain grown in liquid medium and diluted 1:10 into fresh medium every 24 h for 3 days; SynComBac10 composition analyzed by comparing the absolute abundance of the 10 strains in GAM medium; consortium administered to chicks via oral gavage. Cultured without shaking.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40266232"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40266232
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Following a 72-hour growth period at 37°C without shaking under anaerobic conditions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40266232"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40266232
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"absolute abundance of 10 strains in GAM medium"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html b/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html
new file mode 100644
index 00000000..b8e45e5d
--- /dev/null
+++ b/docs/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.html
@@ -0,0 +1,1064 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>SynCom BsBv Cigar Tobacco Leaf Fermentation - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
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+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
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+        h2 {
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+            margin: 2rem 0 1rem;
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+            margin: 1.5rem 0 0.75rem;
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+        }
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+        .metadata-grid {
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+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
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+            margin: 1rem 0;
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+        th, td {
+            padding: 0.75rem 1rem;
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+        th {
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+        tr:not(:last-child) td {
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+        .term-link:hover {
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+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
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+        .legend-circle {
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+        .network-tooltip {
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+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>SynCom BsBv Cigar Tobacco Leaf Fermentation</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000278</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        cigar tobacco leaves (cultivar QX204) undergoing fermentation
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001121"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:01001121
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-species synthetic microbial community (the BsBv SynCom) of Bacillus safensis and Bacillus velezensis, screened for high extracellular cellulase, amylase and protease activities and applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation. The consortium accelerated degradation of cellulose, protein, and starch, shifted the leaf bacterial community toward Firmicutes/Bacillus, and modulated the volatile flavor metabolite profile (e.g. phenylacetic acid, phytol, farnesol) to enhance honey, floral, and baked aromas while reducing irritancy, thereby directionally improving cigar tobacco leaf quality.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus safensis</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=561879"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:561879
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.indcrop.2025.122621"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Bacillus safensis and Bacillus velezensis with high extracellular cellulase, amylase and protease activities were screened out, and synthetic communities were constructed."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus velezensis</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=492670"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:492670
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.indcrop.2025.122621"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Bacillus safensis and Bacillus velezensis with high extracellular cellulase, amylase and protease activities were screened out, and synthetic communities were constructed."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for SynCom BsBv Cigar Tobacco Leaf Fermentation</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Cooperative macromolecule degradation by the BsBv SynCom</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.indcrop.2025.122621"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"The SynCom significantly accelerated the degradation of key macromolecules, reducing cellulose, protein, and starch contents by 52.48 %, 56.36 %, and 68.47 %, respectively, which were markedly greater reductions than those observed in the uninoculated control."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom-driven bacterial community succession and Bacillus enrichment</h3>
+                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.indcrop.2025.122621"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122621</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"inoculation shifted the bacterial community structure, increasing the relative abundance of Firmicutes and significantly enriching the genus Bacillus."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Solid-state fermentation on cigar tobacco leaves (cultivar QX204)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+                <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
+                <table>
+                    <thead>
+                        <tr>
+                            <th>Component</th>
+                            <th>Concentration</th>
+                            <th>Unit</th>
+                            <th>CHEBI</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        
+                        <tr>
+                            <td><strong>cigar tobacco leaves (cultivar QX204)</strong></td>
+                            <td>N/A</td>
+                            <td>N/A</td>
+                            <td>
+                                
+                                N/A
+                                
+                            </td>
+                        </tr>
+                        
+                    </tbody>
+                </table>
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> The two-member BsBv SynCom (Bacillus safensis + Bacillus velezensis) was applied to harvested cigar tobacco leaves of cultivar QX204 and fermented for 42 days. The accessible source (paywalled; abstract only) does not report incubation temperature, humidity, pH, atmosphere, medium composition, or inoculum size for this fermentation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1016/j.indcrop.2025.122621"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1016/j.indcrop.2025.122621
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"This microbial community was applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Bacillus safensis"] = {
+            id: "NCBITaxon:561879",
+            label: "Bacillus safensis",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Bacillus velezensis"] = {
+            id: "NCBITaxon:492670",
+            label: "Bacillus velezensis",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Cooperative macromolecule degradation by the BsBv SynCom",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "NICHE_PARTITIONING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "SynCom-driven bacterial community succession and Bacillus enrichment",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
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+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
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+            .attr("markerWidth", 6)
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+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
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+                var lines = [];
+                var maxWidth = 24;
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+                for (var i = 0; i < words.length; i++) {
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+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
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+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
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+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
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+                tooltip.append("br");
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+                .style("top", (event.offsetY - 12) + "px");
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+        // Tick
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+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
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+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.html b/docs/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.html
new file mode 100644
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--- /dev/null
+++ b/docs/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.html
@@ -0,0 +1,997 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>SynCom + Chlorella sorokiniana Biogas-slurry Coupling System - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
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+
+        * {
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+            margin: 2rem 0 1rem;
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+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>SynCom + Chlorella sorokiniana Biogas-slurry Coupling System</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000285</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        livestock biogas slurry treatment bioreactor
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002123"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002123
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A sequential synthetic microbial community (SynCom)-microalga coupling system engineered to treat livestock biogas slurry. An autochthonous microalga, Chlorella sorokiniana, isolated from the slurry is coupled with a SynCom pretreatment stage. The system operated stably for 60 days, achieving 94.41% nitrate-nitrogen removal, 81.84% total-phosphorus removal, and 6.31% chemical oxygen demand removal. SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana (by 27.15% and 488.10% vs the BG11 control), upregulating Rubisco and glutamine synthetase, providing a strategy for simultaneous pollutant abatement and resource recovery.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Chlorella sorokiniana</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3076"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:3076
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41794300/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41794300</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"an autochthonous microalga Chlorella sorokiniana isolated from the slurry"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>SynCom bacterial members (unnamed)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:2
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41794300/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41794300</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"this study constructed a sequential synthetic microbial community (SynCom)-microalgae coupling system"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for SynCom + Chlorella sorokiniana Biogas-slurry Coupling System</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom pretreatment facilitates Chlorella sorokiniana growth</h3>
+                    <span class="interaction-type">COMMENSALISM</span>
+                </div>
+
+                
+
+                
+                <p><strong>Target Taxon:</strong> Chlorella sorokiniana</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41794300/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41794300</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana by 27.15% and 488.10%, respectively"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    livestock biogas slurry (SynCom-pretreated); BG11 (control)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Chlorella sorokiniana grown on SynCom-pretreated livestock biogas slurry in a sequential SynCom-microalgae coupling system operated stably for 60 days; BG11 medium served as the growth control. Reported slurry effluent typically had total nitrogen 56.5-830 mg/L and total phosphorus 0.2-476 mg/L. System temperature, pH and light regime not stated in the accessible abstract.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41794300"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41794300
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The system operated stably for 60 days and achieved 94.41% removal of nitrate nitrogen"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41794300"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41794300
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"compared to the BG11 group, SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Chlorella sorokiniana"] = {
+            id: "NCBITaxon:3076",
+            label: "Chlorella sorokiniana",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER"]
+        };
+        
+        taxonData["SynCom bacterial members (unnamed)"] = {
+            id: "NCBITaxon:2",
+            label: "SynCom bacterial members (unnamed)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COMMENSALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "SynCom pretreatment facilitates Chlorella sorokiniana growth",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+            var tgtKey = "Chlorella sorokiniana";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
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+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
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+
+        var node = svg.append("g")
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+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
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+            .attr("x", -14)
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+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
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+                        lines.push(line);
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+                    } else {
+                        line = testLine;
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+                if (line) lines.push(line);
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+                // Limit to 3 lines maximum
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+        var tooltip = d3.select("#network-tooltip");
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+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
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+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
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+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
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+        // Tick
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+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
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+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html b/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html
new file mode 100644
index 00000000..0620917b
--- /dev/null
+++ b/docs/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.html
@@ -0,0 +1,1023 @@
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+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience - CommunityMech</title>
+    <style>
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+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000302</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        sugarcane rhizosphere
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00005801"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00005801
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A rhizobacteria synthetic community (SynCom) named MetG2 inoculated onto sugarcane in a greenhouse experiment to enhance stress resilience through targeted modulation of plant-microbe interactions. Shotgun metagenome and metatranscriptome sequencing revealed temporal shifts in the rhizosphere microbial community, with up-regulation of genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation (particularly within Proteobacteria), indicating active microbial movement toward root surfaces, alongside enrichment of genes for nutrient acquisition, hormone synthesis, siderophore production, and VOC synthesis. Sugarcane responded with up-regulation of hormone-related and nutrient-transporter genes and induction of stress-resistance genes, supporting MetG2 as a sustainable strategy to enhance crop productivity and resilience.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>sugarcane (Saccharum officinarum)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4547"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4547
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.rhisph.2025.101142"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.rhisph.2025.101142</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"This study investigated the molecular mechanisms underlying sugarcane responses and the dynamics of its rhizosphere microbial community following inoculation with a SynCom called MetG2"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Proteobacteria (rhizosphere community members)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1224"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1224
+                            </a>
+                        </td>
+                        <td>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.rhisph.2025.101142"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.rhisph.2025.101142</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"particularly within Proteobacteria, indicating active microbial movement toward root surfaces"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Microbial colonization of sugarcane roots</h3>
+                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Proteobacteria (rhizosphere community members)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> sugarcane (Saccharum officinarum)</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.rhisph.2025.101142"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.rhisph.2025.101142</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"an up-regulation of genes related to flagellar assembly, chemotaxis, quorum sensing, and biofilm formation, particularly within Proteobacteria, indicating active microbial movement toward root surfaces"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom-stimulated enhancement of sugarcane stress resilience</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Proteobacteria (rhizosphere community members)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> sugarcane (Saccharum officinarum)</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.rhisph.2025.101142"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.rhisph.2025.101142</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"genes associated with nutrient acquisition, hormone synthesis, siderophore production, and volatile organic compound (VOC) synthesis were enriched, suggesting stimulated beneficial microbial activities"</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.rhisph.2025.101142"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.rhisph.2025.101142</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"Sugarcane plants also exhibited dynamic responses, including the up-regulation of hormone-related genes (auxin, cytokinin, salicylic acid) and nutrient transporter genes"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["sugarcane (Saccharum officinarum)"] = {
+            id: "NCBITaxon:4547",
+            label: "sugarcane (Saccharum officinarum)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER"]
+        };
+        
+        taxonData["Proteobacteria (rhizosphere community members)"] = {
+            id: "NCBITaxon:1224",
+            label: "Proteobacteria (rhizosphere community members)",
+            abundance: "UNKNOWN",
+            roles: []
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COLONIZATION_FACILITATION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Microbial colonization of sugarcane roots",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Proteobacteria (rhizosphere community members)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "sugarcane (Saccharum officinarum)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "SynCom-stimulated enhancement of sugarcane stress resilience",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Proteobacteria (rhizosphere community members)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "sugarcane (Saccharum officinarum)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 4;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html b/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html
new file mode 100644
index 00000000..b401b09a
--- /dev/null
+++ b/docs/communities/SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.html
@@ -0,0 +1,941 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
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+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
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+        body {
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+        .container {
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+            padding: 2rem;
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+
+        header {
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+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
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+        h2 {
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+            border-bottom: 1px solid var(--border);
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+
+        h3 {
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+        .metadata-item {
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+        .badge {
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+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
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+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
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+
+        th, td {
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+
+        th {
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+        tr:not(:last-child) td {
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+        .role-badge {
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+  :root:not([data-theme="light"]) th{background:#232a3d}
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000292</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        rhizosphere of Artemisia argyi in Cd-contaminated agricultural soil
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00005801"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00005801
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A simplified, native rhizosphere synthetic microbial community (SynCom) pairing a Pseudomonas isolate with a Rahnella isolate, assembled by a top-down design from rhizobacteria isolated from cadmium (Cd)-contaminated agricultural soil to partner with the perennial medicinal plant Artemisia argyi. The Pseudomonas-Rahnella pair shows strong Cd tolerance (~2 mM), plant growth-promotion (PGP) traits, and carbon fixation capacity, and was chosen for functional complementarity with minimal antagonism. Under Cd stress the SynCom establishes stable endophytic colonization (10-15%) rather than rhizoplane colonization, improving root biomass, Cd uptake, soil organic carbon accumulation, and essential-oil precursors, thereby coupling phytoremediation, productivity, and carbon sequestration.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas (rhizosphere isolate)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=286"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:286
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.indcrop.2025.122518"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122518</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"The selected Pseudomonas–Rahnella pair exhibited strong Cd tolerance (∼ 2 mM), Plant growth promotion (PGP) traits, and carbon fixation capacity."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Rahnella (rhizosphere isolate)</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=34037"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:34037
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_PRODUCER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://doi.org/10.1016/j.indcrop.2025.122518"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122518</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"The selected Pseudomonas–Rahnella pair exhibited strong Cd tolerance (∼ 2 mM), Plant growth promotion (PGP) traits, and carbon fixation capacity."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism</h3>
+                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Pseudomonas (rhizosphere isolate)</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Rahnella (rhizosphere isolate)</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://doi.org/10.1016/j.indcrop.2025.122518"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.indcrop.2025.122518</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"A top-down design strategy guided the assembly of a simplified, yet functionally complementary SynCom with minimal antagonism."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Pseudomonas (rhizosphere isolate)"] = {
+            id: "NCBITaxon:286",
+            label: "Pseudomonas (rhizosphere isolate)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER"]
+        };
+        
+        taxonData["Rahnella (rhizosphere isolate)"] = {
+            id: "NCBITaxon:34037",
+            label: "Rahnella (rhizosphere isolate)",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_PRODUCER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "NICHE_PARTITIONING";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Functionally complementary Pseudomonas-Rahnella pairing with minimal antagonism",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Pseudomonas (rhizosphere isolate)";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Rahnella (rhizosphere isolate)";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 3;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
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+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
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+                tooltip.append("span").text(d.ontologyId);
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+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
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+                tooltip.append("strong").text(d.label);
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+                if (d.metabolites.length) {
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+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
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+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
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+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
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+                .style("left", (event.offsetX + 12) + "px")
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+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html b/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
new file mode 100644
index 00000000..7b75f862
--- /dev/null
+++ b/docs/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.html
@@ -0,0 +1,1541 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Sesame-flavor Baijiu Fuqu SynCom (13-genus) - CommunityMech</title>
+    <style>
+        :root {
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+}
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Sesame-flavor Baijiu Fuqu SynCom (13-genus)</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000283</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        sesame flavor-type baijiu fermentation (Fuqu starter)
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_03600040"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:03600040
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Thirteen-genus synthetic microbial community (SynCom) designed for Fuqu, the fermentation starter used in sesame flavor-type baijiu (Chinese liquor) production. Multi-omics analysis identified 13 core genera - the fungal/yeast genera Aspergillus, Pichia, Saccharomyces, Trichosporon, Candida, Torulaspora, Clavispora and Wickerhamomyces and the bacterial genera Bacillus, Lactobacillus, Leuconostoc, Pediococcus and Weissella - as the core microbiota driving flavor-compound formation. Assembled into a SynCom, these members yielded the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, and outperformed commercial Fuqu at large scale. The community represents an engineered strategy to enhance sulfur-containing flavor compounds during baijiu fermentation.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Aspergillus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5052"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:5052
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1386"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1386
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Lactobacillus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1578"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1578
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Leuconostoc</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1243"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1243
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pediococcus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1253"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1253
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pichia</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4919"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4919
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Saccharomyces</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4930"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4930
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Trichosporon</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5552"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:5552
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Weissella</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=46255"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:46255
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Candida</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5475"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:5475
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Torulaspora</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=4948"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:4948
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Clavispora</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=36910"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:36910
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Wickerhamomyces</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=599737"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:599737
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">SECONDARY_FERMENTER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"13 genera (Aspergillus, Bacillus, Lactobacillus, Leuconostoc, Pediococcus, Pichia, Saccharomyces, Trichosporon, Weissella, Candida, Torulaspora, Clavispora, and Wickerhamomyces) were identified as core microbiota involved in the production of those flavor compounds"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Sesame-flavor Baijiu Fuqu SynCom (13-genus)</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Emergent flavor-compound co-production by the assembled SynCom</h3>
+                    <span class="interaction-type"></span>
+                </div>
+
+                
+
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    3-(methylthio)-1-propanal
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=49017"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:49017</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42121419/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42121419</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"The resulting SynCom exhibited the highest flavor compound diversity (0.64) and 3-(methylthio)-1-propanal content (618.14"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    sorghum extract medium (simulated fermentation)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Simulated fermentation of the assembled SynCom in sorghum extract medium. Yeast incubated at 30 °C for 24 h (150 rpm); bacteria (except L. acetotolerans) at 37 °C for 14 h (150 rpm); L. acetotolerans anaerobically at 37 °C for 3 d; A. oryzae at 30 °C for 5 d. Strains mixed at an equal concentration of 1 x 10^5 CFU/mL.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42121419"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42121419
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All strains were incubated in the sorghum extract medium. Yeast was incubated at 30 °C for 24 h with shaking at 150 rpm."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42121419"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42121419
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each strain in the SynComs was mixed at an equal concentration of 1 × 10 5 CFU/mL."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Aspergillus"] = {
+            id: "NCBITaxon:5052",
+            label: "Aspergillus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Bacillus"] = {
+            id: "NCBITaxon:1386",
+            label: "Bacillus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Lactobacillus"] = {
+            id: "NCBITaxon:1578",
+            label: "Lactobacillus",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Leuconostoc"] = {
+            id: "NCBITaxon:1243",
+            label: "Leuconostoc",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Pediococcus"] = {
+            id: "NCBITaxon:1253",
+            label: "Pediococcus",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Pichia"] = {
+            id: "NCBITaxon:4919",
+            label: "Pichia",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Saccharomyces"] = {
+            id: "NCBITaxon:4930",
+            label: "Saccharomyces",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Trichosporon"] = {
+            id: "NCBITaxon:5552",
+            label: "Trichosporon",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Weissella"] = {
+            id: "NCBITaxon:46255",
+            label: "Weissella",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Candida"] = {
+            id: "NCBITaxon:5475",
+            label: "Candida",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Torulaspora"] = {
+            id: "NCBITaxon:4948",
+            label: "Torulaspora",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Clavispora"] = {
+            id: "NCBITaxon:36910",
+            label: "Clavispora",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+        taxonData["Wickerhamomyces"] = {
+            id: "NCBITaxon:599737",
+            label: "Wickerhamomyces",
+            abundance: "UNKNOWN",
+            roles: ["SECONDARY_FERMENTER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "UNKNOWN";
+            var metabolites = [];
+            
+            
+            metabolites.push("3-(methylthio)-1-propanal");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Emergent flavor-compound co-production by the assembled SynCom",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 14;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html b/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
new file mode 100644
index 00000000..a7cf55fc
--- /dev/null
+++ b/docs/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.html
@@ -0,0 +1,1233 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
+        }
+
+        .badge {
+            display: inline-block;
+            padding: 0.25rem 0.75rem;
+            border-radius: 12px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .badge-engineered { background: #dbeafe; color: #1e40af; }
+        .badge-natural { background: #d1fae5; color: #065f46; }
+
+        .description {
+            background: var(--card);
+            border-left: 4px solid var(--primary);
+            padding: 1rem 1.5rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        table {
+            width: 100%;
+            background: var(--card);
+            border-radius: 8px;
+            overflow: hidden;
+            border: 1px solid var(--border);
+            margin: 1rem 0;
+        }
+
+        th, td {
+            padding: 0.75rem 1rem;
+            text-align: left;
+        }
+
+        th {
+            background: #f1f5f9;
+            font-weight: 600;
+            color: var(--text);
+            border-bottom: 2px solid var(--border);
+        }
+
+        tr:not(:last-child) td {
+            border-bottom: 1px solid var(--border);
+        }
+
+        .term-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-family: 'Courier New', monospace;
+            font-size: 0.875rem;
+        }
+
+        .term-link:hover {
+            text-decoration: underline;
+        }
+
+        .interaction-card {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin: 1rem 0;
+        }
+
+        .interaction-header {
+            display: flex;
+            justify-content: space-between;
+            align-items: start;
+            margin-bottom: 1rem;
+        }
+
+        .interaction-type {
+            padding: 0.25rem 0.75rem;
+            background: #f0fdf4;
+            color: #166534;
+            border-radius: 4px;
+            font-size: 0.875rem;
+            font-weight: 500;
+        }
+
+        .interaction-flow {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid var(--primary);
+            padding: 1rem;
+            margin: 1rem 0;
+            border-radius: 4px;
+        }
+
+        .flow-item {
+            margin: 0.5rem 0;
+        }
+
+        .flow-arrow {
+            color: var(--primary);
+            margin: 0 0.5rem;
+        }
+
+        .evidence-list {
+            list-style: none;
+            margin: 0.5rem 0;
+        }
+
+        .evidence-item {
+            background: var(--background);
+            color: var(--text);
+            border-left: 3px solid #ca8a04;
+            padding: 0.75rem;
+            margin: 0.5rem 0;
+            border-radius: 4px;
+        }
+
+        .empty-state {
+            background: #f8fafc;
+            border: 1px dashed #cbd5e1;
+            border-radius: 8px;
+            padding: 2rem;
+            text-align: center;
+            color: #64748b;
+        }
+
+        .empty-state p {
+            margin: 0.5rem 0;
+        }
+
+        .empty-state-note {
+            font-size: 0.875rem;
+            color: #94a3b8;
+        }
+
+        .pmid-link {
+            color: var(--primary);
+            text-decoration: none;
+            font-weight: 500;
+        }
+
+        .pmid-link:hover {
+            text-decoration: underline;
+        }
+
+        .snippet {
+            color: var(--text-muted);
+            font-style: italic;
+            font-size: 0.875rem;
+            margin-top: 0.5rem;
+        }
+
+        .roles-list {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 0.5rem;
+        }
+
+        .role-badge {
+            padding: 0.25rem 0.5rem;
+            background: #ede9fe;
+            color: #5b21b6;
+            border-radius: 4px;
+            font-size: 0.75rem;
+            font-weight: 500;
+        }
+
+        .dataset-description {
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        footer {
+            margin-top: 3rem;
+            padding-top: 2rem;
+            border-top: 1px solid var(--border);
+            text-align: center;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+        }
+
+        .back-link {
+            display: inline-block;
+            color: var(--primary);
+            text-decoration: none;
+            margin-bottom: 1rem;
+        }
+
+        .back-link:hover {
+            text-decoration: underline;
+        }
+
+        /* Network diagram */
+        .network-container {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1rem;
+            margin: 1rem 0 2rem;
+            position: relative;
+        }
+
+        .network-container svg {
+            width: 100%;
+            display: block;
+        }
+
+        .network-legend {
+            display: flex;
+            flex-wrap: wrap;
+            gap: 1rem;
+            padding: 0.75rem 0 0;
+            border-top: 1px solid var(--border);
+            margin-top: 0.5rem;
+            font-size: 0.8rem;
+            color: var(--text-muted);
+        }
+
+        .legend-item {
+            display: flex;
+            align-items: center;
+            gap: 0.35rem;
+        }
+
+        .legend-swatch {
+            width: 14px;
+            height: 14px;
+            border-radius: 3px;
+            display: inline-block;
+        }
+
+        .legend-circle {
+            border-radius: 50%;
+        }
+
+        .network-tooltip {
+            position: absolute;
+            background: rgba(30, 41, 59, 0.95);
+            color: #f8fafc;
+            padding: 0.5rem 0.75rem;
+            border-radius: 6px;
+            font-size: 0.8rem;
+            line-height: 1.4;
+            pointer-events: none;
+            opacity: 0;
+            transition: opacity 0.15s;
+            max-width: 280px;
+            z-index: 10;
+        }
+
+        .network-tooltip strong {
+            color: #93c5fd;
+        }
+    /* ---- Dark theme (OS default; superseded by the toggle) ---- */
+@media (prefers-color-scheme: dark){
+  :root:not([data-theme="light"]){--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+  :root:not([data-theme="light"]) header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+  :root:not([data-theme="light"]) th{background:#232a3d}
+  :root:not([data-theme="light"]) .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+  :root:not([data-theme="light"]) .interaction-flow{background:rgba(255,255,255,.04)}
+  :root:not([data-theme="light"]) .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+  :root:not([data-theme="light"]) .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+  :root:not([data-theme="light"]) .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+}
+:root[data-theme="dark"]{--primary:#6ea6f0; --secondary:#99a2b5; --background:#101420; --card:#1a1f2e; --border:#2a3142; --text:#e8ecf4; --text-muted:#99a2b5; --success:#34d399; --warning:#fbbf24; --net-label:#cbd5e1;}
+:root[data-theme="dark"] header{background:linear-gradient(135deg,#1d2740,#101420);border-bottom-color:#2a3142}
+:root[data-theme="dark"] th{background:#232a3d}
+:root[data-theme="dark"] .interaction-type{background:rgba(52,211,153,.14);color:#34d399}
+:root[data-theme="dark"] .interaction-flow{background:rgba(255,255,255,.04)}
+:root[data-theme="dark"] .evidence-item{background:rgba(251,191,36,.10);border-left-color:#fbbf24}
+:root[data-theme="dark"] .empty-state{background:rgba(255,255,255,.03);border-color:#2a3142;color:#99a2b5}
+:root[data-theme="dark"] .role-badge{background:rgba(180,153,240,.16);color:#c4b5fd}
+@media (prefers-reduced-motion: reduce){
+  *,*::before,*::after{animation-duration:.01ms!important;animation-iteration-count:1!important;transition-duration:.01ms!important;scroll-behavior:auto!important;}
+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000272</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        rhizosphere
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00005801"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00005801
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>Two-species synthetic bacterial community (SynCom Y) of Agrobacterium deltaense LSQ16 and Bacillus velezensis WB, simplified from a larger biocontrol SynCom Q by stepwise strain omission. Co-cultivation synergistically enhances multispecies biofilm formation, extracellular polysaccharide production, and metabolic activity, improving suppression of watermelon Fusarium wilt. Genome-scale modeling predicts interspecies metabolite exchange (amino acids, purines, phosphates); exogenous L-ornithine and guanine enhance B. velezensis biofilm formation, consistent with cross-feeding-supported cooperation.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Agrobacterium deltaense LSQ16</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1183412"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1183412
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Co-cultivation of A. deltaense LSQ16 and B. velezensis WB significantly enhanced biofilm formation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus velezensis WB</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=492670"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:492670
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">CROSS_FEEDER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                                    
+                                    - SUPPORT (IN_VITRO)
+                                    
+                                    <div class="snippet">"Co-cultivation of A. deltaense LSQ16 and B. velezensis WB significantly enhanced biofilm formation."</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Synergistic biofilm and EPS formation in co-culture</h3>
+                    <span class="interaction-type">MUTUALISM</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Agrobacterium deltaense LSQ16</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bacillus velezensis WB</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Compared with monocultures, co-cultivation also markedly increased extracellular polysaccharide production and metabolic activity."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Agrobacterium deltaense LSQ16</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Bacillus velezensis WB</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    L-ornithine
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15729"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15729</a>), 
+                    
+                    guanine
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16235"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16235</a>), 
+                    
+                    guanosine
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16750"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16750</a>), 
+                    
+                    (S)-malate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15589"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:15589</a>), 
+                    
+                    phosphate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=26020"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:26020</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                            
+                            - SUPPORT (IN_VITRO)
+                        </div>
+                        
+                        <div class="snippet">"Moreover, exogenous supplementation of l-ornithine and guanine further enhanced the biofilm-forming capacity of B. velezensis WB."</div>
+                        
+                    </li>
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                            
+                            - SUPPORT (COMPUTATIONAL)
+                        </div>
+                        
+                        <div class="snippet">"Predictive results indicated metabolite exchange between the two strains involved amino acids, purines, phosphates, and other compounds."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16</h3>
+                    <span class="interaction-type">CROSS_FEEDING</span>
+                </div>
+
+                
+                <p><strong>Source Taxon:</strong> Bacillus velezensis WB</p>
+                
+
+                
+                <p><strong>Target Taxon:</strong> Agrobacterium deltaense LSQ16</p>
+                
+
+                
+                <p><strong>Metabolites:</strong>
+                    
+                    L-serine
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17115"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17115</a>)
+                    
+                </p>
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42125264/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42125264</a>
+                            
+                            - SUPPORT (COMPUTATIONAL)
+                        </div>
+                        
+                        <div class="snippet">"Predictive results indicated metabolite exchange between the two strains involved amino acids, purines, phosphates, and other compounds."</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    LBGM
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Biofilm formation assay. Strains precultured in TSB overnight at 25 °C with shaking at 150 rpm, OD600 adjusted to 0.8, then inoculated at 10% (v/v) into 2 mL LBGM medium per well. Single-species suspensions added directly to 24-well plates; mixed-species biofilms mixed in equal volumes before plating. Incubated statically at 30 °C and sampled at 24, 48, and 72 h.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42125264"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42125264
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Subsequently, they were inoculated at 10% ( v / v ) into 2 mL of LBGM medium. For single-species biofilms, the bacterial suspension was directly introduced into 24-well plates."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42125264"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42125264
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Samples were incubated statically at 30 °C for 24, 48, and 72 h to compare the biofilm-forming capacities"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/42125264"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:42125264
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Glycerol-preserved strains were inoculated into TSB and cultured overnight at 25 °C with shaking at 150 rpm."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
+    <script src="../d3.v7.min.js"></script>
+    <script>
+    (function() {
+        var interactionColors = {
+            CROSS_FEEDING: "#22c55e",
+            MUTUALISM: "#3b82f6",
+            SYNTROPHY: "#a855f7",
+            COMPETITION: "#ef4444",
+            COMMENSALISM: "#f97316",
+            PREDATION: "#dc2626",
+            NICHE_PARTITIONING: "#14b8a6",
+            STRAIN_COMPETITION: "#fb7185",
+            COLONIZATION_FACILITATION: "#eab308"
+        };
+
+        // Build taxon lookup keyed by preferred_term
+        var taxonData = {};
+        
+        taxonData["Agrobacterium deltaense LSQ16"] = {
+            id: "NCBITaxon:1183412",
+            label: "Agrobacterium deltaense LSQ16",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+        taxonData["Bacillus velezensis WB"] = {
+            id: "NCBITaxon:492670",
+            label: "Bacillus velezensis WB",
+            abundance: "UNKNOWN",
+            roles: ["CROSS_FEEDER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
+        var taxonNodeIds = {};
+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "MUTUALISM";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Synergistic biofilm and EPS formation in co-culture",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Agrobacterium deltaense LSQ16";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bacillus velezensis WB";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:1";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            
+            metabolites.push("L-ornithine");
+            
+            metabolites.push("guanine");
+            
+            metabolites.push("guanosine");
+            
+            metabolites.push("(S)-malate");
+            
+            metabolites.push("phosphate");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 2;
+
+            nodes.push({
+                id: intId,
+                label: "Predicted cross-feeding from A. deltaense LSQ16 to B. velezensis WB",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Agrobacterium deltaense LSQ16";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Bacillus velezensis WB";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+        (function() {
+            var intId = "interaction:2";
+            var intType = "CROSS_FEEDING";
+            var metabolites = [];
+            
+            
+            metabolites.push("L-serine");
+            
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Predicted metabolite return from B. velezensis WB to A. deltaense LSQ16",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+            var srcKey = "Bacillus velezensis WB";
+            if (taxonNodeIds[srcKey]) {
+                links.push({ source: taxonNodeIds[srcKey], target: intId });
+            }
+            
+
+            
+            var tgtKey = "Agrobacterium deltaense LSQ16";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
+            connectedIds.add(typeof l.target === "object" ? l.target.id : l.target);
+        });
+        nodes = nodes.filter(function(n) {
+            return n.type === "interaction" || connectedIds.has(n.id);
+        });
+
+        // D3 setup
+        var container = document.getElementById("network-container");
+        var svg = d3.select("#network-svg");
+        var width = container.clientWidth - 32;
+        // Dynamic height based on node count: minimum 500px, add 40px per node
+        var nodeCount = 5;
+        var height = Math.max(500, 400 + nodeCount * 20);
+        svg.attr("width", width).attr("height", height);
+
+        // Arrow marker
+        svg.append("defs").append("marker")
+            .attr("id", "arrowhead")
+            .attr("viewBox", "0 -5 10 10")
+            .attr("refX", 20)
+            .attr("refY", 0)
+            .attr("markerWidth", 6)
+            .attr("markerHeight", 6)
+            .attr("orient", "auto")
+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
+            .selectAll("line")
+            .data(links)
+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
+            .attr("width", 28)
+            .attr("height", 18)
+            .attr("x", -14)
+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
+                var c = d3.color(interactionColors[d.interactionType] || "#6b7280");
+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
+                var words = d.label.split(/\s+/);
+                var line = "";
+                var lines = [];
+                var maxWidth = 24;
+
+                for (var i = 0; i < words.length; i++) {
+                    var testLine = line + (line ? " " : "") + words[i];
+                    if (testLine.length > maxWidth && line.length > 0) {
+                        lines.push(line);
+                        line = words[i];
+                    } else {
+                        line = testLine;
+                    }
+                }
+                if (line) lines.push(line);
+
+                // Limit to 3 lines maximum
+                if (lines.length > 3) {
+                    lines = lines.slice(0, 3);
+                    lines[2] = lines[2].substring(0, 21) + "...";
+                }
+
+                // Add tspan for each line
+                var lineHeight = 11;
+                var startY = -(lines.length - 1) * lineHeight / 2;
+                lines.forEach(function(lineText, i) {
+                    textElem.append("tspan")
+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
+            });
+        });
+
+        // Stabilize after 300 ticks then stop
+        simulation.alpha(1).alphaDecay(0.02);
+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
+        link.attr("x1", function(d) { return d.source.x; })
+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html b/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
index 122f4d2f..420ac7a4 100644
--- a/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
+++ b/docs/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Azotobacter Photoproduction Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000207</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000207</code>
                     </span>
                 </div>
 
@@ -1113,7 +1115,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The primary abstract supports a designed coculture grown without fixed carbon or nitrogen and supplied conceptually by air, water, phosphate, trace metals, and sunlight; this record does not assert the complete salts, induction, or incubation protocol.
 
                 </p>
diff --git a/docs/communities/Synechococcus_Bacillus_SPC.html b/docs/communities/Synechococcus_Bacillus_SPC.html
index 7e7b5385..7017abcd 100644
--- a/docs/communities/Synechococcus_Bacillus_SPC.html
+++ b/docs/communities/Synechococcus_Bacillus_SPC.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Bacillus Synthetic Photosynthetic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000065</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000065</code>
                     </span>
                 </div>
 
@@ -713,6 +715,84 @@ <h4>Evidence</h4>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    CoB BG-11 (BG-11-based cyanobacteria/bacteria co-culture medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">8.3</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. elongatus propagated in BG-11 + 1 g/L HEPES (pH 8, 35 °C, constant light); prokaryote co-culture medium CoB BG-11 = BG-11 + 106 mM NaCl, 4 mM NH4Cl, 25 mM HEPPSO (pH 8.3). B. subtilis pre-grown at 37 °C; 2% sucrose added to acclimate; IPTG added to induce sucrose export.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All acclimating cultures and co-cultures were grown at 35 °C, 150 rpm, 2% CO2, in light (PAR = ~80 μmol with 15 W Gro-Lux Sylvania fluorescent bulbs) within a Multitron Infors HT incubator"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"CoB BG-11 consists of BG-11 supplemented with 106 mM NaCl, 4 mM NH4Cl and 25 mM HEPPSO, pH 8.3-KOH"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Synechococcus_Ecoli_SPC.html b/docs/communities/Synechococcus_Ecoli_SPC.html
index df97ece3..c0cde422 100644
--- a/docs/communities/Synechococcus_Ecoli_SPC.html
+++ b/docs/communities/Synechococcus_Ecoli_SPC.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-E.coli Synthetic Photosynthetic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000066</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000066</code>
                     </span>
                 </div>
 
@@ -807,6 +809,84 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    CoB BG-11 (BG-11-based cyanobacteria/bacteria co-culture medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">8.3</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. elongatus propagated in BG-11 + 1 g/L HEPES (pH 8, 35 °C, constant light); prokaryote co-culture medium CoB BG-11 = BG-11 + 106 mM NaCl, 4 mM NH4Cl, 25 mM HEPPSO (pH 8.3). E. coli pre-grown at 37 °C; 2% sucrose added to acclimate; IPTG added to induce sucrose export.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All acclimating cultures and co-cultures were grown at 35 °C, 150 rpm, 2% CO2, in light (PAR = ~80 μmol with 15 W Gro-Lux Sylvania fluorescent bulbs) within a Multitron Infors HT incubator"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"CoB BG-11 consists of BG-11 supplemented with 106 mM NaCl, 4 mM NH4Cl and 25 mM HEPPSO, pH 8.3-KOH"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html b/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html
index 28bd7e76..46cbd432 100644
--- a/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html
+++ b/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Halomonas Light-Driven PHB Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000198</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000198</code>
                     </span>
                 </div>
 
@@ -951,7 +953,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The curated source supports a synthetic light-driven coculture and alginate hydrogel encapsulation; this record does not assert the full salts, induction, or encapsulation protocol.
 
                 </p>
diff --git a/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html b/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html
index c56b06e2..dbda32b5 100644
--- a/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html
+++ b/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Pseudomonas Phototrophic PHA and DNT Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000167</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000167</code>
                     </span>
                 </div>
 
@@ -1311,7 +1313,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> BG-11-derived medium was adapted for simultaneous cyanobacterial and P. putida growth; specific recipes varied by publication and experiment.
                 </p>
                 
diff --git a/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html b/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html
index c39c51e7..d910c640 100644
--- a/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html
+++ b/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Shewanella D-Lactate Biophotovoltaic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000211</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000211</code>
                     </span>
                 </div>
 
@@ -1080,7 +1082,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> MBG11 is a modified BG11-based medium adjusted to support both the cyanobacterium and Shewanella in the electrochemical device. The full component table is in the source supplementary material and is not reasserted here.
 
                 </p>
diff --git a/docs/communities/Synechococcus_Yarrowia_SPC.html b/docs/communities/Synechococcus_Yarrowia_SPC.html
index 13ebce16..17808a7a 100644
--- a/docs/communities/Synechococcus_Yarrowia_SPC.html
+++ b/docs/communities/Synechococcus_Yarrowia_SPC.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synechococcus-Yarrowia Synthetic Photosynthetic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000067</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000067</code>
                     </span>
                 </div>
 
@@ -723,6 +725,79 @@ <h4>Evidence</h4>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    BG-11-based photosynthetic co-culture medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">35 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">AEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. elongatus propagated in BG-11 + 1 g/L HEPES (pH 8, 35 °C, constant light). In the source (Hays et al. 2017) the yeast partner tested was Saccharomyces cerevisiae, grown in the yeast co-culture medium CoY BG-11; the general co-culture conditions (35 °C, 150 rpm, 2% CO2, ~80 µmol PAR) apply across all cyanobacterium/heterotroph dyads. 2% sucrose added to acclimate; IPTG induces sucrose export.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All acclimating cultures and co-cultures were grown at 35 °C, 150 rpm, 2% CO2, in light (PAR = ~80 μmol with 15 W Gro-Lux Sylvania fluorescent bulbs) within a Multitron Infors HT incubator"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28127397"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28127397
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"S. elongatus was propagated in BG-11 (Sigma-Aldrich) plus 1 g/L HEPES, pH 8 in constant light at 35 °C"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html b/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html
index 1c9d7738..a20adefd 100644
--- a/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html
+++ b/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synthetic Lichen Synechococcus-Rhodotorula Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000149</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000149</code>
                     </span>
                 </div>
 
@@ -926,7 +928,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Modified BG-11 coculture medium with HEPES, YNB without amino acids, ammonium chloride, IPTG, and NaCl; cyanobacterial inoculum was grown with CO2-enriched aeration.
                 </p>
                 
diff --git a/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html b/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html
index 301e277f..b9669319 100644
--- a/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html
+++ b/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Synthetic Periphyton Freshwater Biofilm</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000130</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000130</code>
                     </span>
                 </div>
 
@@ -702,6 +704,87 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    COMBO freshwater medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">17 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> 26 phototrophic species pre-cultured in COMBO and inoculated in a successional sequence onto glass slides to build the biofilm. Warming (17 to 20 °C) and the herbicide terbuthylazine (0-100 nM) were applied as stressors.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35869094"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35869094
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"to grow in the same freshwater medium COMBO (see Supplementary Table 2 for the detailed composition) 77 at 17 °C and photon irradiance of 40 to 60 µmol s −1"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35869094"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35869094
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"with a photoperiod of 16 h light: 8 h dark"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/35869094"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:35869094
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"sterile 300-mL Erlenmeyer flasks containing 150 mL of COMBO and placed on a shaker operated at 30 rpm"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html b/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html
index 377be1da..e5cea5d3 100644
--- a/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html
+++ b/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophobacter-Methanobacterium Syntrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000068</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000068</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Syntrophobacter-Methanobacterium Syntrophic Consortium</h1>
                     <span class="metadata-value">
                         anaerobic environment
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002229"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001825"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:00002229
+                            ENVO:01001825
                         </a>
                     </span>
                 </div>
@@ -855,6 +857,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    anoxic bicarbonate-buffered basal medium (Stams et al., 1993)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. fumaroxidans (DSM 10017)-M. formicicum (DSM 1535) coculture grown on 30 mM propionate without added electron acceptor under anoxic conditions; batch cultured in triplicate.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29611893"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29611893
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Syntrophobacter fumaroxidans MPOB T (DSM 10017) was cultivated under anoxic conditions in basal medium as described previously"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29611893"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29611893
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All organisms were batch cultured in triplicate at 37°C in 1 l flasks"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/29611893"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:29611893
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Cocultures of S. fumaroxidans with Methanospirillum hungatei strain JF1 T (DSM 864) or Methanobacterium formicicum MF T (DSM 1535) were grown with 30 mM of propionate without electron acceptor"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html b/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html
index 626628b9..78240b72 100644
--- a/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html
+++ b/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophobacter-Methanospirillum Syntrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000069</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000069</code>
                     </span>
                 </div>
 
@@ -400,9 +402,9 @@ <h1>Syntrophobacter-Methanospirillum Syntrophic Consortium</h1>
                     <span class="metadata-value">
                         anaerobic environment
                         <br>
-                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002229"
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_01001825"
                            class="term-link" target="_blank" rel="noopener noreferrer">
-                            ENVO:00002229
+                            ENVO:01001825
                         </a>
                     </span>
                 </div>
@@ -1222,7 +1224,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium prepared under strict anaerobic conditions using modified Hungate technique. Medium boiled and cooled under N2/CO2 atmosphere, dispensed anaerobically into serum bottles or tubes, sealed with butyl rubber stoppers, and autoclaved. Reducing agents (Na2S and cysteine) added from sterile anaerobic stock solutions after autoclaving to establish low redox potential. Final pH adjusted to 7.2. Resazurin used as redox indicator (colorless when reduced). S. fumaroxidans uses both H2 and formate as electron carriers for interspecies electron transfer to M. hungatei, with formate being the preferential carrier during syntrophic propionate oxidation.
 
                 </p>
diff --git a/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html b/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html
index 6dda67cf..de34cff3 100644
--- a/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html
+++ b/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophomonas-Methanococcus Butyrate Growth Coordination Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000189</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000189</code>
                     </span>
                 </div>
 
@@ -1107,7 +1109,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Abstract-level evidence supports a mesophilic S. wolfei and M. maripaludis coculture assayed as a butyrate-oxidizing syntrophic system; detailed medium composition is not asserted here.
 
                 </p>
diff --git a/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html b/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html
index 3a4eccac..fa7da407 100644
--- a/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html
+++ b/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophomonas-Methanospirillum Syntrophic Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000070</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000070</code>
                     </span>
                 </div>
 
@@ -1214,7 +1216,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Medium prepared under strict anaerobic conditions using modified Hungate technique. Medium boiled and cooled under N2/CO2 atmosphere, dispensed anaerobically into serum bottles, sealed with butyl rubber stoppers, and autoclaved. Reducing agents (Na2S and cysteine) added from sterile anaerobic stock solutions after autoclaving. Final pH adjusted to 7.2. Resazurin used as redox indicator (colorless when reduced). Growth requires strict anaerobic conditions; addition of H2 gas to headspace inhibits butyrate degradation.
 
                 </p>
diff --git a/docs/communities/Syntrophus_Benzoate_Degrader.html b/docs/communities/Syntrophus_Benzoate_Degrader.html
index 977354b9..1103137c 100644
--- a/docs/communities/Syntrophus_Benzoate_Degrader.html
+++ b/docs/communities/Syntrophus_Benzoate_Degrader.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophus Benzoate Degrader</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000071</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000071</code>
                     </span>
                 </div>
 
@@ -615,12 +617,6 @@ <h3>Benzoate Degradation and H2/Formate Production</h3>
                             class="term-link" target="_blank" rel="noopener noreferrer">GO:0018874</a>)
                     </li>
                     
-                    <li>
-                        aromatic compound catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0019439"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0019439</a>)
-                    </li>
-                    
                 </ul>
                 
 
@@ -881,6 +877,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    sulfate-free benzoate basal medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> S. aciditrophicus-M. hungatei cocultures grown in sulfate-free (&lt;5 µM) benzoate basal medium; all media prepared anaerobically by the Balch-Wolfe technique; test substrate at 1.2-1.7 mM. Conditions are from a closely related study of the same two organisms (Jackson &amp; McInerney 2001, doi:10.1128/aem.67.12.5520-5525.2001), as the record&#39;s primary reference is not openly accessible.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/aem.67.12.5520-5525.2001"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/aem.67.12.5520-5525.2001
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Cocultures of S. aciditrophicus and M. hungatei were established and grown in sulfate-free (&lt;5 μM) benzoate basal medium as described previously."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/aem.67.12.5520-5525.2001"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/aem.67.12.5520-5525.2001
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All cultures were incubated at 37°C."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.1128/aem.67.12.5520-5525.2001"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.1128/aem.67.12.5520-5525.2001
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All media and stock solutions were prepared anaerobically by using the techniques described by Balch and Wolfe."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -965,8 +1047,6 @@ <h2>Environmental Factors</h2>
             
             processes.push("benzoate metabolic process");
             
-            processes.push("aromatic compound catabolic process");
-            
             
             var evidenceCount = 2;
 
diff --git a/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html b/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
index 024f8182..a82a1bcb 100644
--- a/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
+++ b/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Syntrophus-Methanospirillum Gentianae Benzoate Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000187</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000187</code>
                     </span>
                 </div>
 
@@ -1183,7 +1185,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed abstract supports a methanogenic S. gentianae and M. hungatei coculture degrading benzoate; detailed medium composition is not asserted from abstract-level evidence.
 
                 </p>
diff --git a/docs/communities/THOR_Rhizosphere_Model_Community.html b/docs/communities/THOR_Rhizosphere_Model_Community.html
index 2a062a43..d1fb9d0d 100644
--- a/docs/communities/THOR_Rhizosphere_Model_Community.html
+++ b/docs/communities/THOR_Rhizosphere_Model_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>THOR Rhizosphere Model Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000079</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000079</code>
                     </span>
                 </div>
 
@@ -915,6 +917,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    1/2-strength tryptic soy broth (TSB)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> THOR members propagated on 1/10-strength TSA and grown in liquid 1/2-strength TSB; competition assays also used LB and soybean root exudate, and biofilm assays were incubated at 20°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/30837345"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:30837345
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Bacterial strains were propagated on 1/10-strength tryptic soy agar (TSA) and grown in liquid culture in 1/2-strength tryptic soy broth (TSB) at 28°C with vigorous shaking"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html b/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html
index 97bebdbd..b2bc804a 100644
--- a/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html
+++ b/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>TYQ1 Nematode Biocontrol SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000072</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000072</code>
                     </span>
                 </div>
 
@@ -1053,6 +1055,61 @@ <h2>Associated Datasets</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    tryptic soy agar (TSA) and R2A
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Rhizosphere strains isolated and cultured on TSA and R2A at 28°C; SynCom members co-cultured on TSA (inter-colony/biofilm assays) and grown in TSB and M9 media supplemented with root exudates or TYQ1 supernatant.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41660888"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41660888
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"plated on TSA and R2A media. The plates were then incubated at 28°C for 3–5 days"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html b/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html
index b90fec64..11ee8a1b 100644
--- a/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html
+++ b/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Teosinte-Derived Maize Biofertilizer SynCom7</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000100</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000100</code>
                     </span>
                 </div>
 
@@ -744,6 +746,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    R2A broth
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">28 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Each SynCom strain grown independently to OD600 1.0, centrifuged, and resuspended in sterile 0.85% NaCl to 1 x 10^9 CFU/mL; equal volumes mixed to form the SynCom.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40270813"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40270813
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each bacterial strain was cultured independently in R2A broth media at 28°C with orbital shaking at 150 rpm until reaching an optical density (OD600) of 1.0"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html b/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
index 112f72cb..3fe84bf2 100644
--- a/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
+++ b/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thalassiosira-Marinobacter Marine Snow Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000259</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000259</code>
                     </span>
                 </div>
 
@@ -1061,7 +1063,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Controlled marine laboratory cocultures of T. weissflogii with M. adhaerens HP15 were incubated in aggregation and exudation assays. Detailed medium recipes are not asserted beyond the source-supported marine coculture context.
 
                 </p>
diff --git a/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html b/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
index 67597695..7e5c2f14 100644
--- a/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
+++ b/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thalassiosira-Ruegeria Phycosphere Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000162</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000162</code>
                     </span>
                 </div>
 
@@ -1007,7 +1009,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> T. pseudonana CCMP1335 was grown axenically in organic carbon-free L1 +Si medium; R. pomeroyi DSS-3 was pre-grown in YTSS, washed repeatedly in sterile L1 medium, and inoculated into replicate diatom cultures.
                 </p>
                 
diff --git a/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html b/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
index 220c5de8..c4fa86bf 100644
--- a/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
+++ b/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thermacetogenium-Methanothermobacter Acetate Oxidation Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000182</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000182</code>
                     </span>
                 </div>
 
@@ -1304,7 +1306,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract-level evidence supports acetate-linked thermophilic anaerobic coculture assays and H2/CO2 reverse-direction assays; detailed medium salts are not asserted here.
                 </p>
                 
diff --git a/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html b/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
new file mode 100644
index 00000000..488a2c5f
--- /dev/null
+++ b/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html
@@ -0,0 +1,1223 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Thermophilic Lignocellulose-degrading Composting SynCom - CommunityMech</title>
+    <style>
+        :root {
+            --primary: #3D7DD6;
+            --secondary: #64748b;
+            --background: #f8fafc;
+            --card: #ffffff;
+            --border: #e2e8f0;
+            --text: #1e293b;
+            --text-muted: #64748b;
+            --success: #10b981;
+            --warning: #f59e0b;
+        }
+
+        * {
+            margin: 0;
+            padding: 0;
+            box-sizing: border-box;
+        }
+
+        body {
+            font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
+            background: var(--background);
+            color: var(--text);
+            line-height: 1.6;
+        }
+
+        .container {
+            max-width: 1200px;
+            margin: 0 auto;
+            padding: 2rem;
+        }
+
+        header {
+            background: linear-gradient(135deg, #FBD3E3, #CBDDF6);
+            border-bottom: 1px solid rgba(0, 0, 0, 0.10);
+            padding: 1.5rem 0;
+            margin-bottom: 2rem;
+        }
+
+        h1 {
+            color: var(--primary);
+            font-size: 2rem;
+            margin-bottom: 0.5rem;
+        }
+
+        h2 {
+            color: var(--text);
+            font-size: 1.5rem;
+            margin: 2rem 0 1rem;
+            border-bottom: 1px solid var(--border);
+            padding-bottom: 0.5rem;
+        }
+
+        h3 {
+            color: var(--text);
+            font-size: 1.25rem;
+            margin: 1.5rem 0 0.75rem;
+        }
+
+        .metadata {
+            background: var(--card);
+            border: 1px solid var(--border);
+            border-radius: 8px;
+            padding: 1.5rem;
+            margin-bottom: 2rem;
+        }
+
+        .metadata-grid {
+            display: grid;
+            grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
+            gap: 1rem;
+            margin-top: 1rem;
+        }
+
+        .metadata-item {
+            display: flex;
+            flex-direction: column;
+        }
+
+        .metadata-label {
+            font-weight: 600;
+            color: var(--text-muted);
+            font-size: 0.875rem;
+            text-transform: uppercase;
+            letter-spacing: 0.05em;
+            margin-bottom: 0.25rem;
+        }
+
+        .metadata-value {
+            color: var(--text);
+            font-size: 1rem;
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+
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+  :root:not([data-theme="light"]) th{background:#232a3d}
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+}
+</style>
+</head>
+<body>
+    <header>
+        <div class="container">
+            <a href="../browser.html" class="back-link">← Back to Communities</a>
+            <h1>Thermophilic Lignocellulose-degrading Composting SynCom</h1>
+        </div>
+    </header>
+
+    <main class="container">
+        <!-- Metadata Overview -->
+        <section class="metadata">
+            <div class="metadata-grid">
+                <div class="metadata-item">
+                    <span class="metadata-label">Community ID</span>
+                    <span class="metadata-value">
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000282</code>
+                    </span>
+                </div>
+
+                <div class="metadata-item">
+                    <span class="metadata-label">Ecological State</span>
+                    <span class="metadata-value">
+                        <span class="badge badge-engineered">
+                            ENGINEERED
+                        </span>
+                    </span>
+                </div>
+
+                
+                <div class="metadata-item">
+                    <span class="metadata-label">Environment</span>
+                    <span class="metadata-value">
+                        manure composting
+                        <br>
+                        <a href="https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http://purl.obolibrary.org/obo/ENVO_00002170"
+                           class="term-link" target="_blank" rel="noopener noreferrer">
+                            ENVO:00002170
+                        </a>
+                    </span>
+                </div>
+                
+            </div>
+        </section>
+
+        <!-- Description -->
+        
+        <section class="description">
+            <p>A five-member thermophilic lignocellulose-degrading synthetic microbial community (SynCom) designed for manure composting, comprising the bacteria Bacillus cereus, Achromobacter sp., and Pseudomonas sp. together with the fungi Cladosporium sp. and Trichoderma harzianum. Inoculation drives a metabolic reprogramming from a biofilm-dependent defense-survival mode toward an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), which restricts horizontal gene transfer opportunities. By intensifying thermophilic fermentation, lowering the carbon/nitrogen ratio, and enhancing humification, the SynCom attenuates antibiotic resistance genes and virulence factors, collapses high-risk ARG-mobilome interactomes, and achieves deep bio-sanitization by eliminating high-risk pathogens such as Pseudomonas aeruginosa.</p>
+        </section>
+        
+
+        <!-- Taxonomy -->
+        
+        <section>
+            <h2>Taxonomy</h2>
+            <table>
+                <thead>
+                    <tr>
+                        <th>Taxon</th>
+                        <th>Ontology ID</th>
+                        <th>Functional Roles</th>
+                        <th>Abundance</th>
+                    </tr>
+                </thead>
+                <tbody>
+                    
+                    <tr>
+                        <td>
+                            <strong>Bacillus cereus</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1396"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:1396
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Achromobacter sp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=222"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:222
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Pseudomonas sp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=286"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:286
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Cladosporium sp.</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5498"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:5498
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                    <tr>
+                        <td>
+                            <strong>Trichoderma harzianum</strong>
+                        </td>
+                        <td>
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5544"
+                               class="term-link" target="_blank" rel="noopener noreferrer">
+                                NCBITaxon:5544
+                            </a>
+                        </td>
+                        <td>
+                            
+                            <div class="roles-list">
+                                
+                                <span class="role-badge">PRIMARY_DEGRADER</span>
+                                
+                            </div>
+                            
+                        </td>
+                        <td>N/A</td>
+                    </tr>
+                    
+                    <tr class="evidence-row-container">
+                        <td colspan="4">
+                            <ul class="evidence-list">
+                                
+                                <li class="evidence-item">
+                                    
+                                    <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                                       class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                                    
+                                    - SUPPORT (IN_VIVO)
+                                    
+                                    <div class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum)"</div>
+                                    
+                                </li>
+                                
+                            </ul>
+                        </td>
+                    </tr>
+                    
+                    
+                </tbody>
+            </table>
+        </section>
+        
+
+        <!-- Ecological Interactions -->
+        <section>
+            <h2>Ecological Interactions</h2>
+        
+
+            <!-- Network Diagram -->
+            <div class="network-container" id="network-container">
+                <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
+                <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
+                    <title id="network-svg-title">Ecological interaction network for Thermophilic Lignocellulose-degrading Composting SynCom</title>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).</desc>
+                </svg>
+                <div class="network-legend">
+                    <div class="legend-item">
+                        <span class="legend-swatch legend-circle" style="background: #3b82f6;"></span> Taxon
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #22c55e;"></span> Cross-feeding
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #3b82f6;"></span> Mutualism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #a855f7;"></span> Syntrophy
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #ef4444;"></span> Competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #f97316;"></span> Commensalism
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #14b8a6;"></span> Niche partitioning
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #eab308;"></span> Colonization facilitation
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #fb7185;"></span> Strain competition
+                    </div>
+                    <div class="legend-item">
+                        <span class="legend-swatch" style="background: #dc2626;"></span> Predation
+                    </div>
+                </div>
+            </div>
+
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>Community-level bio-sanitization of high-risk pathogens</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+                <p><strong>Target Taxon:</strong> Pseudomonas aeruginosa</p>
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+            <div class="interaction-card">
+                <div class="interaction-header">
+                    <h3>SynCom-driven suppression of horizontal gene transfer</h3>
+                    <span class="interaction-type">COMPETITION</span>
+                </div>
+
+                
+
+                
+
+                
+
+                
+
+                
+
+                
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
+                    
+                    <li class="evidence-item">
+                        <div>
+                            
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/41839407/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41839407</a>
+                            
+                            - SUPPORT (IN_VIVO)
+                        </div>
+                        
+                        <div class="snippet">"a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly"</div>
+                        
+                    </li>
+                    
+                </ul>
+                
+            </div>
+            
+        
+        </section>
+
+        <!-- Associated Datasets -->
+        
+
+        <!-- Environmental Factors -->
+        
+
+        
+
+        <!-- Growth Media -->
+        
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Thermophilic manure-composting substrate (solid-state)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">thermophilic (no numeric value reported in the abstract) °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> The SynCom is applied to a solid-state manure-composting matrix and drives intensified thermophilic fermentation with a rapid decrease in carbon/nitrogen ratio and enhanced humification. The abstract (source is closed-access, no legal OA full text) reports only a qualitative thermophilic regime; no numeric temperature, pH, medium composition, atmosphere, or incubation time is stated.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41839407"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41839407
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"a thermophilic lignocellulose-degrading synthetic microbial community"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41839407"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41839407
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"intensifying thermophilic fermentation"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/41839407"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:41839407
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
+    </main>
+
+    <footer>
+        <div class="container">
+            <p>Generated by CommunityMech | <a href="https://github.com/CultureBotAI/CommunityMech">View on GitHub</a></p>
+        </div>
+    </footer>
+
+    
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+    <script>
+    (function() {
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+            PREDATION: "#dc2626",
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+            STRAIN_COMPETITION: "#fb7185",
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+        };
+
+        // Build taxon lookup keyed by preferred_term
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+        
+        taxonData["Bacillus cereus"] = {
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+            label: "Bacillus cereus",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Achromobacter sp."] = {
+            id: "NCBITaxon:222",
+            label: "Achromobacter sp.",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Pseudomonas sp."] = {
+            id: "NCBITaxon:286",
+            label: "Pseudomonas sp.",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Cladosporium sp."] = {
+            id: "NCBITaxon:5498",
+            label: "Cladosporium sp.",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+        taxonData["Trichoderma harzianum"] = {
+            id: "NCBITaxon:5544",
+            label: "Trichoderma harzianum",
+            abundance: "UNKNOWN",
+            roles: ["PRIMARY_DEGRADER"]
+        };
+        
+
+        // Build nodes and links
+        var nodes = [];
+        var links = [];
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+
+        // Add taxon nodes
+        Object.keys(taxonData).forEach(function(key) {
+            var t = taxonData[key];
+            var nodeId = "taxon:" + key;
+            taxonNodeIds[key] = nodeId;
+            nodes.push({
+                id: nodeId,
+                label: t.label,
+                type: "taxon",
+                abundance: t.abundance,
+                roles: t.roles,
+                ontologyId: t.id
+            });
+        });
+
+        // Add interaction nodes and edges
+        
+        (function() {
+            var intId = "interaction:0";
+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
+                label: "Community-level bio-sanitization of high-risk pathogens",
+                type: "interaction",
+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+            var tgtKey = "Pseudomonas aeruginosa";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
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+            
+        })();
+        
+        (function() {
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+            var intType = "COMPETITION";
+            var metabolites = [];
+            
+            var processes = [];
+            
+            var evidenceCount = 1;
+
+            nodes.push({
+                id: intId,
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+                interactionType: intType,
+                metabolites: metabolites,
+                processes: processes,
+                evidenceCount: evidenceCount
+            });
+
+            
+
+            
+        })();
+        
+
+        // Remove taxon nodes with no connections
+        var connectedIds = new Set();
+        links.forEach(function(l) {
+            connectedIds.add(typeof l.source === "object" ? l.source.id : l.source);
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+        // Arrow marker
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+            .append("path")
+            .attr("d", "M0,-5L10,0L0,5")
+            .attr("fill", "#94a3b8");
+
+        var simulation = d3.forceSimulation(nodes)
+            .force("link", d3.forceLink(links).id(function(d) { return d.id; }).distance(100))
+            .force("charge", d3.forceManyBody().strength(-400))
+            .force("center", d3.forceCenter(width / 2, height / 2))
+            .force("collision", d3.forceCollide().radius(40))
+            .force("x", d3.forceX(width / 2).strength(0.05))
+            .force("y", d3.forceY(height / 2).strength(0.05));
+
+        var link = svg.append("g")
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+            .join("line")
+            .attr("stroke", "#94a3b8")
+            .attr("stroke-width", 1.5)
+            .attr("marker-end", "url(#arrowhead)");
+
+        var node = svg.append("g")
+            .selectAll("g")
+            .data(nodes)
+            .join("g")
+            .style("cursor", "pointer");
+
+        // Taxon nodes: circles
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("circle")
+            .attr("r", function(d) { return d.abundance === "DOMINANT" ? 18 : 12; })
+            .attr("fill", "#3b82f6")
+            .attr("stroke", "#1e40af")
+            .attr("stroke-width", 1.5);
+
+        // Interaction nodes: rounded rects
+        node.filter(function(d) { return d.type === "interaction"; })
+            .append("rect")
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+            .attr("y", -9)
+            .attr("rx", 5)
+            .attr("fill", function(d) { return interactionColors[d.interactionType] || "#6b7280"; })
+            .attr("stroke", function(d) {
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+                return c ? c.darker(0.5) : "#4b5563";
+            })
+            .attr("stroke-width", 1.5);
+
+        // Labels for taxa (positioned below circle)
+        node.filter(function(d) { return d.type === "taxon"; })
+            .append("text")
+            .text(function(d) {
+                var parts = d.label.split(" ");
+                return parts.length >= 2 ? parts[0][0] + ". " + parts.slice(1).join(" ") : d.label;
+            })
+            .attr("text-anchor", "middle")
+            .attr("dy", function(d) { return d.abundance === "DOMINANT" ? 30 : 24; })
+            .attr("font-size", "10px")
+            .style("fill", "var(--net-label, #475569)");
+
+        // Labels for interactions (multi-line, centered in rectangle)
+        node.filter(function(d) { return d.type === "interaction"; })
+            .each(function(d) {
+                var textElem = d3.select(this).append("text")
+                    .attr("text-anchor", "middle")
+                    .attr("font-size", "9px")
+                    .style("fill", "var(--net-label, #475569)")
+                    .style("pointer-events", "none");
+
+                // Word-wrap text to fit in rectangle (max ~24 chars per line)
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+
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+                        line = words[i];
+                    } else {
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+                    }
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+
+                // Limit to 3 lines maximum
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+
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+                var startY = -(lines.length - 1) * lineHeight / 2;
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+                        .attr("x", 0)
+                        .attr("dy", i === 0 ? startY : lineHeight)
+                        .text(lineText);
+                });
+            });
+
+        // Tooltip
+        var tooltip = d3.select("#network-tooltip");
+
+        node.on("mouseenter", function(event, d) {
+            tooltip.selectAll("*").remove();
+            if (d.type === "taxon") {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.ontologyId);
+                tooltip.append("br");
+                tooltip.append("span").text("Abundance: " + d.abundance);
+                if (d.roles.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Roles: " + d.roles.join(", "));
+                }
+            } else {
+                tooltip.append("strong").text(d.label);
+                tooltip.append("br");
+                tooltip.append("span").text(d.interactionType);
+                if (d.metabolites.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Metabolites: " + d.metabolites.join(", "));
+                }
+                if (d.processes.length) {
+                    tooltip.append("br");
+                    tooltip.append("span").text("Processes: " + d.processes.join(", "));
+                }
+                tooltip.append("br");
+                tooltip.append("span").text("Evidence items: " + d.evidenceCount);
+            }
+            tooltip.style("opacity", 1)
+                .style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mousemove", function(event) {
+            tooltip.style("left", (event.offsetX + 12) + "px")
+                .style("top", (event.offsetY - 12) + "px");
+        })
+        .on("mouseleave", function() {
+            tooltip.style("opacity", 0);
+        });
+
+        // Tick
+        simulation.on("tick", function() {
+            link.attr("x1", function(d) { return d.source.x; })
+                .attr("y1", function(d) { return d.source.y; })
+                .attr("x2", function(d) { return d.target.x; })
+                .attr("y2", function(d) { return d.target.y; });
+
+            node.attr("transform", function(d) {
+                // Constrain nodes within safe boundaries
+                // Account for: node size, label text, and extra padding
+                var nodeRadius = (d.type === "taxon" && d.abundance === "DOMINANT") ? 18 :
+                                (d.type === "taxon") ? 12 : 14; // interaction nodes
+                var labelOffset = d.type === "taxon" ? 35 : 0; // taxon labels below node
+
+                var marginTop = 40;
+                var marginBottom = 60; // extra space for labels
+                var marginSide = 80; // space for long names
+
+                d.x = Math.max(marginSide, Math.min(width - marginSide, d.x));
+                d.y = Math.max(marginTop, Math.min(height - marginBottom, d.y));
+                return "translate(" + d.x + "," + d.y + ")";
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+        for (var i = 0; i < 300; i++) simulation.tick();
+        simulation.stop();
+
+        // Apply final positions
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+            .attr("y1", function(d) { return d.source.y; })
+            .attr("x2", function(d) { return d.target.x; })
+            .attr("y2", function(d) { return d.target.y; });
+
+        node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
+    })();
+    </script>
+    
+    <script src="../theme-toggle.js"></script>
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/communities/Thermophilic_Pyrite_QS_Consortium.html b/docs/communities/Thermophilic_Pyrite_QS_Consortium.html
index 899af97a..2ea35ae1 100644
--- a/docs/communities/Thermophilic_Pyrite_QS_Consortium.html
+++ b/docs/communities/Thermophilic_Pyrite_QS_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thermophilic Pyrite Quorum Sensing Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000073</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000073</code>
                     </span>
                 </div>
 
@@ -733,12 +735,6 @@ <h3>Ferrous Iron Oxidation by Leptospirillum</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -848,12 +844,6 @@ <h3>Sulfur Oxidation by Acidithiobacillus caldus</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         sulfur compound metabolic process
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006790"
@@ -943,12 +933,6 @@ <h3>Dual Iron and Sulfur Oxidation by Sulfobacillus</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1054,12 +1038,6 @@ <h3>Pyrite and Chalcopyrite Dissolution</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         biofilm formation
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0042710"
@@ -1248,12 +1226,12 @@ <h3>AHL Quorum Sensing Regulation</h3>
                         class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:75315</a>), 
                     
                     N-(3-hydroxy-dodecanoyl)-L-homoserine lactone
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=75317"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:75317</a>), 
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=187815"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:187815</a>), 
                     
                     N-(3-hydroxy-tetradecanoyl)-L-homoserine lactone
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=75318"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:75318</a>)
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=55474"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:55474</a>)
                     
                 </p>
                 
@@ -1596,6 +1574,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Mackintosh basal salt solution (Mac medium)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">2.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">40 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Three-species moderately thermophilic consortium grown on 2% (wt/vol) pyrite or chalcopyrite grains plus 34 mM iron(II) in Mac medium; individual strains maintained in Mac medium at pH 2.0-2.5 with FeSO4 and/or elemental sulfur; QS compounds added at or 24 h after inoculation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2025.1592588"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2025.1592588
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The MT consortium bioleaching assays were performed at 40°C in Erlenmeyer flasks with Mac medium pH 2.0 and 2% (wt/vol) pyrite or chalcopyrite grains plus 34 mM iron(II) ions"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2025.1592588"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2025.1592588
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Cultures were incubated at 40°C under constant shaking at 140 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://doi.org/10.3389/fmicb.2025.1592588"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            doi:10.3389/fmicb.2025.1592588
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Mineral dissolution and colonization assays were conducted in 250 mL-Erlenmeyer flasks with 100 mL of medium inoculated with a mixture of the three species each at 2 × 10 7 cells/mL"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1681,8 +1745,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("carbon fixation");
@@ -1726,8 +1788,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("sulfur compound metabolic process");
             
             processes.push("quorum sensing");
@@ -1773,8 +1833,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             processes.push("sulfur compound metabolic process");
@@ -1826,8 +1884,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("biofilm formation");
             
             processes.push("quorum sensing");
diff --git a/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html b/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
index d57e8332..28356c47 100644
--- a/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
+++ b/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thermotoga-Methanocaldococcus Hyperthermophilic Syntrophy</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000186</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000186</code>
                     </span>
                 </div>
 
@@ -1105,7 +1107,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The primary abstract supports an anaerobic T. maritima and M. jannaschii coculture at 85 degrees C; detailed medium composition is not asserted here.
 
                 </p>
diff --git a/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html b/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html
index 64979bb3..3f60415c 100644
--- a/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html
+++ b/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Thiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000239</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000239</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Tinto_River_Iron_Cycling_Community.html b/docs/communities/Tinto_River_Iron_Cycling_Community.html
index edefde29..4b08a72a 100644
--- a/docs/communities/Tinto_River_Iron_Cycling_Community.html
+++ b/docs/communities/Tinto_River_Iron_Cycling_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Tinto River Iron Cycling Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000074</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000074</code>
                     </span>
                 </div>
 
@@ -777,17 +779,6 @@ <h3>Iron Oxidation and Acid Generation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
                 <div class="interaction-flow">
@@ -836,17 +827,6 @@ <h3>Heterotrophic Carbon-Iron Coupling</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -963,12 +943,6 @@ <h3>Complementary Iron and Sulfur Oxidation</h3>
                 <p><strong>Biological Processes:</strong></p>
                 <ul>
                     
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
                     <li>
                         iron ion transport
                         (<a href="http://amigo.geneontology.org/amigo/term/GO:0006826"
@@ -1039,17 +1013,6 @@ <h3>Fungal Organic Matter Degradation and Biofilm Formation</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:1901575"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:1901575</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -1312,10 +1275,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1345,10 +1304,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
@@ -1427,8 +1382,6 @@ <h2>Environmental Factors</h2>
             var processes = [];
             
             
-            processes.push("oxidation-reduction process");
-            
             processes.push("iron ion transport");
             
             
@@ -1470,10 +1423,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("organic substance catabolic process");
-            
-            
             var evidenceCount = 1;
 
             nodes.push({
diff --git a/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html b/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
index 8b26bdaf..c9cd66bc 100644
--- a/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
+++ b/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Tobacco Chemotactic Biocontrol SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000106</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000106</code>
                     </span>
                 </div>
 
@@ -660,6 +662,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    tryptic soy broth (TSB)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Chemotactic SynCom strains (two Pseudomonas, one Bacillus) grown in TSB (tryptone 15 g/L, soy peptone 5 g/L, NaCl 5 g/L); activated on TSB agar at 30°C for 12 h before inoculum preparation.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/40670700"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:40670700
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Chemotactic bacterial strains were first grown overnight in TSB medium at 30 °C with shaking at 150 rpm"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Tomato_Oxylipin_SynCom3.html b/docs/communities/Tomato_Oxylipin_SynCom3.html
index c3446766..d77c7199 100644
--- a/docs/communities/Tomato_Oxylipin_SynCom3.html
+++ b/docs/communities/Tomato_Oxylipin_SynCom3.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Tomato Oxylipin-Protective SynCom3</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000107</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000107</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html b/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html
index 5b86eb02..0589b01c 100644
--- a/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html
+++ b/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Tribromophenol Anaerobic Bioremediation SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000112</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000112</code>
                     </span>
                 </div>
 
@@ -702,6 +704,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    anaerobic mineral medium (unspecified)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Optimum glucose 0.5 or 2.5 mM, sulfate (SO4 2-) 1.0 or 2.5 mM, and inoculum density equivalent to 10^4 16S rRNA gene copies/mL; complete mineralization of 23 uM 2,4,6-TBP within 35 days (0.58 umol/L/d).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/25461007"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:25461007
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a synthetic anaerobe community"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/25461007"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:25461007
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The optimum concentrations of glucose, SO4(2-), and inoculum densities were 0.5 or 2.5mM, 1.0 or 2.5mM, and the densities equivalent to 10(4)copiesmL(-1) of the 16S rRNA genes, respectively. This resulted in the complete mineralization of 23μM 2,4,6-TBP within 35days"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
index 3aa12a14..0961904e 100644
--- a/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
+++ b/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Trichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000188</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000188</code>
                     </span>
                 </div>
 
@@ -1207,7 +1209,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Abstract-level evidence supports an anaerobic syntrophic coculture assayed for butyrate oxidation and methane generation; detailed medium composition is not asserted here.
 
                 </p>
diff --git a/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html b/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html
index 69d0a31f..ae0d8452 100644
--- a/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html
+++ b/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Trichoderma-E. coli Cellulosic Isobutanol Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000205</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000205</code>
                     </span>
                 </div>
 
@@ -1092,7 +1094,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The PubMed abstract supports microcrystalline cellulose and pretreated corn stover as feedstocks and does not provide complete medium composition. The full article reports Trichoderma minimal medium and engineered E. coli strains, but this record keeps the curated growth condition at the abstract-supported species and feedstock level.
                 </p>
                 
diff --git a/docs/communities/Trichoderma_Lactate_Platform.html b/docs/communities/Trichoderma_Lactate_Platform.html
index 4739979a..4fd6636b 100644
--- a/docs/communities/Trichoderma_Lactate_Platform.html
+++ b/docs/communities/Trichoderma_Lactate_Platform.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Trichoderma Lactate Platform for SCFA Production</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000075</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000075</code>
                     </span>
                 </div>
 
@@ -902,6 +904,79 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    Mandels medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Reactor autoclaved with microcrystalline cellulose or pretreated beechwood; remaining medium components added at inoculation. Three-step sequential inoculation: T. reesei (5% v/v), then the lactic acid bacteria to OD600 0.5 after 48 h, then the lactate-fermenting anaerobe (5% v/v) after a further 48 h. The membrane was continuously flushed with air (140 mL/min per liter liquid phase), generating an aerobic-to-anaerobic oxygen gradient. pH controlled with 4 N phosphoric acid / 4 M sodium hydroxide.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32855308"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32855308
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The temperature was set to 30°C and the pH to 6.0 using 4 N phosphoric acid and 4 M sodium hydroxide."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/32855308"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:32855308
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The remaining medium components were added when the reactor was inoculated with 5% (v/v) T. reesei. After 48 hours, the lactic acid bacteria were inoculated to an optical density (OD600) of 0.5 by centrifuging the cells at 3000 rpm for 10 min and suspending them in fresh Mandels medium."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html b/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html
index bf811822..325698c0 100644
--- a/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html
+++ b/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Trichoderma-Streptomyces Filamentous Cellulose Coculture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000270</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000270</code>
                     </span>
                 </div>
 
@@ -1042,7 +1044,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The abstract supports a cellulose-fed synthetic filamentous coculture but does not specify the full mineral medium formulation in the PubMed text.
 
                 </p>
diff --git a/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html b/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
index ef5ffb72..7639b539 100644
--- a/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
+++ b/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Trichodesmium-Alteromonas Marine Consortium</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000147</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000147</code>
                     </span>
                 </div>
 
@@ -694,17 +696,6 @@ <h3>Alteromonas Helper Functions in Trichodesmium Colonies</h3>
                 
 
                 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-                    
-                    <li>
-                        oxidation-reduction process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0055114"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0055114</a>)
-                    </li>
-                    
-                </ul>
-                
 
                 
 
@@ -927,6 +918,61 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    YBC-II
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">26 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> YBC-II is an artificial seawater medium for oceanic cyanobacteria (Chen et al., 1996). Trichodesmium erythraeum IMS101 consortium enrichments grown with continuous shaking under fluorescent light to avoid cell sedimentation; associated Alteromonas macleodii epibionts were isolated from these Trichodesmium cultures on soft-agar RMP medium.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/28440800"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:28440800
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Enrichments were grown in 1 l of YBC-II media (Chen et al., 1996) in 2 l polycarbonate baffled flasks at 26 °C under a 14:10 light:dark cycle (150 μM m−2 s−1) with fluorescent light. Enrichments were continuously shaken to avoid cell sedimentation."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
@@ -1049,10 +1095,6 @@ <h2>Environmental Factors</h2>
             
             var processes = [];
             
-            
-            processes.push("oxidation-reduction process");
-            
-            
             var evidenceCount = 2;
 
             nodes.push({
diff --git a/docs/communities/Urine_Nitrification_SynCom.html b/docs/communities/Urine_Nitrification_SynCom.html
index 0c0c250c..fda1b190 100644
--- a/docs/communities/Urine_Nitrification_SynCom.html
+++ b/docs/communities/Urine_Nitrification_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Urine Nitrification Synthetic Microbial Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000117</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000117</code>
                     </span>
                 </div>
 
@@ -786,6 +788,69 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    synthetic/real urine nitrification medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Reactor 1: ammonium-fed AOB/NOB co-culture salt-adapted up to 45 mS/cm conductivity (resembling undiluted nitrified urine). Reactor 2: fed with 1% and 10% synthetic and fresh real urine; organics removal 69±15%.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31623889"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31623889
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"In reactor 1, salt adaptation of the ammonium-fed AOB and NOB co-culture was possible up to 45mScm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/31623889"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:31623889
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"In reactor 2, the nitrifiers and ureolytic heterotrophs were fed with urine"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html b/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html
index a29fa69d..a9ccb34e 100644
--- a/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html
+++ b/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Variovorax-Cryptococcus Vitamin Cross-Feeding Microcosm</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000213</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000213</code>
                     </span>
                 </div>
 
@@ -951,7 +953,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Minimal defined media were used to assay vitamin-driven dependencies; thiamine and pantothenate are produced by community members (Variovorax and Cryptococcus respectively) rather than added exogenously, and full media composition is not enumerated in the abstract.
                 </p>
                 
diff --git a/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html b/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html
index 315334bf..3c79eb66 100644
--- a/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html
+++ b/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Watermelon Rhizosphere Fusarium-Protective SynCom8</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000098</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000098</code>
                     </span>
                 </div>
 
@@ -660,6 +662,100 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    beef extract peptone broth (NB) medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">37 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> SynCom members were each grown overnight in NB medium, then centrifuged and re-suspended in sterile water to OD600 0.1 and mixed in equal volume (v/v) to establish the SynCom. The SynCom was applied to ungrafted watermelon seedlings (cultivar Zaojia 8424) in polypropylene pots filled with 600 g of non-sterile soil in a greenhouse (daytime 16 h at 30 °C, night 8 h at 26 °C).
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38840214"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38840214
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"each of the 16 core strains was inoculated in beef extract peptone broth (NB) medium and incubated overnight at 37℃ at 170 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38840214"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38840214
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The fermentation broth of each strain was centrifuged at 4000 × g for 5 min and re-suspended in sterile water with OD600 adjusted to 0.1. The suspensions of the 16 strains were mixed in equal volume (v/v) to establish the SynCom."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38840214"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38840214
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The pot experiments were run in a greenhouse (daytime: 16 h long at 30°C, night: 8 h long at 26°C) located in Nanjing Agriculture University."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38840214"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38840214
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each replicate was run in polypropylene pots filled with 600 g of dry, non-sterile soil with no history of watermelon cultivation."</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html b/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
index ad16d746..a20aca29 100644
--- a/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
+++ b/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000255</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000255</code>
                     </span>
                 </div>
 
@@ -864,8 +866,8 @@ <h3>Lactate-Sulfate Carbon And Sulfur Subnetwork</h3>
                     
                     <li>
                         organic substance catabolic process
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0071704"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0071704</a>)
+                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0008152"
+                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0008152</a>)
                     </li>
                     
                 </ul>
diff --git a/docs/communities/Wheat_Consortium_C1.html b/docs/communities/Wheat_Consortium_C1.html
index 039a5540..9bc6ddbb 100644
--- a/docs/communities/Wheat_Consortium_C1.html
+++ b/docs/communities/Wheat_Consortium_C1.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Wheat Synthetic Consortium C1</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000076</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000076</code>
                     </span>
                 </div>
 
@@ -777,6 +779,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    1/4 x tryptic soy agar (TSA)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Wheat-rhizosphere strains maintained on 1/4x TSA / 1x TSB at 25°C; SynCom members grown on 1/4x TSA plates before assembly. Liquid TSB cultures grown shaking at 250 rpm, 25°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36118206"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36118206
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each bacterium was grown in a Petri dish with 1/4 x TSA medium at 25°C for 48 h"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36118206"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36118206
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were grown on 1/4 x tryptic soy agar/1 x tryptic soy broth (TSA/TSB, BD, Franklin Lakes, NJ) at 25°C"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Wheat_Consortium_C6.html b/docs/communities/Wheat_Consortium_C6.html
index a5c17c05..03acfe05 100644
--- a/docs/communities/Wheat_Consortium_C6.html
+++ b/docs/communities/Wheat_Consortium_C6.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Wheat Synthetic Consortium C6</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000077</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000077</code>
                     </span>
                 </div>
 
@@ -785,6 +787,74 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    1/4 x tryptic soy agar (TSA)
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">25 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Wheat-rhizosphere strains maintained on 1/4x TSA / 1x TSB at 25°C; SynCom members grown on 1/4x TSA plates before assembly. Liquid TSB cultures grown shaking at 250 rpm, 25°C.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36118206"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36118206
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each bacterium was grown in a Petri dish with 1/4 x TSA medium at 25°C for 48 h"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36118206"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36118206
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"were grown on 1/4 x tryptic soy agar/1 x tryptic soy broth (TSA/TSB, BD, Franklin Lakes, NJ) at 25°C"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html b/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
index 1171cdb8..c56eb0bb 100644
--- a/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
+++ b/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Wheat Straw Biogas Pretreatment SynCom</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000118</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000118</code>
                     </span>
                 </div>
 
diff --git a/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html b/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
index 9d20d25e..50ad50b9 100644
--- a/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
+++ b/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Yogurt Two-Species Starter Culture</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000164</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000164</code>
                     </span>
                 </div>
 
@@ -1140,7 +1142,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> S. thermophilus and L. delbrueckii subsp. bulgaricus were co-inoculated into milk for thermophilic fermentation; exact strains, inoculum ratios, and temperature vary by study.
                 </p>
                 
@@ -1208,7 +1210,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> Industrial starter strains S. thermophilus 1131 and L. delbrueckii subsp. bulgaricus 2038 were studied during yogurt fermentation in milk/skim-milk medium.
                 </p>
                 
diff --git a/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html b/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
index 963c888d..aeff2323 100644
--- a/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
+++ b/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>Zymomonas-E. coli Exometabolomics-Designed Obligate Mutualism</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000210</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000210</code>
                     </span>
                 </div>
 
@@ -1037,7 +1039,7 @@ <h3>
                 
 
                 
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> The curated source text supports spent-medium exometabolomics, auxotroph pairing, optical-density monitoring, and flow-cytometry confirmation. The complete medium recipe is not asserted in this record because it was not verified from the cited snippets.
 
                 </p>
diff --git a/docs/communities/hCom2_Complex_Gut_Microbiome.html b/docs/communities/hCom2_Complex_Gut_Microbiome.html
index 1cee95c2..a3000050 100644
--- a/docs/communities/hCom2_Complex_Gut_Microbiome.html
+++ b/docs/communities/hCom2_Complex_Gut_Microbiome.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>hCom2 Complex Gut Microbiome</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000123</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000123</code>
                     </span>
                 </div>
 
@@ -618,6 +620,100 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    SAAC complete defined medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Atmosphere</span>
+                        <span class="metadata-value">ANAEROBIC</span>
+                    </div>
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Individual strains were propagated in Mega Medium (MM) or Chopped Meat Medium (CMM) and diluted 1:10 every 24 h before assembly; the assembled community was propagated in vitro in SAAC complete defined medium.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36070752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36070752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The community was propagated in vitro in SAAC medium"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36070752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36070752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"All culturing was done in an anaerobic chamber (Coy Laboratories) at 10% CO 2 , 5% H 2 , and 85% N 2 atmosphere."</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36070752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36070752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"each of our 104 strains can be propagated in Mega Medium (MM), Chopped Meat Medium (CMM), or both"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/36070752"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:36070752
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Strains were diluted 1:10 every 24 h for 2 days into fresh growth medium in 2.2-mL deep well plates"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/docs/communities/mCAFEs_Brachypodium_RCC.html b/docs/communities/mCAFEs_Brachypodium_RCC.html
index 383b6b77..2e07ffac 100644
--- a/docs/communities/mCAFEs_Brachypodium_RCC.html
+++ b/docs/communities/mCAFEs_Brachypodium_RCC.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>m-CAFEs Brachypodium Reduced Complexity Consortia</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000078</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">CommunityMech:000078</code>
                     </span>
                 </div>
 
@@ -1099,6 +1101,92 @@ <h2>Environmental Factors</h2>
 
         <!-- Growth Media -->
         
+        <section>
+            <h2>Growth Media</h2>
+            
+            <div class="metadata">
+                <h3>
+                    modified RCH2 minimal medium
+                    
+                </h3>
+
+                
+
+                <div class="metadata-grid" style="margin-top: 1rem;">
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">pH</span>
+                        <span class="metadata-value">6.0</span>
+                    </div>
+                    
+
+                    
+                    <div class="metadata-item">
+                        <span class="metadata-label">Temperature</span>
+                        <span class="metadata-value">30 °C</span>
+                    </div>
+                    
+
+                    
+                </div>
+
+                
+
+                
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
+                    <strong>Preparation notes:</strong> Base RCH2 minimal medium at pH 6.0 amended with 10 mL/L Wolfe&#39;s vitamins and a single carbon source at 2 mM (citrate, malate, glucose, asparagine, glutamine, glucuronic acid, or a mixture), or 1/10 R2A; enrichments transferred every 3 or 7 days for 10 generations.
+                </p>
+                
+
+                
+                <div style="margin-top: 1rem;">
+                    <h4 style="color: var(--text);">Evidence</h4>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38846575"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38846575
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"The base media for all but one enrichment was a modified RCH2 media (minimal media) at pH 6.0 to mimic the field pH"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38846575"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38846575
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Plates were incubated in the 30°C shaking incubator at 130 rpm"</p>
+                        
+                    </div>
+                    
+                    <div class="evidence-item">
+                        
+                        <a href="https://pubmed.ncbi.nlm.nih.gov/38846575"
+                           class="pmid-link" target="_blank" rel="noopener">
+                            PMID:38846575
+                        </a>
+                        
+
+                        
+                        <p class="snippet">"Each well had 1.8 mL volume in total with 10% inoculum (180 μL)"</p>
+                        
+                    </div>
+                    
+                </div>
+                
+            </div>
+            
+        </section>
+        
     </main>
 
     <footer>
diff --git a/kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml b/kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml
index fff41145..b2847371 100644
--- a/kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml
+++ b/kb/communities/ANME_SRB_Marine_Methane_Seep_Consortium.yaml
@@ -205,4 +205,55 @@ curation_history:
     syntrophy at resolved clade level (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1). Both records describe
     the same natural community type from different studies; candidates for future consolidation.'
   llm_assisted: true
+growth_media:
+- name: Anaerobic artificial seawater sediment/rock microcosm (methane seep AOM incubation)
+  composition:
+  - name: methane
+  - name: sulfate
+  - name: pyruvate
+  atmosphere: ANAEROBIC
+  headspace_gas: Methane (CH4) supplied as the electron-donor substrate; some rock microcosms
+    incubated without added electron donor or with pyruvate
+  temperature: variable by sample (4, 24, or 50 degrees C)
+  temperature_unit: °C
+  temperature_range: '4-50'
+  salinity: artificial seawater (NaCl-based marine salinity; exact concentration not stated)
+  inoculum_source: Push-core seafloor sediment, carbonate rock, and microbial-mat samples from
+    marine methane seeps (Costa Rica margin, southern Pescadero Basin, Santa Monica Basin)
+  vessel_type: sediment/rock microcosm incubation
+  preparation_notes: Samples were stored under an N2 atmosphere at 4°C prior to microcosm
+    incubation. ANME-SRB consortia were incubated in (anaerobic) artificial seawater; sediment
+    horizons received CH4 plus 250 μM L-Homopropargylglycine (HPG) at 4°C, and metabolic
+    activity was confirmed by sulfide accumulation and BONCAT/HPG incorporation. Rock and
+    push-core variants were incubated with CH4 (50°C), with pyruvate (24°C), or without added
+    electron donor (24°C). Single active ANME:SRB aggregates were subsequently FACS-sorted for
+    metagenomics.
+  evidence:
+  - reference: PMID:37747940
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: was incubated in anaerobic artificial sea water without electron donor at 24°C
+    explanation: Supports anaerobic artificial-seawater medium and 24°C incubation of the seep
+      ANME-SRB material.
+  - reference: PMID:37747940
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: artificial sea water supplemented with pyruvate at 24°C
+    explanation: Supports a pyruvate-amended artificial-seawater incubation variant at 24°C.
+  - reference: PMID:37747940
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 250 μM L-Homopropargylglycine (HPG) at 4°C
+    explanation: Supports the CH4/HPG sediment microcosm incubation at 4°C for detecting active
+      ANME-SRB consortia.
+  - reference: PMID:37747940
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: atmosphere at 4°C for sediment microcosm incubations
+    explanation: Supports N2 storage atmosphere at 4°C prior to sediment microcosm incubation.
+  - reference: PMID:37747940
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Push-core samples of seafloor sediment were collected from different locations on the Costa Rica margin
+    explanation: Supports the seafloor methane-seep sediment origin of the incubated inoculum.
 
diff --git a/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml
index 5f6fb1d0..66796c6b 100644
--- a/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml
+++ b/kb/communities/Aerobic_Denitrification_Disturbance_SynCom.yaml
@@ -139,3 +139,20 @@ related_ingredients:
       the quinone pool to complex III, resulting in an increase in electron transfer activity
     explanation: Establishes phenazine-1-carboxylic acid as the DBP-induced redox metabolite driving
       SMC adaptation.
+growth_media:
+- name: unspecified (aerobic denitrification medium)
+  atmosphere: AEROBIC
+  preparation_notes: Three-member aerobic denitrification synthetic microbial community cultivated
+    under dibutyl phthalate (DBP) and levofloxacin (LOFX) disturbance treatments; medium composition,
+    temperature and pH are not reported in the accessible (subscription-only) abstract.
+  evidence:
+  - reference: PMID:40020349
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: aerobic denitrification efficiency could be maintained at about 93 %
+    explanation: Establishes aerobic cultivation of the denitrifying synthetic microbial community.
+  - reference: PMID:40020349
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: dibutyl phthalate (DBP) and levofloxacin (LOFX) were used as environmental disturbances
+    explanation: Names the two disturbance treatments applied during cultivation.
diff --git a/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml
index ac9ee5f5..2a1925ae 100644
--- a/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml
+++ b/kb/communities/Aerobic_Denitrification_QQ_SynCom.yaml
@@ -148,3 +148,16 @@ environmental_factors:
   description: Single-culture, co-culture, and three-member SMC denitrification systems were compared.
   evidence:
   - *id001
+growth_media:
+- name: nitrate wastewater (aerobic denitrification medium)
+  atmosphere: AEROBIC
+  preparation_notes: Synthetic microbial community cultivated under aerobic conditions for aerobic
+    denitrification of nitrate wastewater. Medium composition, temperature, and pH are not reported
+    in the accessible (paywalled) abstract.
+  evidence:
+  - reference: PMID:38277828
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: the application of aerobic denitrification technology in wastewater treatment
+    explanation: Establishes aerobic (AEROBIC) cultivation of the SMC for denitrification of nitrate
+      wastewater.
diff --git a/kb/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.yaml b/kb/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.yaml
index f9c7088c..63f206e4 100644
--- a/kb/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.yaml
+++ b/kb/communities/BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia.yaml
@@ -123,3 +123,35 @@ ecological_interactions:
       associated with improved protein conversion performance in the tested SynCom.
     explanation: Bacillus proteolysis and the partners' protein-conversion association imply a division
       of labor / cross-feeding of proteolysis-derived amino acids.
+growth_media:
+- name: Gnotobiotic BSFL host reared on organic-waste feedstock
+  composition:
+  - name: chicken manure
+  - name: kitchen waste
+  preparation_notes: In-vivo cultivation of the SynCom in germ-free (gnotobiotic) black soldier fly
+    larvae under controlled conditions; the larvae were reared on organic-waste feedstocks (chicken
+    manure and kitchen waste). No defined medium composition, temperature, pH value, atmosphere,
+    incubation time, or shaking is reported in the accessible source (full text paywalled in
+    Bioresource Technology; abstract only). The larval gut presents a spatial pH gradient along which
+    the SynCom members show distinct spatiotemporal distribution.
+  evidence:
+  - reference: PMID:42167379
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: employed multi-omics and synthetic microbial communities (SynCom) in germ-free models to
+      examine microbiota-associated protein conversion under controlled conditions
+    explanation: The SynCom is cultivated in vivo in germ-free (gnotobiotic) larval hosts under
+      controlled conditions.
+  - reference: PMID:42167379
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: when applied to chicken manure and kitchen waste, the SynCom-BSFL system showed
+      improvements in selected performance metrics
+    explanation: Chicken manure and kitchen waste are the organic-waste feedstock substrates on which
+      the SynCom-BSFL system was cultivated.
+  - reference: PMID:42167379
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: distinct spatiotemporal distribution patterns along the gut pH gradient
+    explanation: The cultivation environment is the larval gut, which presents a spatial pH gradient
+      shaping member distribution.
diff --git a/kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml b/kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml
index c124aaf9..e07d9ff4 100644
--- a/kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml
+++ b/kb/communities/BioModels_MODEL2209060002_DPigrum_SAureus_Community.yaml
@@ -118,6 +118,52 @@ associated_datasets:
   accession: doi:10.3389/fcimb.2022.925215
   url: https://doi.org/10.3389/fcimb.2022.925215
   description: Community GEM and use-case for nasal microbiome-relevant interaction modeling.
+growth_media:
+- name: SNM3 (synthetic nasal medium, in silico)
+  composition:
+  - name: oxygen
+  - name: iron
+  headspace_gas: Oxygen available in silico (nose provides both aerobic and anaerobic conditions);
+    oxygen exchange lower bound set to -20 mmol/(gDW*h)
+  preparation_notes: In silico constraint-based (FBA/FVA) medium, not a bench culture. Main
+    medium is SNM3, a defined synthetic medium developed to mimic the human nose environment;
+    exchange-reaction lower bounds for metabolites present in SNM3 were set to -10 mmol/(gDW*h),
+    except -20 (oxygen) and -0.1 (iron); all other exchanges set to 0. Two additional derived
+    media were also used - a rich medium (COMPM) and a poor medium (COOPM). No temperature, pH,
+    or physical cultivation parameters are reported because the study is purely computational.
+  evidence:
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: The main medium applied herein is SNM3
+    explanation: Names SNM3 as the defined medium used for the community metabolic model.
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: a unique SNM3 has been developed
+    explanation: Establishes SNM3 as a defined medium formulated to mimic the human nasal habitat.
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: to mimic the human nose environment
+    explanation: SNM3 was designed to represent the nasal environment simulated by this community model.
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: except oxygen and iron
+    explanation: Oxygen and iron receive special exchange bounds in the SNM3 medium definition,
+      indicating oxygen availability in the model.
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: provides both aerobic and anaerobic living conditions
+    explanation: The modeled nasal habitat provides both aerobic and anaerobic conditions, so no
+      single atmosphere enum is asserted.
+  - reference: doi:10.3389/fcimb.2022.925215
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: one medium as rich in the nutrients of the human nose and the other one as poor in the nutrients
+    explanation: Two additional derived media (rich COMPM and poor COOPM) were used alongside SNM3.
 external_resources:
 - name: BioModels entry
   repository: BIOMODELS
diff --git a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml
index 39dc6214..c176b652 100644
--- a/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml
+++ b/kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml
@@ -676,3 +676,39 @@ metals_present:
 metal_relevance: PRIMARY
 metal_notes: Metal/REE detected via environmental factor measurements; Metal/REE detected via keyword
   matching in description (context-validated)
+growth_media:
+- name: Aerobic acetate mineral medium for chromate reduction (dominant Intrasporangium
+    strain characterization conditions)
+  composition:
+  - name: acetate
+  - name: chromate
+  ph: '8.0'
+  ph_range: 7.5-8.5
+  temperature: '37'
+  temperature_unit: °C
+  temperature_range: 30-37
+  atmosphere: AEROBIC
+  preparation_notes: Aerobic Cr(VI) reduction by the dominant Intrasporangiaceae/Intrasporangium
+    strain, optimal at pH 8.0 and 37°C with acetate (1 mmol/L) as the most efficient
+    carbon source; strain tolerates Cr(VI) to an MIC of 17 mmol/L. Conditions are drawn
+    from the characterization of the closely related dominant strain Intrasporangium
+    sp. Q5-1; the enrichment community source (BioProject PRJNA1272773) reports no explicit
+    medium recipe.
+  evidence:
+  - reference: doi:10.1007/s11274-009-0047-x
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The best condition of Cr(VI) reduction for Q5-1 is pH 8.0 at 37°C
+    explanation: States the optimal pH (8.0) and temperature (37°C) for chromate reduction
+      by the dominant Intrasporangium strain.
+  - reference: doi:10.1007/s11274-009-0047-x
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: is able to reduce Cr(VI) aerobically
+    explanation: Establishes the aerobic atmosphere for chromate reduction by the dominant
+      strain.
+  - reference: doi:10.1007/s11274-009-0047-x
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: the most efficient carbon source for stimulating Cr(VI) reduction
+    explanation: Identifies acetate as the carbon source stimulating chromate reduction.
diff --git a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
index 006c5035..9ecbaa55 100644
--- a/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
+++ b/kb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml
@@ -107,3 +107,40 @@ related_ingredients:
       environmental problems and mitigate greenhouse gas emissions
     explanation: Names mitigation of greenhouse gas emissions (N2O is the key denitrification-derived
       GHG) as a motivating application of the phylogenetically diverse SDCs.
+growth_media:
+- name: Modified marine broth 2216 supplemented with 20 mM NaNO3 (nitrate as electron acceptor)
+  composition:
+  - name: marine broth 2216 (modified)
+  - name: sodium nitrate
+  temperature: '25'
+  temperature_unit: °C
+  atmosphere: ANAEROBIC
+  vessel_type: Balch tubes (three replicate)
+  preparation_notes: Conditions are drawn from the same group's closely related, open-access
+    all-Shewanella denitrifying-SynCom study (Wu et al. 2023, Microbiol Spectr), which describes the
+    identical cultivation used to build the Shewanella (closely related, CR) synthetic denitrifying
+    communities of this record; the paywalled primary paper (PMID:37207729) reports no Methods in its
+    abstract. Strains cultured anaerobically in a modified marine broth 2216 (Becton, Dickinson) with
+    20 mM NaNO3 as electron acceptor, at 25°C in replicate Balch tubes, then serially transferred for
+    experimental evolution.
+  evidence:
+  - reference: doi:10.1128/spectrum.04528-22
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: cultured anaerobically in three replicate Balch tubes at 25°C in the modified marine broth
+      2216 (Becton, Dickinson)
+    explanation: States the anaerobic atmosphere, 25°C incubation temperature, marine broth 2216 base
+      medium, and Balch-tube vessel for the same group's all-Shewanella denitrifying SynCom (the CR
+      community type in this record).
+  - reference: doi:10.1128/spectrum.04528-22
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: cultivated in a modified 2216 medium
+    explanation: Confirms the modified marine broth 2216 as the defined base medium for constructing
+      the synthetic denitrifying communities.
+  - reference: doi:10.1128/spectrum.04528-22
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: as the electron acceptor
+    explanation: Supports 20 mM nitrate (NaNO3) supplied as the terminal electron acceptor for
+      anaerobic denitrification in the medium.
diff --git a/kb/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml b/kb/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml
index bda0bc2f..6d22c30b 100644
--- a/kb/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml
+++ b/kb/communities/Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium.yaml
@@ -118,3 +118,29 @@ ecological_interactions:
       for denitrification enzymes, intracellular electron transfer proteins, and quorum sensing of
       P. aeruginosa
     explanation: Electron cross-feeding upregulates denitrification and electron-transfer gene expression in P. aeruginosa.
+growth_media:
+- name: Anaerobic Fe0-fed denitrification medium
+  composition:
+  - name: metallic iron (Fe0)
+  - name: nitrate
+  atmosphere: ANAEROBIC
+  preparation_notes: Metallic iron (Fe0) supplied as the sole electron donor; nitrate serves as the
+    terminal electron acceptor for denitrification by P. aeruginosa. No medium composition detail,
+    temperature, pH, or reactor configuration was recoverable — the primary source (Water Research,
+    PMID:39504696) is paywalled and only abstract-level conditions could be extracted.
+  evidence:
+  - reference: PMID:39504696
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: In natural or engineered anaerobic environments
+    explanation: Establishes anaerobic cultivation conditions for the Fe0-dependent denitrification consortium.
+  - reference: PMID:39504696
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: using Fe0 as the sole electron donor
+    explanation: Metallic iron (Fe0) is the sole electron donor supplied to the consortium.
+  - reference: PMID:39504696
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: P. aeruginosa can accept electrons for nitrate reduction
+    explanation: Nitrate is the terminal electron acceptor driving denitrification in the medium.
diff --git a/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml b/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml
index 2306b3c1..2a26c224 100644
--- a/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml
+++ b/kb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml
@@ -99,3 +99,22 @@ ecological_interactions:
     snippet: inoculation shifted the bacterial community structure, increasing the relative abundance
       of Firmicutes and significantly enriching the genus Bacillus.
     explanation: SynCom inoculation restructured the resident bacterial community, enriching Bacillus.
+growth_media:
+- name: Solid-state fermentation on cigar tobacco leaves (cultivar QX204)
+  composition:
+  - name: cigar tobacco leaves (cultivar QX204)
+  incubation_time: "42"
+  incubation_time_unit: days
+  vessel_type: cigar tobacco leaf solid-state fermentation
+  preparation_notes: The two-member BsBv SynCom (Bacillus safensis + Bacillus velezensis) was applied
+    to harvested cigar tobacco leaves of cultivar QX204 and fermented for 42 days. The accessible
+    source (paywalled; abstract only) does not report incubation temperature, humidity, pH,
+    atmosphere, medium composition, or inoculum size for this fermentation.
+  evidence:
+  - reference: doi:10.1016/j.indcrop.2025.122621
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: This microbial community was applied to cigar tobacco leaves (cultivar QX204) during a
+      42-day fermentation.
+    explanation: States the fermentation substrate (cigar tobacco leaves, cultivar QX204) and the
+      42-day incubation duration.
diff --git a/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml b/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
index 4c4c317d..800c089c 100644
--- a/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
+++ b/kb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml
@@ -153,3 +153,29 @@ ecological_interactions:
       active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and
       enriched flagellar assembly
     explanation: Community-level metabolic reprogramming that restricts horizontal gene transfer.
+growth_media:
+- name: Thermophilic manure-composting substrate (solid-state)
+  temperature: thermophilic (no numeric value reported in the abstract)
+  preparation_notes: The SynCom is applied to a solid-state manure-composting matrix and drives
+    intensified thermophilic fermentation with a rapid decrease in carbon/nitrogen ratio and enhanced
+    humification. The abstract (source is closed-access, no legal OA full text) reports only a
+    qualitative thermophilic regime; no numeric temperature, pH, medium composition, atmosphere, or
+    incubation time is stated.
+  evidence:
+  - reference: PMID:41839407
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: a thermophilic lignocellulose-degrading synthetic microbial community
+    explanation: States the community is cultivated under a thermophilic regime.
+  - reference: PMID:41839407
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: intensifying thermophilic fermentation
+    explanation: Confirms thermophilic fermentation as the operative cultivation condition during
+      composting.
+  - reference: PMID:41839407
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification
+    explanation: Names the C/N ratio decrease and humification that characterize the composting
+      substrate over time.
diff --git a/reports/growth_conditions_sweep/INDEX.md b/reports/growth_conditions_sweep/INDEX.md
new file mode 100644
index 00000000..7b59eb60
--- /dev/null
+++ b/reports/growth_conditions_sweep/INDEX.md
@@ -0,0 +1,56 @@
+# Growth-conditions sweep — prep index
+
+- Records prepped: **45**
+- OA full text (Methods reachable): **24**
+- Abstract-only (paywalled): **21**
+- No citable reference: **0**
+
+| Record | Primary ref | Access | Method | Methods URL |
+|---|---|---|---|---|
+| Aerobic_Denitrification_Disturbance_SynCom | `PMID:40020349` | ABSTRACT_ONLY | none | — |
+| Aerobic_Denitrification_QQ_SynCom | `PMID:38277828` | ABSTRACT_ONLY | none | — |
+| Bacillus_Bradyrhizobium_Straw_Humification_SynCom | `PMID:41264879` | ABSTRACT_ONLY | none | — |
+| Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium | `PMID:42343824` | ABSTRACT_ONLY | none | — |
+| Chromium_Sulfur_Reduction_Enrichment | `PMID:21441371` | ABSTRACT_ONLY | none | — |
+| Miscanthus_REE_Tailings_Nitrogen_SynCom10 | `PMID:39481489` | ABSTRACT_ONLY | none | — |
+| Peanut_Seed_Bacterial_CS_SynCom | `PMID:38520150` | ABSTRACT_ONLY | none | — |
+| Phylogenetically_Diverse_Denitrifying_SynCom | `PMID:37207729` | ABSTRACT_ONLY | none | — |
+| Pinus_armandii_Endophytic_Biocontrol_SynCom | `PMID:42322490` | ABSTRACT_ONLY | none | — |
+| Pleuromutilin_Degrading_Artificial_Consortium_5_Strain | `PMID:42133144` | ABSTRACT_ONLY | none | — |
+| Polaromonas_Vanadium_Reduction_Community | `PMID:33125214` | ABSTRACT_ONLY | none | — |
+| Populus_Salt_Tolerant_SynComs | `PMID:40904019` | ABSTRACT_ONLY | none | — |
+| Rice_Acid_Soil_Bioinoculant_SynCom | `PMID:38324131` | ABSTRACT_ONLY | none | — |
+| Shewanella_Pseudomonas_Fe0_Electrosyntrophic_Denitrifying_Consortium | `PMID:39504696` | ABSTRACT_ONLY | none | — |
+| Shewanella_oneidensis_Rhodopseudomonas_palustris_Electrosyntrophic_Coculture | `PMID:42285537` | ABSTRACT_ONLY | none | — |
+| SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation | `doi:10.1016/j.indcrop.2025.122621` | ABSTRACT_ONLY | none | — |
+| SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience | `doi:10.1016/j.rhisph.2025.101142` | ABSTRACT_ONLY | none | — |
+| SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation | `doi:10.1016/j.indcrop.2025.122518` | ABSTRACT_ONLY | none | — |
+| Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization | `PMID:41839407` | ABSTRACT_ONLY | none | — |
+| Tomato_Oxylipin_SynCom3 | `PMID:37549573` | ABSTRACT_ONLY | none | — |
+| Wheat_Straw_Biogas_Pretreatment_SynCom | `PMID:38748977` | ABSTRACT_ONLY | none | — |
+| AMD_Acidophile_Heterotroph_Network | `doi:10.3389/fmicb.2024.1374800` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11141062/fullTextXML) |
+| AMD_Nitrososphaerota_Archaeal | `PMID:29209281` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5701628/fullTextXML) |
+| ANME_SRB_Marine_Methane_Seep_Consortium | `PMID:37747940` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10553843/fullTextXML) |
+| Australian_Lead_Zinc_Polymetallic | `PMID:22092956` | OA_FULLTEXT | unpaywall | [link](https://academic.oup.com/femsec/article-pdf/79/2/298/19525950/79-2-298.pdf) |
+| BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia | `PMID:42167379` | OA_FULLTEXT | unpaywall | [link](https://research.wur.nl/en/publications/engineering-a-gut-synthetic-microbial-community-to-enhance-protei) |
+| Bayan_Obo_REE_Tailings_Consortium | `PMID:38310848` | OA_FULLTEXT | unpaywall | [link](http://hdl.handle.net/10261/352237) |
+| BioModels_MODEL1806250003_Spittlebug_Sulcia_Sodalis | `PMID:30254121` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6156193/fullTextXML) |
+| BioModels_MODEL1806250004_Sharpshooter_Sulcia_Baumannia | `PMID:30254121` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6156193/fullTextXML) |
+| BioModels_MODEL1806250005_Cicada_Sulcia_Hodgkinia | `PMID:30254121` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC6156193/fullTextXML) |
+| BioModels_MODEL2209060002_DPigrum_SAureus_Community | `doi:10.3389/fcimb.2022.925215` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9810029/fullTextXML) |
+| BioModels_MODEL2310020001_Mouse_Metaorganism_Model | `doi:10.1101/2024.03.28.587009` | OA_FULLTEXT | unpaywall | [link](https://www.biorxiv.org/content/biorxiv/early/2024/03/31/2024.03.28.587009.full.pdf) |
+| BioModels_MODEL2407300002_Sponge_Holobiont_Network | `PMID:39738126` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11685487/fullTextXML) |
+| Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium | `doi:10.1371/journal.pgen.1002357` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3213167/fullTextXML) |
+| East_River_Floodplain_Core_Microbiome | `PMID:34022966` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8141241/fullTextXML) |
+| Hanford_300_Area_Unconfined_Aquifer_Community | `PMID:22456444` | OA_FULLTEXT | unpaywall | [link](https://www.nature.com/articles/ismej201226.pdf) |
+| Iberian_Pit_Lake_Stratified_Community | `PMID:36123522` | OA_FULLTEXT | unpaywall | [link](https://www.ncbi.nlm.nih.gov/pmc/articles/9666448) |
+| KBase_Models_for_Zahmeeth_Original_PLOS | `doi:10.1101/2023.08.23.554558` | OA_FULLTEXT | unpaywall | [link](https://www.biorxiv.org/content/biorxiv/early/2023/08/24/2023.08.23.554558.full.pdf) |
+| KBase_ORT_Workflow_Community_Model | `PMID:34726691` | OA_FULLTEXT | unpaywall | [link](https://www.osti.gov/biblio/1828774) |
+| Mercury_SFA_EFPC_Sediment_Community | `PMID:33927032` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8086206/fullTextXML) |
+| Naica_Deep_Subsurface_Thermophilic | `doi:10.3389/fmicb.2013.00037` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3589807/fullTextXML) |
+| Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community | `PMID:22988623` | OA_FULLTEXT | unpaywall | [link](https://hdl.handle.net/2027.42/191248) |
+| SPRUCE_Peatland_Methane_Cycling_Community | `PMID:40715043` | OA_FULLTEXT | europepmc_oa | [link](https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12296737/fullTextXML) |
+| Saanich_Inlet_OMZ_Redox_Gradient_Community | `PMID:27655888` | OA_FULLTEXT | unpaywall | [link](https://www.pnas.org/content/pnas/113/40/E5925.full.pdf) |
+| Tinto_River_Iron_Cycling_Community | `doi:10.1128/aem.69.8.4853-4865.2003` | OA_FULLTEXT | unpaywall | [link](https://www.ncbi.nlm.nih.gov/pmc/articles/169134) |
+
+Per-record source bundles are in this directory (`<Record>.md`).
\ No newline at end of file
diff --git a/src/communitymech/templates/community.html b/src/communitymech/templates/community.html
index 43c00a56..9ea46c8b 100644
--- a/src/communitymech/templates/community.html
+++ b/src/communitymech/templates/community.html
@@ -177,7 +177,8 @@
         }
 
         .interaction-flow {
-            background: #fafafa;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid var(--primary);
             padding: 1rem;
             margin: 1rem 0;
@@ -199,7 +200,8 @@
         }
 
         .evidence-item {
-            background: #fefce8;
+            background: var(--background);
+            color: var(--text);
             border-left: 3px solid #ca8a04;
             padding: 0.75rem;
             margin: 0.5rem 0;
@@ -381,7 +383,7 @@ <h1>{{ community.name }}</h1>
                 <div class="metadata-item">
                     <span class="metadata-label">Community ID</span>
                     <span class="metadata-value">
-                        <code style="background: #f1f5f9; padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">{{ community.id }}</code>
+                        <code style="background: var(--border); color: var(--text); padding: 0.25rem 0.5rem; border-radius: 4px; font-size: 0.9rem;">{{ community.id }}</code>
                     </span>
                 </div>
 
@@ -893,7 +895,7 @@ <h4 style="margin-top: 1rem; color: var(--text);">Composition</h4>
                 {% endif %}
 
                 {% if medium.preparation_notes %}
-                <p style="margin-top: 1rem; padding: 0.75rem; background: #f8fafc; border-radius: 4px;">
+                <p style="margin-top: 1rem; padding: 0.75rem; background: var(--background); color: var(--text); border: 1px solid var(--border); border-radius: 4px;">
                     <strong>Preparation notes:</strong> {{ medium.preparation_notes }}
                 </p>
                 {% endif %}