diff --git a/.claude/skills/add-community-record/SKILL.md b/.claude/skills/add-community-record/SKILL.md new file mode 100644 index 000000000..31137ed68 --- /dev/null +++ b/.claude/skills/add-community-record/SKILL.md @@ -0,0 +1,75 @@ +--- +name: add-community-record +description: Discover and add evidence-backed CommunityMech communities through local + scouting, identifier allocation and validated record writing; do not promote scouting + stubs as records. +--- + +# Add a CommunityMech record + +Use [scout-communities](../scout-communities/SKILL.md) to build a bounded candidate +frontier; inspect primary papers and reuse previously acquired research. +[deep-research-community](../deep-research-community/SKILL.md) is a separate +provider workflow whose spending requires existing authorization. +Search community names, source identifiers, exact membership and prior decisions +across `kb/communities/`, `data/isolates/`, `kb/taxa/`, research and history with +ignored files included. A title overlap is only a lead, not identity proof. + +Read [manage-identifiers](../manage-identifiers/SKILL.md) and +[the current schema](../../../src/communitymech/schema/communitymech.yaml). +Allocate `CommunityMech:` IDs across **both** communities and isolates; check +again immediately before creation to avoid another session's allocation. +Scouting stubs under `research/scouting/stubs/` contain placeholder IDs and `_scout` +metadata and are not valid `MicrobialCommunity` records. Build from the current +class and nearest appropriate validated record, not historical skill examples. + +Establish exact community scope, verified membership/strains, source-backed +interactions, environmental/growth context and claim evidence. Write with +`communitymech.validation.write_validated.write_validated_community` using the +correct root class; the default is `MicrobialCommunity`, while reusable taxon +records use `CommonTaxon`. Preserve native key order and use the curation event +helper plus append-only `just new-history` for actual additions. +Run `just validate `, `just validate-strict `, +`just validate-terms `, `just validate-references-explained `, +`just validate-history`, `just audit-writers`, `just gen-html`, +`just check-docs-current` and `just qc`. Reuse +[review-communities](../review-communities/SKILL.md) for its native rubric. + +For an open discovery goal, maintain added/already-present/rejected/blocked +candidate dispositions. Re-query the recorded frontier after curation and report +no further admissible candidates only within that bounded source/query scope; +never claim that no undiscovered microbial communities exist. +## Scope and completion + +For one target, read the whole maintained record and its generated projection or +components. For a corpus goal, first freeze an inventory of record IDs, paths, +input hashes and applicable graph/protein elements; resume that ledger after an +interruption. Include hidden and ignored inputs when establishing absence. +Classify each target as checked, changed, evidence-limited, excluded, not +applicable or blocked, with reasons and inspected sources. A sample, a provider +report and a validator pass do not establish whole-corpus scientific completion. + +Use [curate-yaml-record](../curate-yaml-record/SKILL.md) for the local evidence, +write, history and status contract; this adapter does not replace its managed +method. Record actual agent identity. Preserve scientific status rules and +unrelated edits. Use inspected primary evidence for mechanistic claims and exact +active identifiers for instances; never infer causality from association or +coverage from an empty query. A quotation is source text; interpretation belongs +in the native notes/explanation field. + +Save final scientific assessments through +[review-yaml-record](../review-yaml-record/SKILL.md), +[record reviews](../../../docs/record-reviews.md), and the +[local profile](../../../docs/record-review-profile.md), including their native +persistence exceptions. Keep coverage/checkpoint accounting even when a clean +review should not produce a bundle. Unavailable prerequisites remain blocked; +a skipped target is not a completed enrichment. This skill authorizes no paid +provider call by itself. + +After a completed goal, follow the user's authorized commit, push/PR, +adversarial review, issue/fix, merge and branch-cleanup sequence under the current +repository guidance. Carry forward existing authorization without asking again. +Use fresh required checks and native merge-queue rules. Verify actual merge and +landed content before deleting that feature branch or starting the next goal. +Only genuine review findings become issues; a no-diff goal needs a documented +no-op receipt rather than an artificial commit. diff --git a/.claude/skills/add-uniprot-protein-examples/SKILL.md b/.claude/skills/add-uniprot-protein-examples/SKILL.md new file mode 100644 index 000000000..045e2dce6 --- /dev/null +++ b/.claude/skills/add-uniprot-protein-examples/SKILL.md @@ -0,0 +1,74 @@ +--- +name: add-uniprot-protein-examples +description: Review CommunityMech taxon gene annotations and add verified UniProt + identifiers with evidence linking exact proteins to community roles or interactions. +--- + +# CommunityMech UniProt gene/protein annotations + +Read [the schema](../../../src/communitymech/schema/communitymech.yaml), +[ground-causal-graph-taxa](../ground-causal-graph-taxa/SKILL.md) and the full +community plus linked reusable taxon. The native protein route is +`CommonTaxon.genes[]` (`GeneAnnotation`), not a new `protein_examples` field on +community interactions. `gene_id` accepts a UniProtKB CURIE, with gene symbol, +locus, genome, GO terms, supported role/interaction and claim evidence where +appropriate under the current schema. + +Inventory communities/isolates and referenced `kb/taxa/` genes. Resolve the +protein in the exact parent taxon and experimental context. Confirm any versioned +genome matches the parent's declared genome and that the source establishes the +role/interaction claimed. A gene annotation must not assert a role merely because +the family is present or a neighbor carries it. If a community-specific protein +example lacks a suitable native owner or relationship, record the representation +gap instead of inserting unsupported fields. + +Write through `communitymech.validation.write_validated.write_validated_community` +with `target_class="CommonTaxon"` for reusable taxa, and append truthful curation +and repository history. Run `just validate-taxa`, `just validate-terms-taxa`, +`just validate-history`, `just audit-writers` and `just qc`; run the appropriate +community/reference and page-current gates when linked community content changes. +## Protein identity and evidence + +Inspect live UniProt entry metadata or a release-pinned, provenance-verifiable +native snapshot. Check primary accession and active/merged/deleted state, +organism and strain, sequence/isoform, gene/locus mapping and source identity. +Prefer an exact assayed protein over a convenient ortholog. A named gene alone +is not a unique protein match. Keep family, whole complex, individual subunit, +native protein and experimental construct distinct. UniProt identity metadata +supports identity; primary role evidence supports participation in the record's +mechanism. Retain the original accession and an explicit mapping rationale when +resolving a changed identifier. Do not silently substitute species or isoforms. +## Scope and completion + +For one target, read the whole maintained record and its generated projection or +components. For a corpus goal, first freeze an inventory of record IDs, paths, +input hashes and applicable graph/protein elements; resume that ledger after an +interruption. Include hidden and ignored inputs when establishing absence. +Classify each target as checked, changed, evidence-limited, excluded, not +applicable or blocked, with reasons and inspected sources. A sample, a provider +report and a validator pass do not establish whole-corpus scientific completion. + +Use [curate-yaml-record](../curate-yaml-record/SKILL.md) for the local evidence, +write, history and status contract; this adapter does not replace its managed +method. Record actual agent identity. Preserve scientific status rules and +unrelated edits. Use inspected primary evidence for mechanistic claims and exact +active identifiers for instances; never infer causality from association or +coverage from an empty query. A quotation is source text; interpretation belongs +in the native notes/explanation field. + +Save final scientific assessments through +[review-yaml-record](../review-yaml-record/SKILL.md), +[record reviews](../../../docs/record-reviews.md), and the +[local profile](../../../docs/record-review-profile.md), including their native +persistence exceptions. Keep coverage/checkpoint accounting even when a clean +review should not produce a bundle. Unavailable prerequisites remain blocked; +a skipped target is not a completed enrichment. This skill authorizes no paid +provider call by itself. + +After a completed goal, follow the user's authorized commit, push/PR, +adversarial review, issue/fix, merge and branch-cleanup sequence under the current +repository guidance. Carry forward existing authorization without asking again. +Use fresh required checks and native merge-queue rules. Verify actual merge and +landed content before deleting that feature branch or starting the next goal. +Only genuine review findings become issues; a no-diff goal needs a documented +no-op receipt rather than an artificial commit. diff --git a/.claude/skills/curate-causal-graphs/SKILL.md b/.claude/skills/curate-causal-graphs/SKILL.md new file mode 100644 index 000000000..c49e92bf6 --- /dev/null +++ b/.claude/skills/curate-causal-graphs/SKILL.md @@ -0,0 +1,67 @@ +--- +name: curate-causal-graphs +description: Review and curate CommunityMech ecological interaction downstream graphs + with evidence for each directed causal claim, preserving taxon and experimental + scope. +--- + +# CommunityMech causal interaction graphs + +Read [the schema](../../../src/communitymech/schema/communitymech.yaml), +[ground-causal-graph-taxa](../ground-causal-graph-taxa/SKILL.md) and +[evidence-curation](../evidence-curation/SKILL.md). +The native graph is `MicrobialCommunity.ecological_interactions` with +`EcologicalInteraction.downstream` (`InteractionDownstream`), not a copied +TraitMech nodes/edges list. Inventory `kb/communities/*.yaml` and +`data/isolates/*.yaml`; read reusable `kb/taxa/` records that support a claim. + +Review each interaction and downstream target, direction, mechanism, participant +and organism/condition scope against inspected primary sources. Preserve stable +interaction names and their `downstream[].target` references. Taxon membership, co-occurrence +and a metabolite correlation do not prove a causal chain. If evidence supports +only an interaction but not the proposed downstream link, retain the narrower +supported claim and record the unresolved step. Do not fabricate native slots. +The causal-edge mode of +[deep-research-community](../deep-research-community/SKILL.md) may supply leads; +it does not itself curate the graph or satisfy scientific review. + +Use `communitymech.curate.curation_event.record_curation_event` and +`communitymech.validation.write_validated.write_validated_community`; append +actual repository history. Run community validation/strict/term/reference gates, +`just validate-history`, `just audit-writers`, `just qc`, then `just gen-html` and +`just check-docs-current` for changed communities. Verify downstream references +and citations explicitly even if a structural validator accepts them. +## Scope and completion + +For one target, read the whole maintained record and its generated projection or +components. For a corpus goal, first freeze an inventory of record IDs, paths, +input hashes and applicable graph/protein elements; resume that ledger after an +interruption. Include hidden and ignored inputs when establishing absence. +Classify each target as checked, changed, evidence-limited, excluded, not +applicable or blocked, with reasons and inspected sources. A sample, a provider +report and a validator pass do not establish whole-corpus scientific completion. + +Use [curate-yaml-record](../curate-yaml-record/SKILL.md) for the local evidence, +write, history and status contract; this adapter does not replace its managed +method. Record actual agent identity. Preserve scientific status rules and +unrelated edits. Use inspected primary evidence for mechanistic claims and exact +active identifiers for instances; never infer causality from association or +coverage from an empty query. A quotation is source text; interpretation belongs +in the native notes/explanation field. + +Save final scientific assessments through +[review-yaml-record](../review-yaml-record/SKILL.md), +[record reviews](../../../docs/record-reviews.md), and the +[local profile](../../../docs/record-review-profile.md), including their native +persistence exceptions. Keep coverage/checkpoint accounting even when a clean +review should not produce a bundle. Unavailable prerequisites remain blocked; +a skipped target is not a completed enrichment. This skill authorizes no paid +provider call by itself. + +After a completed goal, follow the user's authorized commit, push/PR, +adversarial review, issue/fix, merge and branch-cleanup sequence under the current +repository guidance. Carry forward existing authorization without asking again. +Use fresh required checks and native merge-queue rules. Verify actual merge and +landed content before deleting that feature branch or starting the next goal. +Only genuine review findings become issues; a no-diff goal needs a documented +no-op receipt rather than an artificial commit. diff --git a/.claude/skills/ground-taxa-gtdb/SKILL.md b/.claude/skills/ground-taxa-gtdb/SKILL.md index 6ac163604..40743a807 100644 --- a/.claude/skills/ground-taxa-gtdb/SKILL.md +++ b/.claude/skills/ground-taxa-gtdb/SKILL.md @@ -297,7 +297,7 @@ taxonomy entries and their id anchors do not line up. *Chlorobium* went unprotected — it survived earlier sweeps only because its recompute happened to fail (#376). - **`is_reclassified: true`** — GTDB uses a different name than NCBI at that - rank. Read it as exactly that and no more: 51 of 138 true values (37%) are a + rank. Read it as exactly that and no more: 53 of 141 true values (38%) are a dropped strain designation, a polyphyly suffix, a GTDB placeholder epithet, or a nomenclatural ending rather than any kind of reclassification (#441, #480) diff --git a/docs/404.html b/docs/404.html index b20a9bcea..ae028fced 100644 --- a/docs/404.html +++ b/docs/404.html @@ -60,7 +60,7 @@

Page Not Found (404)

Explore CommunityMech

-

CommunityMech Knowledge Base (458 communities) • +

CommunityMech Knowledge Base (473 communities) • Schema: https://w3id.org/communitymech • Source: kb/communities/ • License: BSD-3-Clause

diff --git a/docs/browser.html b/docs/browser.html index 8d194413d..cd6f3e80f 100644 --- a/docs/browser.html +++ b/docs/browser.html @@ -855,7 +855,7 @@

+ +

Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture

+

Engineered probiotic co-culture of oxygen-sensitive anaerobic Bifidobacterium longum DSM20219 and biofilm-forming Bacillus subtilis SOM8 co-encapsulated in sodium alginate hydrogel beads. Bacillus subtilis SOM8 promotes interspecies cell aggregation, extracellular polymeric matrix development, and biofilm formation within the alginate matrix, enhancing B. longum DSM20219 survival by ~3-log CFU/g (>7-log CFU/g) in simulated gastric and intestinal fluids and maintaining >6-log CFU/g over 28 days of aerobic storage.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia + +

Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community

+

Simplified four-isolate bacterial synthetic community (SynCom) constructed from keystone taxa—Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter—identified in a natural microbial consortium enriched from herbicide-stressed agricultural black soil in Northeast China. Activated by glucose supplementation that fuels glycolytic and TCA cycle energy supply and environmental acidification, the SynCom co-metabolically degrades a recalcitrant mixture of nicosulfuron (97.27%), mesotrione (68.00%), and atrazine (22.91%) via enriched catabolic genes including atzF (allophanate hydrolase) and gst (glutathione S-transferase).

+
+
+ + + + + + + 3 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Clostridial isoDCA Mini Consortium + +

Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture

+

High-cell-density syntrophic bacterial coculture pairing genetically engineered Clostridium acetobutylicum (CACas9 delta-hbd-p95ace02_atoB, lacking 4-C metabolism and overexpressing an acetone-formation pathway) with the acetogen and ketoreductase partner Clostridium ljungdahlii in a 3.6-L perfusion bioreactor. C. acetobutylicum ferments glucose to acetone, CO2, and H2; C. ljungdahlii consumes dissolved H2—relieving the thermodynamic bottleneck of NADH-driven H2 evolution in C. acetobutylicum—and reduces cross-fed acetone to isopropanol at supratheoretical yields in continuous carbon-negative glucose fermentation.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Coastal Forested Wetland Seawater-Ion Microcosm Community + +

Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium

+

Syntrophic consortium of anaerobic methane-oxidizing archaea (ANME-2b, family Candidatus Methanocomedenaceae / Candidatus Methanomarinus) and sulfate-reducing bacteria (Seep-SRB1g, phylum Thermodesulfobacteriota) from deep-sea methane seep sediments on the Costa Rica margin capable of oxidizing carbon monoxide (CO) in the absence of methane. CO oxidation is coupled syntrophically to dissimilatory sulfate reduction and, under sulfate-free conditions, to CO2 (bicarbonate) reduction to methane by ANME-2b to support cellular maintenance.

+
+
+ + + + + + + 2 + + PERTURBED +
+ SYNTROPHY +
+ + Crystal Geyser CO2-Rich Aquifer Autotrophic CPR Lysolipid Community + +

Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community

+

Cross-kingdom synthetic microbial community (13 bacterial and 6 fungal strains) assembled from signature taxa enriched in the low-phosphorus rhizosphere of cucumber (Cucumis sativus): bacterial genera Bacillus, Cupriavidus, Sphingopyxis, and Devosia together with fungal genera Aspergillus and Amesomyces (reported as Amesia). Recruited and sustained by low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the cross-kingdom SynCom engages in mutualistic biofilm and hyphal facilitation and reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85-99%, suppressing cucumber Fusarium wilt even under high-phosphorus conditions.

+
+
+ + + + + + + 6 + + ENGINEERED +
+ RHIZOSPHERE +
+ + DCPP DBS4-DCP-4-DCP-11d Degradation SynCom + +

Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium

+

Anaerobic deep-sea whale-fall sediment microbial consortium and reconstituted defined co-culture enriched in potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. SHE mimicking iron-reducing conditions. Primary chitin-degrading Vallitalea sp. hydrolyzes insoluble crystalline chitin and ferments oligomers to soluble intermediates (N-acetylglucosamine, glucose, acetate) that are cross-fed to iron-reducing, electrogenic Trichloromonas sp. performing extracellular electron transfer (EET) to electrodes or iron oxides.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ DIET +
+ + Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture + +

Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture

+

Catalyst-free, light-driven defined bacterial co-culture pairing the light-responsive electroactive bio-photosensitizer bacterium Delftia acidovorans YP-3 with hydrogen-producing and nitrate-reducing Klebsiella oxytoca DX-3 for simultaneous wastewater nitrogen removal and biohydrogen recovery. Through direct contact and soluble redox-active mediators that lower electron-transfer resistance and stimulate NADH metabolism, the YP-3/DX-3 co-culture generates 345.52 mL/L H2 in 48 h and achieves 90.25% nitrate removal with minimal nitrite accumulation in synthetic swine wastewater.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ BIOTECHNOLOGY +
+ + Gulf of Mexico Oil-Degrading Consortium + +

Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance

+

Compatible three-strain halophilic plant growth-promoting bacterial (HPGPB) consortium comprising Halobacillus marinus MKM3, Halobacillus halophilus MKM4, and Halobacillus halophilus MKM11 applied to black gram (Vigna mungo L. varieties VBN8 and VBN11) under 50 and 100 mM NaCl stress. The consortium improves ionic balance, reduces Na+ accumulation and lipid peroxidation, enhances antioxidant enzyme activities, and increases grain yield by up to 38% under saline greenhouse conditions.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ RHIZOSPHERE +
+ + Human Gut Four-Member Proteome-Complementarity Consortium + +

Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction

+

Four-strain core endophytic synthetic bacterial community (SynCom-NS)—composed of Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi (Ochrobactrum anthropi) SaOA1, and Novosphingobium lindaniclasticum SaNL1 originally isolated from the hyperaccumulator Sedum alfredii—applied to the high-biomass crop Brassica juncea under cadmium stress. SynCom-NS increases soil Cd bioavailability, upregulates root HMA4 metal transporter expression and glutathione-mediated antioxidant defenses, increases plant fresh weight by 82%, and amplifies shoot Cd accumulation 4.07-fold.

+
+
+ + + + + + + 4 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Eng + +

Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium

+

Defined 1:1:1 synthetic bacterial consortium composed of Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 isolated from long-term prometryn-contaminated cornfield soil in Harbin, China. The consortium synergistically degrades the methylthio-s-triazine herbicide prometryn (96.87% removal in 12 h in liquid culture and 96.3% removal over 30 days in soil microcosms) and alleviates prometryn phytotoxicity in maize (Zea mays).

+
+
+ + + + + + + 3 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Rhodococcus-Pseudomonas Plastic Pyrolysis Oil Waste Consortium + +

Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture

+

Defined synthetic bacterial coculture pairing phototrophic nitrogen-fixing Rhodopseudomonas palustris CGA676 with fermentative Escherichia coli PFM2 in an obligate bidirectional carbon-and-nitrogen cross-feeding relationship evolved for 650-800 generations alongside matched monocultures. Beyond engineered carbon (organic acids from glucose fermentation) and nitrogen (ammonium from N2 fixation) exchange, the coculture engages in additional cross-feeding of adenine and iron that represses biosynthesis and scavenging gene expression in the recipient and limits rather than promotes emergent metabolic dependencies.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ SYNTROPHY +
+ + Trichoderma Lactate Platform for SCFA Production + +

Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium

+

Cross-kingdom fungal-bacterial synthetic consortium pairing the atrazine-degrading fungus Trichoderma lentiforme HN154 with rhizosphere Burkholderia isolates (strains Bur-4, Bur-5, and Bur-14) to remediate atrazine-contaminated corn-soybean rotation soil and protect soybean (Glycine max) from residual phytotoxicity. Trichoderma lentiforme HN154 transforms atrazine into hydroxyatrazine and biuret intermediates that stimulate Burkholderia chemotaxis, swarming, and swimming motility; cross-feeding on these intermediates harnesses bacterial atzB, atzC, atzE, and atzF catabolic enzymes to achieve 86.3% atrazine degradation within 168 h while boosting soybean SOD, POD, and CAT antioxidant defenses.

+
+
+ + + + + + + 2 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Watermelon Rhizosphere Fusarium-Protective SynCom8 + +

Wetland Lindane-Degrading Organochlorine Bacterial Consortium

+

Functional anaerobic organochlorine-degrading bacterial consortia (top-down consortium M and bottom-up consortium Y13) constructed around generalist non-obligate organochlorine-degrading Enterococcus strains (Enterococcus casseliflavus PseS3, R1, R3, R12) alongside organohalide-respiring and fermentative partners (Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) for gamma-hexachlorocyclohexane (lindane) bioremediation in coastal wetland sediment microcosms while suppressing CO2-reduction methanogenesis.

+
+
+ + + + + + + 5 + + ENGINEERED +
+ BIOREMEDIATION +
+ + Zymomonas-E. coli Exometabolomics-Designed Obligate Mutualism diff --git a/docs/communities.json b/docs/communities.json index 0d4d91023..8f53ee711 100644 --- a/docs/communities.json +++ b/docs/communities.json @@ -388,6 +388,28 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom", + "name": "Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom", + "description": "Synthetic lignocellulose-degrading cross-kingdom microbial consortium (SynCom) composed of Bacillus licheniformis, Bacillus subtilis, Aspergillus nidulans, and Aspergillus rugulosus applied at 5% inoculation during earthworm (Eisenia fetida) co-vermicomposting of high-lignin green waste and cattle manure. The SynCom stimulates lignocellulolytic enzyme and urease activities, enriches carbohydrate esterases, glycosyltransferases, and nitrification gene hao, reduces the C/N ratio, and increases humic substance and nitrate nitrogen content.", + "ecological_state": "ENGINEERED", + "community_category": "LIGNOCELLULOSE", + "member_count": 4, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, + { + "id": "Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7", + "name": "Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot", + "description": "Synthetic bacterial community (T7 SynCom) constructed from core antagonistic rhizosphere biomarker isolates of Bacillus and Pseudomonas depleted during prolonged continuous cropping of chili pepper (Capsicum annuum). T7 SynCom directly antagonizes the root rot pathogen Fusarium solani, reduces chili root rot incidence, and induces systemic plant resistance by activating MAPK, ethylene, jasmonic acid, and salicylic acid immune signaling pathways.", + "ecological_state": "ENGINEERED", + "community_category": "RHIZOSPHERE", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom", "name": "Bacillus G12-Y4-X25 Tobacco Biocontrol SynCom", @@ -550,6 +572,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture", + "name": "Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture", + "description": "Engineered probiotic co-culture of oxygen-sensitive anaerobic Bifidobacterium longum DSM20219 and biofilm-forming Bacillus subtilis SOM8 co-encapsulated in sodium alginate hydrogel beads. Bacillus subtilis SOM8 promotes interspecies cell aggregation, extracellular polymeric matrix development, and biofilm formation within the alginate matrix, enhancing B. longum DSM20219 survival by ~3-log CFU/g (>7-log CFU/g) in simulated gastric and intestinal fluids and maintaining >6-log CFU/g over 28 days of aerobic storage.", + "ecological_state": "ENGINEERED", + "community_category": "BIOTECHNOLOGY", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Bifidobacterium_Faecalibacterium_2FL_FOS_Butyrate_Coculture", "name": "Bifidobacterium-Faecalibacterium 2′-FL/FOS Butyrate Coculture", @@ -723,6 +756,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom", + "name": "Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community", + "description": "Simplified four-isolate bacterial synthetic community (SynCom) constructed from keystone taxa—Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter—identified in a natural microbial consortium enriched from herbicide-stressed agricultural black soil in Northeast China. Activated by glucose supplementation that fuels glycolytic and TCA cycle energy supply and environmental acidification, the SynCom co-metabolically degrades a recalcitrant mixture of nicosulfuron (97.27%), mesotrione (68.00%), and atrazine (22.91%) via enriched catabolic genes including atzF (allophanate hydrolase) and gst (glutathione S-transferase).", + "ecological_state": "ENGINEERED", + "community_category": "BIOREMEDIATION", + "member_count": 3, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Bosea_Pseudomonas_Dimethachlon_Degradation_Consortium", "name": "Bosea-Pseudomonas Dimethachlon-Degradation Consortium", @@ -1115,6 +1159,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture", + "name": "Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture", + "description": "High-cell-density syntrophic bacterial coculture pairing genetically engineered Clostridium acetobutylicum (CACas9 delta-hbd-p95ace02_atoB, lacking 4-C metabolism and overexpressing an acetone-formation pathway) with the acetogen and ketoreductase partner Clostridium ljungdahlii in a 3.6-L perfusion bioreactor. C. acetobutylicum ferments glucose to acetone, CO2, and H2; C. ljungdahlii consumes dissolved H2—relieving the thermodynamic bottleneck of NADH-driven H2 evolution in C. acetobutylicum—and reduces cross-fed acetone to isopropanol at supratheoretical yields in continuous carbon-negative glucose fermentation.", + "ecological_state": "ENGINEERED", + "community_category": "BIOTECHNOLOGY", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Clostridium_Acetobutylicum_Ljungdahlii_Fusion_Coculture", "name": "Clostridium acetobutylicum-Clostridium ljungdahlii Syntrophic Fusion Coculture", @@ -1291,6 +1346,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium", + "name": "Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium", + "description": "Syntrophic consortium of anaerobic methane-oxidizing archaea (ANME-2b, family Candidatus Methanocomedenaceae / Candidatus Methanomarinus) and sulfate-reducing bacteria (Seep-SRB1g, phylum Thermodesulfobacteriota) from deep-sea methane seep sediments on the Costa Rica margin capable of oxidizing carbon monoxide (CO) in the absence of methane. CO oxidation is coupled syntrophically to dissimilatory sulfate reduction and, under sulfate-free conditions, to CO2 (bicarbonate) reduction to methane by ANME-2b to support cellular maintenance.", + "ecological_state": "PERTURBED", + "community_category": "SYNTROPHY", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Community_G_GenX_Biodegradation_Consortium", "name": "Community G GenX Biodegradation Consortium", @@ -1393,6 +1459,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom", + "name": "Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community", + "description": "Cross-kingdom synthetic microbial community (13 bacterial and 6 fungal strains) assembled from signature taxa enriched in the low-phosphorus rhizosphere of cucumber (Cucumis sativus): bacterial genera Bacillus, Cupriavidus, Sphingopyxis, and Devosia together with fungal genera Aspergillus and Amesomyces (reported as Amesia). Recruited and sustained by low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the cross-kingdom SynCom engages in mutualistic biofilm and hyphal facilitation and reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85-99%, suppressing cucumber Fusarium wilt even under high-phosphorus conditions.", + "ecological_state": "ENGINEERED", + "community_category": "RHIZOSPHERE", + "member_count": 6, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Cultivated_Meat_Contaminant_SynCom", "name": "Cultivated Meat Contaminant SynCom", @@ -1451,6 +1528,19 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium", + "name": "Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium", + "description": "Anaerobic deep-sea whale-fall sediment microbial consortium and reconstituted defined co-culture enriched in potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. SHE mimicking iron-reducing conditions. Primary chitin-degrading Vallitalea sp. hydrolyzes insoluble crystalline chitin and ferments oligomers to soluble intermediates (N-acetylglucosamine, glucose, acetate) that are cross-fed to iron-reducing, electrogenic Trichloromonas sp. performing extracellular electron transfer (EET) to electrodes or iron oxides.", + "ecological_state": "ENGINEERED", + "community_category": "DIET", + "member_count": 2, + "metals_present": [ + "IRON" + ], + "rare_earth_elements_present": [], + "metal_relevance": "PRIMARY" + }, { "id": "Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession", "name": "Deepwater Horizon Deep-Sea Oil Plume Succession", @@ -1550,6 +1640,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture", + "name": "Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture", + "description": "Catalyst-free, light-driven defined bacterial co-culture pairing the light-responsive electroactive bio-photosensitizer bacterium Delftia acidovorans YP-3 with hydrogen-producing and nitrate-reducing Klebsiella oxytoca DX-3 for simultaneous wastewater nitrogen removal and biohydrogen recovery. Through direct contact and soluble redox-active mediators that lower electron-transfer resistance and stimulate NADH metabolism, the YP-3/DX-3 co-culture generates 345.52 mL/L H2 in 48 h and achieves 90.25% nitrate removal with minimal nitrite accumulation in synthetic swine wastewater.", + "ecological_state": "ENGINEERED", + "community_category": "BIOTECHNOLOGY", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Shewanella_Anammox_Delta_nrfA_Nitrite_Coupled_Consortium", "name": "Delta nrfA Shewanella-Anammox Nitrite Coupled Consortium", @@ -2101,6 +2202,17 @@ "rare_earth_elements_present": [], "metal_relevance": "SIGNIFICANT" }, + { + "id": "Halobacillus_Black_Gram_Halophilic_PGPR_Consortium", + "name": "Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance", + "description": "Compatible three-strain halophilic plant growth-promoting bacterial (HPGPB) consortium comprising Halobacillus marinus MKM3, Halobacillus halophilus MKM4, and Halobacillus halophilus MKM11 applied to black gram (Vigna mungo L. varieties VBN8 and VBN11) under 50 and 100 mM NaCl stress. The consortium improves ionic balance, reduces Na+ accumulation and lipid peroxidation, enhances antioxidant enzyme activities, and increases grain yield by up to 38% under saline greenhouse conditions.", + "ecological_state": "ENGINEERED", + "community_category": "RHIZOSPHERE", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "HAMBI_Carbon_Gradient_SynCom16", "name": "HAMBI Carbon-Gradient 16-species SynCom", @@ -2216,6 +2328,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium", + "name": "Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction", + "description": "Four-strain core endophytic synthetic bacterial community (SynCom-NS)—composed of Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi (Ochrobactrum anthropi) SaOA1, and Novosphingobium lindaniclasticum SaNL1 originally isolated from the hyperaccumulator Sedum alfredii—applied to the high-biomass crop Brassica juncea under cadmium stress. SynCom-NS increases soil Cd bioavailability, upregulates root HMA4 metal transporter expression and glutathione-mediated antioxidant defenses, increases plant fresh weight by 82%, and amplifies shoot Cd accumulation 4.07-fold.", + "ecological_state": "ENGINEERED", + "community_category": "BIOREMEDIATION", + "member_count": 4, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "PRIMARY" + }, { "id": "Iberian_Pit_Lake_Stratified_Community", "name": "Iberian Pit Lake Stratified Community", @@ -3677,6 +3800,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium", + "name": "Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium", + "description": "Defined 1:1:1 synthetic bacterial consortium composed of Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 isolated from long-term prometryn-contaminated cornfield soil in Harbin, China. The consortium synergistically degrades the methylthio-s-triazine herbicide prometryn (96.87% removal in 12 h in liquid culture and 96.3% removal over 30 days in soil microcosms) and alleviates prometryn phytotoxicity in maize (Zea mays).", + "ecological_state": "ENGINEERED", + "community_category": "BIOREMEDIATION", + "member_count": 3, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Pseudomonas_Acidovorax_Aniline_Degradation_SynCom", "name": "Pseudomonas-Acidovorax Aniline-Degradation SynCom", @@ -3860,6 +3994,19 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture", + "name": "Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture", + "description": "Defined synthetic bacterial coculture pairing phototrophic nitrogen-fixing Rhodopseudomonas palustris CGA676 with fermentative Escherichia coli PFM2 in an obligate bidirectional carbon-and-nitrogen cross-feeding relationship evolved for 650-800 generations alongside matched monocultures. Beyond engineered carbon (organic acids from glucose fermentation) and nitrogen (ammonium from N2 fixation) exchange, the coculture engages in additional cross-feeding of adenine and iron that represses biosynthesis and scavenging gene expression in the recipient and limits rather than promotes emergent metabolic dependencies.", + "ecological_state": "ENGINEERED", + "community_category": "SYNTROPHY", + "member_count": 2, + "metals_present": [ + "IRON" + ], + "rare_earth_elements_present": [], + "metal_relevance": "INCIDENTAL" + }, { "id": "Rhodopseudomonas_Ecoli_CrossFeeding_Coculture", "name": "Rhodopseudomonas-E. coli Cross-Feeding Coculture", @@ -4947,6 +5094,17 @@ "rare_earth_elements_present": [], "metal_relevance": "INCIDENTAL" }, + { + "id": "Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium", + "name": "Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium", + "description": "Cross-kingdom fungal-bacterial synthetic consortium pairing the atrazine-degrading fungus Trichoderma lentiforme HN154 with rhizosphere Burkholderia isolates (strains Bur-4, Bur-5, and Bur-14) to remediate atrazine-contaminated corn-soybean rotation soil and protect soybean (Glycine max) from residual phytotoxicity. Trichoderma lentiforme HN154 transforms atrazine into hydroxyatrazine and biuret intermediates that stimulate Burkholderia chemotaxis, swarming, and swimming motility; cross-feeding on these intermediates harnesses bacterial atzB, atzC, atzE, and atzF catabolic enzymes to achieve 86.3% atrazine degradation within 168 h while boosting soybean SOD, POD, and CAT antioxidant defenses.", + "ecological_state": "ENGINEERED", + "community_category": "BIOREMEDIATION", + "member_count": 2, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture", "name": "Trichoderma-E. coli Cellulosic Isobutanol Coculture", @@ -5061,6 +5219,17 @@ "rare_earth_elements_present": [], "metal_relevance": "NOT_APPLICABLE" }, + { + "id": "Wetland_Lindane_Degrading_Organochlorine_Consortium", + "name": "Wetland Lindane-Degrading Organochlorine Bacterial Consortium", + "description": "Functional anaerobic organochlorine-degrading bacterial consortia (top-down consortium M and bottom-up consortium Y13) constructed around generalist non-obligate organochlorine-degrading Enterococcus strains (Enterococcus casseliflavus PseS3, R1, R3, R12) alongside organohalide-respiring and fermentative partners (Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) for gamma-hexachlorocyclohexane (lindane) bioremediation in coastal wetland sediment microcosms while suppressing CO2-reduction methanogenesis.", + "ecological_state": "ENGINEERED", + "community_category": "BIOREMEDIATION", + "member_count": 5, + "metals_present": [], + "rare_earth_elements_present": [], + "metal_relevance": "NOT_APPLICABLE" + }, { "id": "Wetland_Oxygen_Sulfate_GHG_Microcosm_Community", "name": "Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community", diff --git a/docs/communities.tsv b/docs/communities.tsv index 13cfdf963..f6bf11ba8 100644 --- a/docs/communities.tsv +++ b/docs/communities.tsv @@ -33,6 +33,8 @@ Avena_Rhizosphere_Detritusphere_Niche_Succession Avena Rhizosphere and Detritusp Avena_Rhizosphere_CrossKingdom_SIP_Community Avena Rhizosphere Cross-Kingdom 13C-SIP Community RHIZOSPHERE STABLE 5 NOT_APPLICABLE A rhizosphere community of Avena fatua traced with stable isotope probing (SIP) by growing the plant in a 13CO2 atmosphere. Paired rhizosphere and nonrhizosphere soils sampled at 6 and 9 weeks were density-fractionated and sequenced to recover 55 bacterial genomes (>=70 percent complete), complete 18S rRNA sequences of 13C-enriched microeukaryotic bacterivores and fungi, and 10 circularized bacteriophage genomes. Some phages were the most labeled entities in the rhizosphere, suggesting phage are important agents of turnover of plant-derived carbon in soil. CRISPR spacer targeting linked one phage to a Burkholderiales host predicted to be a plant pathogen and another to a Catenulispora sp. predicted to be a plant growth-promoting bacterium. Heavily 13C-labeled bacterial genes include those involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing. Bacillales_Lignin_Degrading_LDSynCom Bacillales Lignin-Degrading LDSynCom LIGNOCELLULOSE ENGINEERED 11 NOT_APPLICABLE An engineered eleven-strain Bacillales synthetic community assembled for aerobic beechwood-lignin degradation in M9 minimal medium. Zhou et al. 2026 screened a 121-strain Bacillales collection with a bottom-up clear-halo lignin-utilization assay and a top-down M9-lignin enrichment, distilled 15 candidates with crystal-violet biofilm and methylene-blue/Azure-B dye-decolorization assays, and retained 11 strains for the lignin-degrading SynCom. The final LDSynCom formed biofilms on lignin particles, accumulated more Folin-Ciocalteu-reactive phenolics than uninoculated and 11B-dropout controls, and produced extracellular proteomes whose lignin-induced proteins included Paenibacillus sp. 11B ring-cleaving dioxygenase candidates. Bacillus_A1_A3_Naphthalene_Biofilm_Consortium Bacillus A1-A3 Naphthalene Biofilm Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A defined two-isolate Bacillus consortium, Consortium 3, assembled from Bacillus paranthracis isolate A1 and Bacillus licheniformis isolate A3 after enrichment of petroleum-contaminated soil from Ras Gharib, Egypt on polycyclic aromatic hydrocarbons. The A1/A3 pair was one of four consortia built from the three strongest phenanthrene- and naphthalene-degrading isolates. Consortium 3 was induced to grow as a glass-attached biofilm, showed the highest reported synergistic interaction during planktonic naphthalene degradation, reached 94.69% naphthalene degradation as a biofilm culture, and its preformed biofilm degraded 81.47% of naphthalene in artificially contaminated soil. Phenanthrene behaved differently: individual isolates outperformed the consortia, and the authors attributed the lower consortium rates to antagonistic interactions under the more complex PAH substrate. +Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom LIGNOCELLULOSE ENGINEERED 4 NOT_APPLICABLE Synthetic lignocellulose-degrading cross-kingdom microbial consortium (SynCom) composed of Bacillus licheniformis, Bacillus subtilis, Aspergillus nidulans, and Aspergillus rugulosus applied at 5% inoculation during earthworm (Eisenia fetida) co-vermicomposting of high-lignin green waste and cattle manure. The SynCom stimulates lignocellulolytic enzyme and urease activities, enriches carbohydrate esterases, glycosyltransferases, and nitrification gene hao, reduces the C/N ratio, and increases humic substance and nitrate nitrogen content. +Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7 Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot RHIZOSPHERE ENGINEERED 2 NOT_APPLICABLE Synthetic bacterial community (T7 SynCom) constructed from core antagonistic rhizosphere biomarker isolates of Bacillus and Pseudomonas depleted during prolonged continuous cropping of chili pepper (Capsicum annuum). T7 SynCom directly antagonizes the root rot pathogen Fusarium solani, reduces chili root rot incidence, and induces systemic plant resistance by activating MAPK, ethylene, jasmonic acid, and salicylic acid immune signaling pathways. Bacillus_G12_Y4_X25_Tobacco_Biocontrol_SynCom Bacillus G12-Y4-X25 Tobacco Biocontrol SynCom RHIZOSPHERE ENGINEERED 3 NOT_APPLICABLE A three-member Bacillus synthetic microbial community assembled from Bacillus amyloliquefaciens G12, Bacillus pumilus Y4, and Bacillus velezensis X25 to combine complementary antagonistic activities against Fusarium oxysporum and Phytophthora nicotianae, the causal agents of tobacco Fusarium root rot and black shank. G12 was isolated from the tobacco rhizosphere and the Y4 and X25 endophytes from tobacco tissues in Luoyang, China. The strains showed only mild mutual inhibition in pairwise plate confrontations, the 1:1:1 SynCom produced more indole-3-acetic acid than any single strain, and glasshouse and two-site field assays linked the consortium to reduced soil-borne disease, improved tobacco root traits, and higher middle-leaf-based estimated yield. Bacillus_siamensis_vallismortis_HT_Masson_Pine_SynCom Bacillus siamensis-vallismortis HT Masson Pine SynCom RHIZOSPHERE ENGINEERED 2 NOT_APPLICABLE A two-strain HT synthetic plant growth-promoting rhizobacterial community assembled from Trichoderma koningiopsis-conditioned Pinus massoniana rhizosphere isolates. The community combines Bacillus siamensis RW5 and Bacillus vallismortis RW8 and was tested against Fusarium oxysporum damping-off in Masson pine seedlings. Relative to the pathogen challenge control, HT reduced disease incidence by 36.67%, increased seedling height by 9.44%, enhanced protective enzyme activity, alleviated membrane damage, and activated the resistance genes PR1, FLS2, and CAT1. Bacillus_Bradyrhizobium_Straw_Humification_SynCom Bacillus-Bradyrhizobium Straw Humification SynCom LIGNOCELLULOSE ENGINEERED 2 NOT_APPLICABLE A two-member Bacillus siamensis and Bradyrhizobium japonicum SynCom that promotes maize straw humification and soil organic carbon. @@ -47,6 +49,7 @@ Banana_Fusarium_Biocontrol_SynCom12 Banana Fusarium Wilt Biocontrol SynCom1.2 RH Barley_DT_Rhizosphere_SynCom Barley DT Rhizosphere SynCom RHIZOSPHERE ENGINEERED 16 NOT_APPLICABLE A defined sixteen-strain drought-tolerant bacterial synthetic community assembled from barley-rhizosphere isolates collected at the Global Change Experimental Facility in Bad Lauchstadt. Rigerte et al. selected isolates with overlapping 16S rDNA sequences to drought- or future-climate-associated amplicon sequence variants, cultured the barley isolate set on YME agar, combined equal proportions of the sixteen single-strain suspensions, and applied the Barley DT-SynCom to barley seedlings before Blumeria graminis f. sp. hordei challenge and pre-challenge rhizosphere multi-omics assays. Bayan_Obo_REE_Tailings_Consortium Bayan Obo REE Tailings Consortium BIOMINING ENGINEERED 3 PRIMARY IRON CERIUM;LANTHANUM;NEODYMIUM;PRASEODYMIUM;SAMARIUM An acid-producing bacterial consortium engineered to extract rare earth elements (REE) from tailings at the Bayan Obo mine in Inner Mongolia, China, the world's largest rare earth deposit. This functional bacterial consortium achieves exceptional REE recovery rates of 82-83% for the five main light rare earth elements (La, Ce, Pr, Nd, Sm) after 18 days of bioleaching using one-step or two-step processes. The tailings are iron extraction residues from medium-poor oxidized ores containing bastnaesite (REE(CO₃)F) and monazite as primary REE minerals. The consortium employs acid-producing bacteria including actinomycetes (Streptomyces sp.), autotrophic acidophiles (Acidithiobacillus ferrooxidans), and heterotrophic acidophiles (Acidiphilium cryptum) that work synergistically to mobilize REE through acidolysis and organic acid complexation. Key mechanisms include production of organic acids (citric, oxalic, lactic, pyruvic), siderophores, and complexing ligands that solubilize REE from carbonate-fluoride minerals. The two-step process (sequential inoculation with heterotrophs followed by autotrophs) achieves 83.51% recovery versus 82.78% for one-step (simultaneous inoculation), demonstrating synergistic enhancement through pH control and organic acid accumulation. This system represents a critical sustainable biotechnology for recovering strategic REE materials essential for clean energy technologies, permanent magnets, and electronics while remediating millions of tons of existing Bayan Obo tailings. Bifidobacterium_Trichomonas_Vaginal_Coculture Bifidobacterium breve-Trichomonas vaginalis Vaginal Co-culture OTHER ENGINEERED 3 NOT_APPLICABLE A defined two-member co-culture of the vaginal commensal Bifidobacterium breve with the sexually transmitted protozoan parasite Trichomonas vaginalis, assayed against HeLa epithelial cells. The result runs counter to the expectation that a beneficial commensal antagonises the parasite: over 4 h the protozoan proliferated 1.2-fold more while bacterial abundance fell 27%, microscopy showed direct physical association between the two organisms, and transcriptomics of T. vaginalis showed upregulation of fatty acid metabolism and DNA replication genes together with virulence-associated genes including adhesins, corroborated by metabolomic changes in long-chain fatty acids. B. breve conferred no protection on host epithelial cells, and the effects on the parasite were transient. The record captures a commensal-parasite association in which the commensal is depleted while the parasite is enhanced. +Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE Engineered probiotic co-culture of oxygen-sensitive anaerobic Bifidobacterium longum DSM20219 and biofilm-forming Bacillus subtilis SOM8 co-encapsulated in sodium alginate hydrogel beads. Bacillus subtilis SOM8 promotes interspecies cell aggregation, extracellular polymeric matrix development, and biofilm formation within the alginate matrix, enhancing B. longum DSM20219 survival by ~3-log CFU/g (>7-log CFU/g) in simulated gastric and intestinal fluids and maintaining >6-log CFU/g over 28 days of aerobic storage. Bifidobacterium_Faecalibacterium_2FL_FOS_Butyrate_Coculture Bifidobacterium-Faecalibacterium 2′-FL/FOS Butyrate Coculture DIET ENGINEERED 2 NOT_APPLICABLE Defined two-strain anaerobic gut coculture containing Bifidobacterium bifidum JCM1254 and Faecalibacterium prausnitzii A2-165 (JCM31915). The strains were grown in 48-well batch cultures of sugar- and volatile-fatty-acid-free YCFA broth supplied with 0.5% total carbohydrate as 2′-fucosyllactose, fructooligosaccharides, or mixtures of the two. Monocultures showed B. bifidum responding to 2′-FL-rich substrates and F. prausnitzii growing in FOS-containing conditions; in the two-member coculture, total OD600 and lactate/acetate accumulation increased under 2′-FL-rich conditions, but butyrate peaked specifically at 10% 2′-FL plus 90% FOS, indicating ratio-dependent substrate complementarity and metabolite-mediated interaction. Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding Bifidobacterium-Ruminococcus Infant HMO Cross-Feeding Coculture OTHER ENGINEERED 2 NOT_APPLICABLE An infant gut microbiome cross-feeding system reconstructed from individualized cultivations with three infant fecal inocula and supplemented with the human milk oligosaccharide 2'-fucosyllactose (2'FL). Bifidobacterium breve typically cannot metabolize 2'FL on its own, but extracellular fucosidases encoded by coexisting Ruminococcus gnavus release lactose from 2'FL and unlock extensive B. breve growth. Targeted cocultures and supplementation of R. gnavus into an infant microbiome showed that R. gnavus promotes B. breve growth through HMO breakdown, demonstrating that infant HMO utilization depends on synergistic interactions among coexisting species. BioAsteroid_ISS_Chondrite_Biomining_Consortium BioAsteroid ISS Chondrite Biomining Consortium BIOMINING ENGINEERED 2 PRIMARY PALLADIUM;IRON;COPPER;NICKEL;COBALT;VANADIUM;ZINC EUROPIUM;LUTETIUM The BioAsteroid experiment tested microbial biomining of asteroidal (L-chondrite) material under microgravity aboard the International Space Station (ISS). Two heterotrophic microorganisms — the bacterium Sphingomonas desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078 — were flown both as single strains and as an artificial two-member consortium on crushed Northwest Africa (NWA) 869 L-chondrite meteorite fragments, in a 50% v/v R2A medium, inside BioMining Reactors housed in KUBIK incubators. The study measured leaching of 44 elements (including the platinum-group elements ruthenium, palladium and platinum, and other elements of industrial interest) from the meteorite and compared microbial versus abiotic (non-biological) leaching under microgravity and terrestrial gravity. Penicillium simplicissimum was the most effective bioleaching organism in microgravity, enhancing release of palladium, platinum and other elements relative to non-biological controls, while Sphingomonas desiccabilis formed a contiguous biofilm on the rock surface but performed similarly or worse than the abiotic control for most platinum-group elements. In the consortium, the fungus alone outperformed the mixture for palladium, suggesting an antagonistic effect of the bacterium. Metabolomic analysis showed distinct, microgravity-dependent changes in microbial metabolism, particularly for P. simplicissimum, with increased production of carboxylic acids and other molecules of potential biomining or pharmaceutical interest. The work demonstrates proof of principle for microbe-driven transformation of asteroidal material for in situ resource utilization in space. @@ -60,6 +63,7 @@ BioModels_MODEL2405300001_Infant_Gut_HMO_SynCom BioModels MODEL2405300001 Infant BioModels_MODEL2407300002_Sponge_Holobiont_Network BioModels MODEL2407300002 Sponge Holobiont Network OTHER STABLE 3 NOT_APPLICABLE BioModels record MODEL2407300002 provides simulations and model assets for an eight-species sponge microbiome network, modeling interactions among symbiont clades in a Stylissa holobiont. BioRock_ISS_Basalt_Biomining_Consortium BioRock ISS Basalt Biomining Consortium BIOMINING ENGINEERED 3 PRIMARY IRON;VANADIUM LANTHANUM;CERIUM;PRASEODYMIUM;NEODYMIUM;SAMARIUM;EUROPIUM;GADOLINIUM;TERBIUM;DYSPROSIUM;HOLMIUM;ERBIUM;THULIUM;YTTERBIUM;LUTETIUM;YTTRIUM A defined three-species bacterial panel flown as the ESA BioRock experiment on board the International Space Station to test microbial bioleaching of economically important elements from basaltic rock under microgravity, simulated Mars gravity, and simulated Earth gravity (with ground 1 x g controls). Sphingomonas desiccabilis CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans CH34 (DSM 2839) were each cultivated on slides of olivine basalt (collected near Gufunes, Reykjavik, Iceland; chosen as an analogue of Moon/Mars surface material) inside a purposely designed miniature biomining reactor housed in the KUBIK incubator. Sphingomonas desiccabilis enhanced mean leached concentrations of rare earth elements (the lanthanides plus yttrium) relative to non-biological controls in all gravity regimes, while Bacillus subtilis reduced REE bioleaching efficacy and Cupriavidus metallidurans showed no difference, demonstrating the microbial specificity of the process as on Earth. A companion analysis showed that Sphingomonas desiccabilis and Bacillus subtilis both enhanced vanadium leaching by 184.92 to 283.22% relative to sterile controls, and a third study found no significant differences in final bacterial cell concentrations between gravity regimes. Gravity level had no significant effect on mean leaching in any case, establishing the principle of biomining and associated bioindustrial processes on Solar System bodies with non-1 x g gravity. BSFL_Gut_SynCom_Bacillus_Lactobacillus_Issatchenkia Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia) BIOTECHNOLOGY ENGINEERED 3 NOT_APPLICABLE 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%. +Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community BIOREMEDIATION ENGINEERED 3 NOT_APPLICABLE Simplified four-isolate bacterial synthetic community (SynCom) constructed from keystone taxa—Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter—identified in a natural microbial consortium enriched from herbicide-stressed agricultural black soil in Northeast China. Activated by glucose supplementation that fuels glycolytic and TCA cycle energy supply and environmental acidification, the SynCom co-metabolically degrades a recalcitrant mixture of nicosulfuron (97.27%), mesotrione (68.00%), and atrazine (22.91%) via enriched catabolic genes including atzF (allophanate hydrolase) and gst (glutathione S-transferase). Bosea_Pseudomonas_Dimethachlon_Degradation_Consortium Bosea-Pseudomonas Dimethachlon-Degradation Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A defined two-strain consortium reconstructed from the dimethachlon-enriched community JHJ-2. Bosea sp. S6 transforms dimethachlon into the toxic intermediate 3,5-dichloroaniline, and Pseudomonas sp. KH-1 consumes that intermediate, completing a sequential degradation and detoxification handoff. Bothnian_Bay_GAC_Dependent_CIET_SAO_Consortium Bothnian Bay GAC-Dependent CIET-SAO Consortium DIET STABLE 5 NOT_APPLICABLE A coastal-sediment-derived, granular-activated-carbon-dependent enrichment consortium serially transferred for about a decade from Bothnian Bay sediments. In anaerobic, acetate-fed cultures amended with granular activated carbon (GAC), the consortium couples syntrophic acetate oxidation to methane formation by moving electrons from the dominant electrogenic syntroph Candidatus Geosyntrophus acetoxidans through the GAC matrix to a Methanosarcina-related electrotrophic methanogen. Long-read metagenomics recovered 24 MAGs from the GAC-propagated enrichment, including MAGs for the core acetate-oxidizing and methanogenic partners plus GAC-enriched Lentimicrobium, Sedimentibacter, and Desulforhopalus lineages. Brachypodium_Young_Root_Rhizosphere_EcoFAB_Community Brachypodium Young Root Rhizosphere EcoFAB Community RHIZOSPHERE STABLE 4 NOT_APPLICABLE A young Brachypodium distachyon primary-root rhizosphere community analyzed at two spatially distinct zones (root tip and root base) using EcoFABs fabricated ecosystems and conventional pot and tube containers with natural soil. 16S rRNA gene analysis shows a strong rhizosphere effect with significant enrichment of OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, while community composition did not differ between root tips and root base or across growth containers. Bulk metagenomic functional analysis revealed enrichment of metabolic-pathway and root-colonization genes in root tips, whereas nutrient-limitation and environmental-stress genes were enriched in bulk soil, indicating root-driven gradients in labile carbon and nutrient availability. @@ -95,6 +99,7 @@ Chromium_Sulfur_Reduction_Enrichment Chromium Sulfur Oxidation Enrichment METAL_ Multispecies_Probiotic_MV_Luteolin_Consortium CICC Three-Strain Probiotic M-MV Luteolin Consortium BIOTECHNOLOGY ENGINEERED 3 NOT_APPLICABLE Defined anaerobic co-culture of Bifidobacterium longum CICC25033, Clostridium butyricum CICC23847, and Limosilactobacillus reuteri CICC6131 used to produce mixed-species probiotic membrane vesicles (M-MVs). Hou et al. grew the strains singly, pairwise, and as a 1:1:1 three-strain combination in MRS broth, observed higher viable counts in co-culture and with cell-free supernatants from partner strains, isolated M-MVs from the supernatant of the co-culture, found a distinct M-MV proteomic profile with antioxidant activity, and loaded luteolin into the resulting M-MVs for in-vitro and DSS-induced mouse-colitis assays. Cinnamate_Degradation_Consortium Cinnamate β-Oxidation Consortium SYNTROPHY STABLE 3 SIGNIFICANT A syntrophic 3-member anaerobic consortium for degradation of cinnamate via β-oxidation to benzoate, consisting of Papillibacter cinnamivorans, Syntrophus sp., and Methanobacterium formicicum. P. cinnamivorans performs β-oxidation of cinnamate to benzoate, followed by syntrophic benzoate degradation by Syntrophus sp. to acetate, H2, and CO2, with the methanogen consuming H2 to produce methane. This stepwise aromatic compound degradation pathway is important for anaerobic bioremediation. Clostridial_isoDCA_Mini_Consortium Clostridial isoDCA Mini Consortium OTHER ENGINEERED 2 NOT_APPLICABLE A two-member engineered Clostridia consortium pairing Peptacetobacter hiranonis with Ruminococcus gnavus VPI C7-9 WT so the community converts host-derived taurocholic acid through cholic acid and deoxycholic acid to isodeoxycholic acid. Ionescu et al. also built a matched P. hiranonis plus R. gnavus KO consortium with rumgna_00694 disrupted as an isoDCA-negative control, enabling in vitro bile-acid conversion assays and antibiotic-treated mouse engraftment experiments that isolate the host effects of isoDCA. +Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE High-cell-density syntrophic bacterial coculture pairing genetically engineered Clostridium acetobutylicum (CACas9 delta-hbd-p95ace02_atoB, lacking 4-C metabolism and overexpressing an acetone-formation pathway) with the acetogen and ketoreductase partner Clostridium ljungdahlii in a 3.6-L perfusion bioreactor. C. acetobutylicum ferments glucose to acetone, CO2, and H2; C. ljungdahlii consumes dissolved H2—relieving the thermodynamic bottleneck of NADH-driven H2 evolution in C. acetobutylicum—and reduces cross-fed acetone to isopropanol at supratheoretical yields in continuous carbon-negative glucose fermentation. Clostridium_Acetobutylicum_Ljungdahlii_Fusion_Coculture Clostridium acetobutylicum-Clostridium ljungdahlii Syntrophic Fusion Coculture SYNTROPHY ENGINEERED 2 NOT_APPLICABLE A defined two-member anaerobic coculture of the solventogen Clostridium acetobutylicum ATCC 824 and the acetogen Clostridium ljungdahlii DSM 13528. CO2 and H2 produced by C. acetobutylicum feed C. ljungdahlii, and the pairing also produces interspecies cell fusion with large-scale exchange of protein, RNA, and DNA between the two organisms. RNA sequencing of the coculture against the two monocultures, and of membrane-separated against unseparated cocultures in a transwell system, separates the effect of soluble signals from the effect of direct cell-to-cell contact. The transcriptional program shows differential regulation of the C. ljungdahlii Wood-Ljungdahl pathway and of the motility machinery, and of amino-acid biosynthesis and degradation; arginine and histidine made by C. acetobutylicum are proposed to be metabolized by C. ljungdahlii for extra ATP and carbon. The authors read the pairing as mutualistic rather than the commensalism previously assumed. This record is scoped to the WILD-TYPE pairing. The same laboratory has since reported much higher isopropanol and butanol titers from the same species pair using genetically modified C. acetobutylicum; those are properties of the engineered pairing and are deliberately not curated here. Clostridium_Autoethanogenum_Kluyveri_Syngas_Coculture Clostridium autoethanogenum-Clostridium kluyveri Syngas Coculture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE A defined anaerobic synthetic coculture combining the acetogenic syngas fermenter Clostridium autoethanogenum with the chain-elongating bacterium Clostridium kluyveri. C. autoethanogenum converts carbon monoxide or syngas into acetate and ethanol, while C. kluyveri consumes these products for chain elongation, producing C4 and C6 fatty acids and higher alcohols. The system is relevant to DOE carbon utilization and renewable fuels because it couples gas fermentation with microbial upgrading of CO/syngas-derived intermediates in one growth vessel. Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture Clostridium carboxidivorans-Clostridium kluyveri CO Chain-Elongation Coculture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE A defined anaerobic synthetic coculture pairing the autotrophic solventogenic acetogen Clostridium carboxidivorans with the chain-elongating bacterium Clostridium kluyveri. In CO/CO2-fed stirred-tank bioreactors, C. kluyveri elongates C2 products to organic acids, and C. carboxidivorans reduces those acids to longer-chain alcohols such as butanol and hexanol. The system is DOE-relevant because it couples waste-gas/syngas fermentation, carbon utilization, and production of liquid fuels and platform chemicals. @@ -111,6 +116,7 @@ Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture Clostridium-Saccharomyces Clostridium_Thermoanaerobacter_Cellulosic_Bioethanol_Coculture Clostridium-Thermoanaerobacter Cellulosic Bioethanol Coculture LIGNOCELLULOSE ENGINEERED 2 NOT_APPLICABLE A thermophilic, anaerobic, two-member laboratory coculture for consolidated cellulosic bioethanol production. The cellulolytic Clostridium thermocellum LQRI member hydrolyzes and ferments cellulose, while the non-cellulolytic Thermoanaerobacter pseudethanolicus strain X514 partner improves ethanol production from cellulose-derived fermentation intermediates. The system is DOE-relevant because it uses a defined coculture to increase ethanolic fermentation of recalcitrant cellulosic material under batch and cyclic fed-batch bioprocess conditions. Clostridium_Thermoanaerobacterium_JN4_GD17_Cellulosic_Biofuel_Coculture Clostridium-Thermoanaerobacterium JN4-GD17 Cellulosic Biofuel Coculture LIGNOCELLULOSE ENGINEERED 2 NOT_APPLICABLE A thermophilic two-member cellulosic biofuel coculture composed of Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17. The system improves overall cellulosic biofuel production efficiency relative to C. thermocellum alone, but later mechanistic work indicates that GD17 also competitively hampers C. thermocellum JN4 growth while using glucose and cellobiose released during cellulose degradation. Coastal_Forested_Wetland_Seawater_Ion_Microcosm_Community Coastal Forested Wetland Seawater-Ion Microcosm Community METHANOGENESIS PERTURBED 3 NOT_APPLICABLE A restored coastal forested freshwater wetland soil community from the Timberlake Observatory for Wetland Restoration in North Carolina, curated around a manipulative laboratory microcosm experiment that disentangled sulfate from other seawater ions. Intact wetland soil cores received deionized water, artificial seawater, artificial seawater without sulfate, or sulfate alone, followed by DNA sequencing, biogeochemical measurements, and greenhouse gas flux measurements. The experiment found that artificial seawater altered microbial richness, composition, functional genes, and emissions of carbon dioxide, methane, and nitrous oxide whether sulfate was present or absent, whereas sulfate alone did not alter emissions or enrich sulfate-reducing bacteria or sulfur cycling genes. The record is DOE-relevant because authors were affiliated with the DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, and sequencing followed DOE JGI methods. +Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium SYNTROPHY PERTURBED 2 NOT_APPLICABLE Syntrophic consortium of anaerobic methane-oxidizing archaea (ANME-2b, family Candidatus Methanocomedenaceae / Candidatus Methanomarinus) and sulfate-reducing bacteria (Seep-SRB1g, phylum Thermodesulfobacteriota) from deep-sea methane seep sediments on the Costa Rica margin capable of oxidizing carbon monoxide (CO) in the absence of methane. CO oxidation is coupled syntrophically to dissimilatory sulfate reduction and, under sulfate-free conditions, to CO2 (bicarbonate) reduction to methane by ANME-2b to support cellular maintenance. Community_G_GenX_Biodegradation_Consortium Community G GenX Biodegradation Consortium BIOREMEDIATION ENGINEERED 6 NOT_APPLICABLE A Prospector nanowell-derived bacterial consortium from cotton detritusphere enrichments that was re-tested for hexafluoropropylene oxide dimer acid (GenX) degradation. Community G underwent rapid taxonomic restructuring in sterile agricultural-soil microcosms amended with GenX: Salmonella enterica, Pseudomonas tolaasii, Stenotrophomonas sp. LM091, and Stenotrophomonas sp. MYb57 expanded by day 3, while Stenotrophomonas cyclobalanopsidis and Pseudomonas arcuscaelestis declined or disappeared. Active Community G removed 80.6% of GenX in the 3-day soil microcosm and reached 69.6% defluorination. Coniochaeta_Sphingobacterium_Citrobacter_Wheat_Straw_Consortium Coniochaeta-Sphingobacterium-Citrobacter Wheat Straw Consortium LIGNOCELLULOSE ENGINEERED 3 NOT_APPLICABLE A three-member bacterial-fungal synthetic consortium cultivated on wheat straw to study division of labor during lignocellulose degradation. The community combines the fungus Coniochaeta sp. 2T2.1 with the bacterium originally reported as Sphingobacterium multivorum w15 and later proposed as Sphingobacterium paramultivorum w15, plus Citrobacter freundii so4. The system is relevant to DOE bioenergy because it links a Joint Genome Institute fungal genome resource to transcriptomic and metatranscriptomic evidence for cellulose, xylan, hemicellulose, lignin-modification, detoxification, and vitamin B2-associated functions in a model lignocellulose-degrading consortium. Copper_Biomining_Heap_Leach Copper Biomining Heap Leach Consortium BIOMINING ENGINEERED 5 PRIMARY COPPER;IRON An industrial microbial consortium used for commercial copper bioleaching from low-grade sulfide ores in heap leach operations. This acidophilic community oxidizes ferrous iron and reduced sulfur compounds, generating ferric iron (Fe³⁺) and sulfuric acid that solubilize copper from chalcopyrite (CuFeS₂) and other copper sulfide minerals. The consortium demonstrates temporal succession over the 200-300 day leaching cycle, with Acidithiobacillus ferrooxidans dominating early stages (pH >2, low Fe, ~10⁷ copies/ml at 200 days), followed by Leptospirillum ferriphilum and Ferroplasma acidiphilum in aged heaps (pH 1.67-1.83, high Fe³⁺ ~1.9 g/L, ~10⁵ copies/ml at >250 days). Acidithiobacillus thiooxidans maintains constant sulfur oxidation activity (10⁵ copies/ml) throughout the cycle. Sulfobacillus species contribute at low abundance (10³-10⁴ copies/ml) with increased activity in older heaps. The community operates at pH 1.5-2.5, temperatures 20-60°C depending on thermophilic strains, and produces the Fe³⁺ oxidant critical for copper dissolution (reaching 1.86-1.9 g/L Fe³⁺). This biohydrometallurgical process extracts copper from ores uneconomical for conventional smelting, with industrial operations achieving commercial-scale metal recovery through percolation of acidic leach solutions through heaps of crushed ore. @@ -120,11 +126,13 @@ Coscinodiscus_Synthetic_Community Coscinodiscus Synthetic Community PHYTOPLANKTO CRC_Fusobacterium_Control_SynCom CRC Fusobacterium Control SynCom OTHER ENGINEERED 1 NOT_APPLICABLE A bottom-up designed seven-species synthetic microbial community for ecological control of Fusobacterium nucleatum-associated colorectal cancer models. Crucian_Carp_Gut_Disease_Resistance_SynCom Crucian Carp Gut Disease-resistance SynCom OTHER ENGINEERED 3 NOT_APPLICABLE 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. Crystal_Geyser_CO2_Aquifer_CPR_Lipid_Community Crystal Geyser CO2-Rich Aquifer Autotrophic CPR Lysolipid Community EXTREME_ENVIRONMENT STABLE 2 NOT_APPLICABLE A deep CO2-rich subsurface aquifer community below the Colorado Plateau, sampled from groundwater brought to the surface by eruptions of Crystal Geyser. Coupled lipidomic and metagenomic analyses show that bacterial and archaeal CO2 fixation in the deep subsurface provides the organic carbon pool, supporting an autotrophy-based deep biosphere. Candidate Phyla Radiation (CPR) bacterial putative symbionts lack complete lipid biosynthesis pathways but still possess regular lipid membranes, which may originate from other community members; these other members also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. +Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community RHIZOSPHERE ENGINEERED 6 NOT_APPLICABLE Cross-kingdom synthetic microbial community (13 bacterial and 6 fungal strains) assembled from signature taxa enriched in the low-phosphorus rhizosphere of cucumber (Cucumis sativus): bacterial genera Bacillus, Cupriavidus, Sphingopyxis, and Devosia together with fungal genera Aspergillus and Amesomyces (reported as Amesia). Recruited and sustained by low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the cross-kingdom SynCom engages in mutualistic biofilm and hyphal facilitation and reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85-99%, suppressing cucumber Fusarium wilt even under high-phosphorus conditions. Cultivated_Meat_Contaminant_SynCom Cultivated Meat Contaminant SynCom BIOTECHNOLOGY ENGINEERED 1 NOT_APPLICABLE A six-isolate synthetic microbial community assembled from microbial contaminants that originated in the cultivated-meat cell-culture environment. Whole-genome functional mapping suggested potential metabolic complementarity and ecological robustness among the contaminants, and the SynCom was used as a severe cell-cultured-meat contamination model for antimicrobial-peptide intervention tests. In a screen of 11 antimicrobial peptides and proteins, the synthetic peptide 1018-k6 was the most effective agent, with a 37.5 μg/mL minimum inhibitory concentration against the SynCom and complete microbial inhibition across a 14-day production-cycle assay challenged with 10^6 CFU/mL bacteria. Cyantraniliprole_Fahmy_Consortium_T4 Cyantraniliprole Fahmy Consortium T4 BIOREMEDIATION ENGINEERED 6 NOT_APPLICABLE A defined six-member bacterial consortium, designated T4 or Fahmy-consortia, that was previously characterized for pesticide bioremediation and was re-evaluated as a cyantraniliprole-removal benchmark in simulated contaminated water. The consortium contains Bacillus subtilis subsp. subtilis AZFS3, Bacillus pumilus AZFS5, Bacillus mojavensis AZFS15, Bacillus paramycoides AZFS18, Pseudomonas aeruginosa KZFS4, and Alcaligenes aquatilis KZFS11. In 20-day, 30 C simulated-water microcosms seeded with standardized bacterial inocula, T4 achieved the highest tested cyantraniliprole removal: HPLC measured 98.27% removal from the 57.79 mg/L zero-day residue and a 1.00 mg/L residue after 20 days in the nominal 60 mg/L treatment. Cyprus_Copper_Sulphide_Bioleaching_Consortium Cyprus Copper Sulphide Bioleaching Consortium BIOMINING ENGINEERED 4 PRIMARY COPPER;IRON An acidophilic copper bioleaching consortium established from a copper bioleaching column in Cyprus on chalcopyrite (CuFeS2) and sub-cultured to chalcocite (Cu2S) to test how mineral type and surface chemistry shape community composition. Genome-resolved metagenomics after 4 and 8 weeks of cultivation identified dominant members including Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum, and Thermoplasmatales archaea, with abundance trends linked to mineralogy and to surface-attached versus planktonic lifestyles. Many bacteria carried plasmids encoding metal resistance, sulphur metabolism, and CRISPR-Cas loci, with evidence of intra-plasmid competition via CRISPR spacers on an Acidithiobacillus plasmid targeting plasmid-borne conjugal transfer genes. Dairy_Wastewater_Algal_Cyanobacterial_Cultivation_Panel Dairy Wastewater Algal-Cyanobacterial Cultivation Panel BIOREMEDIATION ENGINEERED 4 NOT_APPLICABLE A bounded non-sterile laboratory panel that compared mono-, co-, and sequential cultures of the screened phototrophs Chlorella sorokiniana, Euglena gracilis, Synechocystis sp., and Desertifilum tharense during dairy-wastewater treatment. The 12-day experiment grew four monocultures, four 1:1 dry-weight co-cultures, and four sequential cyanobacterium/microalga cultures in 50% diluted raw dairy wastewater in 500 mL bottles with 250 mL working volume. Samples were fractionated into phycosphere-attached and free-living bacteria for V3-V4 16S rRNA MiSeq profiling, with raw sequence data deposited under NCBI BioProject PRJNA1265442. This is a panel record: the four named taxa were assayed across the treatment bottles rather than all co-occurring in every bottle, and indigenous dairy-wastewater bacteria were intentionally retained by non-sterile sample handling. DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom DCPP DBS4-DCP-4-DCP-11d Degradation SynCom BIOREMEDIATION ENGINEERED 3 NOT_APPLICABLE A metabolic-model-selected three-strain synthetic community composed of Sphingopyxis sp. DBS4, Sphingopyxis sp. DCP-4, and Achromobacter sp. DCP-11d. Lin et al. built genome-scale metabolic models from five DCPP-enrichment isolates, simulated 15 DBS4-containing two- to five-strain combinations, selected DBS4&DCP-4&DCP-11d as the optimal three-member DCPP degrader, and experimentally verified its DCPP removal and predicted metabolite exchange in mineral medium and DCPP-contaminated soil. +Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium DIET ENGINEERED 2 PRIMARY IRON Anaerobic deep-sea whale-fall sediment microbial consortium and reconstituted defined co-culture enriched in potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. SHE mimicking iron-reducing conditions. Primary chitin-degrading Vallitalea sp. hydrolyzes insoluble crystalline chitin and ferments oligomers to soluble intermediates (N-acetylglucosamine, glucose, acetate) that are cross-fed to iron-reducing, electrogenic Trichloromonas sp. performing extracellular electron transfer (EET) to electrodes or iron oxides. Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession Deepwater Horizon Deep-Sea Oil Plume Succession BIOREMEDIATION PERTURBED 5 NOT_APPLICABLE A natural, perturbed deep-sea hydrocarbon-plume microbial community that developed during the 2010 Deepwater Horizon blowout in the Gulf of Mexico. The plume selected indigenous hydrocarbon-degrading Gammaproteobacteria, with early enrichment of Oceanospirillales-like petroleum degraders followed by Colwellia, Cycloclasticus, methylotrophic bacteria, and other taxa with non-redundant hydrocarbon degradation capacities. Defined_Multispecies_Enamel_Caries_Model Defined Multispecies Enamel Caries Model ORAL ENGINEERED 4 NOT_APPLICABLE A defined four-member oral biofilm model for in vitro enamel caries development, composed of Lactobacillus casei, Streptococcus mutans, Streptococcus salivarius, and Streptococcus sanguinis on salivary-pellicle-coated enamel slabs. The system was used to quantify how sucrose, fluoride, and calcium shift biofilm growth and enamel demineralization. Defined_ThreeStrain_Organic_Nitrogen_Nitrifying_Community Defined Three-Strain Organic-Nitrogen Nitrifying Community BIOTECHNOLOGY ENGINEERED 3 NOT_APPLICABLE A simplified synthetic nitrifying microbial community pairing Bacillus badius NBRC 15713 with Nitrosomonas europaea NBRC 14298 and Nitrobacter winogradskyi NBRC 14297 for sequential ammonification and nitrification under organic nitrogen conditions. The co-culture achieved complete ammonification and nitrification under selected organic nitrogen conditions, accumulated approximately 56 mg-N/L nitrate-nitrogen with no residual nitrite-nitrogen, and yielded RT-qPCR profiles linking N. europaea and N. winogradskyi abundance changes to inorganic nitrogen concentrations during cultivation. @@ -134,6 +142,7 @@ Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture Dehalococcoides-Des Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture Dehalococcoides-Methanosarcina DMB-Guided Cobalamin Coculture BIOREMEDIATION ENGINEERED 2 INCIDENTAL A defined two-member chlorinated-ethene bioremediation coculture pairing Dehalococcoides mccartyi strain BAV1 with Methanosarcina barkeri strain Fusaro. D. mccartyi BAV1 is corrinoid auxotrophic and requires a cobalamin-type cofactor for organohalide respiration. M. barkeri Fusaro produces extracellular factor III, which did not by itself support Dehalococcoides reductive dechlorination activity, but addition of 5,6-dimethylbenzimidazole enabled guided biosynthesis of cobalamin that supported Dehalococcoides activity and growth. The system is relevant to DOE chlorinated-solvent groundwater bioremediation because it resolves a cofactor-mediated interaction controlling reductive dechlorination. Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture Dehalococcoides-Pelobacter Acetylene TCE Coculture BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A defined anaerobic laboratory coculture in which the acetylene-fermenting bacterium historically reported as Pelobacter strain SFB93 is paired with Dehalococcoides mccartyi strain 195 to sustain reductive dechlorination of trichloroethene when acetylene is provided as electron donor and carbon source. The system is relevant to chlorinated-solvent groundwater bioremediation because acetylene can be generated during abiotic TCE degradation and can inhibit dechlorination at high concentrations. Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture BIOREMEDIATION STABLE 2 NOT_APPLICABLE A defined two-member anaerobic syntrophic coculture in which Dehalococcoides mccartyi strain 195 reductively dechlorinates trichloroethene while Syntrophomonas wolfei ferments butyrate or crotonate-derived carbon to provide hydrogen and acetate. The system is relevant to chlorinated-solvent groundwater bioremediation because it models interspecies hydrogen transfer and metabolite exchange that support TCE dechlorination by Dehalococcoides-containing communities. +Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE Catalyst-free, light-driven defined bacterial co-culture pairing the light-responsive electroactive bio-photosensitizer bacterium Delftia acidovorans YP-3 with hydrogen-producing and nitrate-reducing Klebsiella oxytoca DX-3 for simultaneous wastewater nitrogen removal and biohydrogen recovery. Through direct contact and soluble redox-active mediators that lower electron-transfer resistance and stimulate NADH metabolism, the YP-3/DX-3 co-culture generates 345.52 mL/L H2 in 48 h and achieves 90.25% nitrate removal with minimal nitrite accumulation in synthetic swine wastewater. Shewanella_Anammox_Delta_nrfA_Nitrite_Coupled_Consortium Delta nrfA Shewanella-Anammox Nitrite Coupled Consortium BIOTECHNOLOGY ENGINEERED 3 NOT_APPLICABLE Engineered anaerobic batch-culture consortium pairing activated anammox sludge from a full-scale municipal wastewater process with an nrfA-deficient Shewanella oneidensis MR-1 mutant. The Delta nrfA strain was inoculated into nitrate- and ammonium-containing mixed medium with sludge from an up-flow anaerobic sludge blanket reactor; blocking the terminal nitrite-to-ammonium DNRA step favored nitrite accumulation, enriched Candidatus Brocadia anammox bacteria, and made the 5:1 anammox-sludge-to-mutant culture the fastest and highest total-nitrogen removal treatment at 97%. Desert_Tomato_Salt_Stress_SynCom5 Desert-Derived Tomato Salt Stress SynCom5 RHIZOSPHERE ENGINEERED 5 NOT_APPLICABLE A five-member desert-root bacterial SynCom that protects tomato plants from high salt stress in non-sterile soil. Desulfovibrio_Methanococcus_Syntrophy Desulfovibrio-Methanococcus Syntrophic Consortium SYNTROPHY STABLE 2 SIGNIFICANT IRON A syntrophic, obligate two-member anaerobic consortium consisting of Desulfovibrio vulgaris Hildenborough, which oxidizes lactate to acetate, H2, and CO2 in the absence of sulfate, and Methanococcus maripaludis S2, a hydrogenotrophic methanogen. D. vulgaris can reduce sulfate when available, but in sulfate-free environments it must grow syntrophically by coupling lactate oxidation to interspecies hydrogen transfer. M. maripaludis consumes the H2 and CO2 produced by D. vulgaris to produce methane, maintaining the low H2 partial pressure thermodynamically required for continued lactate oxidation. This syntrophic relationship is fundamental to understanding microbial metabolism in sulfate-depleted anaerobic environments and represents a classic model system for studying syntrophic electron transfer mechanisms. @@ -183,6 +192,7 @@ Glutamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom Glutamicibacter S11 Aqua Grassland_Soil_WetUp_Virus_Host_Community Grassland Soil Wet-Up Virus-Host Community CARBON_SEQUESTRATION PERTURBED 2 NOT_APPLICABLE A grassland soil virus-host community whose dynamics were measured following rewetting of a seasonally dry California Mediterranean-climate soil. Dry soil holds a diverse but low-biomass reservoir of virions, of which only a subset thrives following wet-up. Quantitative isotope tracing, time-resolved metagenomics, and viromics show viral richness declines by 50 percent within 24 hours post wet-up while viral biomass increases four-fold within one week. Lytic, not lysogenic, cycles dominate the response. Viruses drive a measurable and continuous rate of cell lysis, accounting for up to 46 percent of microbial death one week after wet-up, contributing to microbial biomass turnover and the widely reported post-wet-up CO2 efflux. Groundwater_Elusimicrobia_Diverse_Metabolisms Groundwater Elusimicrobia Diverse Metabolisms Community EXTREME_ENVIRONMENT STABLE 2 NOT_APPLICABLE A genomic survey of 94 draft-quality, non-redundant Elusimicrobia genomes (30 newly reconstructed) from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 previously lacking reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, oxygen- or nitrate/nitrite-dependent respiration, degradation of a variety of organic compounds, and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis using hydrogen and carbon dioxide. Two groundwater-associated clades often encode a new nitrogenase paralog co-occurring with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. Similar genomic loci occur in Gracilibacteria and Myxococcales genomes and are predicted to reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated clades nest within free-living clades, supporting an evolutionary trajectory from free-living to animal-associated lifestyles via genome reduction. GOM_Oil_Degrading_Consortium Gulf of Mexico Oil-Degrading Consortium BIOREMEDIATION STABLE 4 SIGNIFICANT A marine bacterial consortium from the Gulf of Mexico designed for bioremediation of oil-contaminated seawater. The consortium consists of four bacteria: Pseudomonas sp., Halopseudomonas aestusnigri GOM5, Paenarthrobacter sp. GOM3, and Alcanivorax sp. Together, they achieve 62% oil removal over 75 days, degrading both n-alkanes and 12 polyaromatic hydrocarbons (PAHs) including fluorene, dibenzothiophene, phenanthrenes, and pyrene. The consortium exhibits stable population dynamics with distributed metabolic loads across members. +Halobacillus_Black_Gram_Halophilic_PGPR_Consortium Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance RHIZOSPHERE ENGINEERED 2 NOT_APPLICABLE Compatible three-strain halophilic plant growth-promoting bacterial (HPGPB) consortium comprising Halobacillus marinus MKM3, Halobacillus halophilus MKM4, and Halobacillus halophilus MKM11 applied to black gram (Vigna mungo L. varieties VBN8 and VBN11) under 50 and 100 mM NaCl stress. The consortium improves ionic balance, reduces Na+ accumulation and lipid peroxidation, enhances antioxidant enzyme activities, and increases grain yield by up to 38% under saline greenhouse conditions. HAMBI_Carbon_Gradient_SynCom16 HAMBI Carbon-Gradient 16-species SynCom OTHER ENGINEERED 16 NOT_APPLICABLE A 16-species HAMBI synthetic bacterial community serially transferred for 16 days in a fully factorial panel of 96 glucose/R2A resource environments spanning eight total-carbon concentrations and 12 levels of R2A-derived carbon. The experiment tested how total carbon availability and resource complexity structure community-state shifts, with Aeromonas caviae, Pseudomonas chlororaphis, and Citrobacter koseri dominating low-, intermediate-, and high-carbon states. Hanford_300_Area_Unconfined_Aquifer_Community Hanford 300 Area Unconfined Aquifer Community BIOREMEDIATION PERTURBED 4 SIGNIFICANT URANIUM A natural, contaminant-impacted groundwater microbial community from the Hanford Site 300 Area Integrated Field Research Challenge site in eastern Washington. 16S rRNA gene pyrosequencing of groundwater bacteria and archaea across three well clusters and multiple depths showed strong temporal and spatial community dynamics linked to Columbia River water intrusion, depth, nitrate, uranium, and redox conditions. The community includes Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, OP3, low-abundance archaea, and functional guilds such as putative methane oxidizers, sulfur oxidizers, ammonia-oxidizing archaea, and metal reducers. hCom2_Complex_Gut_Microbiome hCom2 Complex Gut Microbiome OTHER ENGINEERED 1 NOT_APPLICABLE A complex defined human gut microbiome assembled from hCom1 and iteratively augmented after fecal challenge to improve stability and colonization resistance in gnotobiotic mice. @@ -193,6 +203,7 @@ Honeybee_Core20_Defined_Microbiota Honeybee Core-20 Defined Microbiota OTHER ENG Horonobe_Mizunami_URL_Subsurface_Microbiome Horonobe and Mizunami Underground Research Laboratory Subsurface Microbiome EXTREME_ENVIRONMENT STABLE 2 NOT_APPLICABLE A multi-year, depth-resolved groundwater microbiome study of the Horonobe (sedimentary rock) and Mizunami (granitic rock) Underground Research Laboratories in Japan, sampling defined intervals between 140 and 400 m below the surface over four years. Draft genomes were reconstructed for more than 90 percent of all detected organisms. The Horonobe and Mizunami microbiomes are dissimilar at the community level, but hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds, and sulfate reduction are well represented in both, while methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and tunnel proximity select for candidate phyla radiation bacteria in the Mizunami URL. Approximately one third of genomically defined organisms have near-identical genotypes at multiple depths within Horonobe, and closely-related species recur in three other USA subsurface environments, constraining expectations of global subsurface biodiversity. Hualgayoc_Acidic_Sulfate_Reducing_AMD_Consortium Hualgayoc Acidic Sulfate-Reducing AMD Consortium AMD ENGINEERED 2 PRIMARY IRON;ZINC An engineered acidophilic sulfate-reducing bacterial enrichment derived from acidic sediments of the abandoned BSA-100 mining tunnel in Hualgayoc, Cajamarca, Peru, and assayed for bioremediation of synthetic acid mine drainage at pH 2.9. The glycerol-fed, sulfate-amended enrichment raised the synthetic AMD pH to 6.1 and removed 100% of Zn2+, more than 99% of Fe2+, and more than 94% of Al3+ after 160-200 days. Genome-resolved metagenomics recovered two high-quality dominant sulfate-reducing MAGs, Desulfosporosinus sp. MAG003 and Acididesulfobacillus sp. MAG013, whose inferred carbon metabolisms suggest a cooperative route in which Desulfosporosinus starts sulfate reduction on glycerol at pH around 3.0 and Acididesulfobacillus continues sulfate reduction on acetate once the culture rises to pH around 4.0. Human_Gut_FourMember_Proteome_Complementarity_Consortium Human Gut Four-Member Proteome-Complementarity Consortium DIET ENGINEERED 4 NOT_APPLICABLE A defined four-member consortium of metabolically distinct human gut anaerobes — Eubacterium hallii, Roseburia intestinalis, Marvinbryantia formatexigens and Faecalibacterium prausnitzii — assembled in all pairwise combinations and as the full community, on distinct carbon sources, and profiled by species-resolved proteomics. The finding is regulatory rather than compositional: bacteria modulate protein abundance in response to specific partners, and those partner-specific shifts reduce functional overlap between members and are frequently associated with increased community productivity. Biotic interactions, not the carbon source, dominated proteomic variation. The record captures a community whose members divide labour by changing what they express in each other's presence, so metabolic complementarity is an outcome of regulation rather than a fixed property of the members. +Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction BIOREMEDIATION ENGINEERED 4 PRIMARY Four-strain core endophytic synthetic bacterial community (SynCom-NS)—composed of Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi (Ochrobactrum anthropi) SaOA1, and Novosphingobium lindaniclasticum SaNL1 originally isolated from the hyperaccumulator Sedum alfredii—applied to the high-biomass crop Brassica juncea under cadmium stress. SynCom-NS increases soil Cd bioavailability, upregulates root HMA4 metal transporter expression and glutathione-mediated antioxidant defenses, increases plant fresh weight by 82%, and amplifies shoot Cd accumulation 4.07-fold. Iberian_Pit_Lake_Stratified_Community Iberian Pit Lake Stratified Community AMD STABLE 8 PRIMARY COPPER;IRON;ZINC A permanently stratified (meromictic) acidic pit lake community from the Iberian Pyrite Belt in southwestern Spain/Portugal, distinguished by dramatic vertical metabolic zonation and subsurface anaerobic processes in an extreme acid mine drainage environment. The pit lake ecosystem exhibits three distinct layers: an upper oxic mixolimnion (pH 2.2-3.1, 0-3m depth), a chemocline transition zone (11m), and an anoxic monimolimnion (pH 3.0-4.5, 35m depth). The upper layer is dominated by acidophilic green algae (Coccomyxa onubensis) and heterotrophic bacteria (Acidiphilium), while the chemocline hosts intense sulfate reduction and iron cycling by specialized Proteobacteria (Desulfomonile, Candidatus Acidulodesulfobacterium). The deep anoxic layer harbors archaeal heterotrophs (Thermoplasmatales, 46% of sequences) that scavenge organic carbon and perform sulfide oxidation using trace oxygen, along with iron-reducing bacteria (Geobacter) and subsurface methanogens (Methanobrevibacter, Methanospirillum). The permanent stratification creates steep geochemical gradients with iron concentrations increasing from 2 mM Fe³⁺ in surface waters to 113 mM Fe²⁺ at depth, sulfate ranging from 26-126 mM, and oxygen transitioning from oxic to completely anoxic conditions. This system represents a natural laboratory for studying coupled aerobic-anaerobic metabolism, metal cycling, biosulfidogenesis, and subsurface methanogenesis under polyextreme conditions (acidity, metals, anoxia). The Iberian Pyrite Belt pit lakes demonstrate how microbial stratification can support complex biogeochemical cycling and potential natural attenuation of toxic metals through sulfide precipitation. Industrial_Bioreactor_Consortium Industrial Bioleaching Reactor Consortium BIOMINING ENGINEERED 8 PRIMARY COPPER;IRON An industrial-scale moderately thermophilic acidophilic microbial consortium operating in continuous and batch bioreactors for metal extraction from sulfide ores and concentrates. This consortium represents a unique system with complete genomic characterization of six key organisms: Acidiplasma sp., Acidithiobacillus caldus, Cuniculiplasma divulgatum, Ferroplasma acidiphilum, Ferroplasma sp., and Thermoplasmatales archaeon. The community operates at moderate thermophilic temperatures (40-50°C) and extremely low pH (1.5-2.0), oxidizing ferrous iron and reduced sulfur compounds to generate ferric iron (Fe³⁺) and sulfuric acid for dissolving chalcopyrite (CuFeS₂) and other metal sulfides. Comparative analysis across reactor modes reveals distinct population dynamics, with Acidithiobacillus caldus predominating early, Sulfobacillus acidophilus predominating in the middle stage, and Ferroplasma thermophilum accounting for the greatest proportion in the final stage. The adapted consortium achieves exceptional copper extraction of 60.4% from 20% pulp density chalcopyrite concentrate in 25 days. Operating under controlled carbon sources (CO₂, molasses) and temperature gradients (40-50°C), this system demonstrates how operational parameters shape microbial community structure and metal recovery efficiency. The availability of six complete reference genomes (PRJNA976529) enables genomic-level investigation of biooxidation mechanisms, making this the most comprehensively characterized industrial bioleaching consortium for biotechnological applications in extractive metallurgy. Industrial_Milk_Line_FourSpecies_Model_Biofilm Industrial Milk-Line Four-Species Model Biofilm BIOTECHNOLOGY ENGINEERED 4 NOT_APPLICABLE A laboratory four-species bacterial biofilm model derived from an industrial milk pasteurization-line biofilm. The community contains Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus, forms reproducible biofilms, and was used to resolve dynamic positive and negative interspecies interactions, including a Bacillus cereus thiocillin I-mediated negative interaction that shapes species distribution and robustness. @@ -320,6 +331,7 @@ Pseudonitzschia_Sulfitobacter_Association Pseudo-nitzschia-Sulfitobacter Marine Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom Pseudomonas aeruginosa Eight-Strain Full-Factorial SynCom BIOTECHNOLOGY ENGINEERED 8 NOT_APPLICABLE A full-factorial synthetic community panel built from eight Pseudomonas aeruginosa mutants: pAOV, PA14, NfxB, ParR-CAZ, mexZ, OrfN, NfxB-CAZ, and MDR6-CAZ. Diaz-Colunga et al. assembled all 256 strain combinations in LB medium in 96-well plates, measured post-growth absorbance spectra after 40 h at 37 C, and identified the three-member 00001101 consortium containing strains 1, 3, and 4 as the highest-Abs600 combination. Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE 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. Pseudomonas_stutzeri_Rhodococcus_Naphthalene_Biochar_Engineered_Consortium Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE 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 >98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks. +Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium BIOREMEDIATION ENGINEERED 3 NOT_APPLICABLE Defined 1:1:1 synthetic bacterial consortium composed of Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 isolated from long-term prometryn-contaminated cornfield soil in Harbin, China. The consortium synergistically degrades the methylthio-s-triazine herbicide prometryn (96.87% removal in 12 h in liquid culture and 96.3% removal over 30 days in soil microcosms) and alleviates prometryn phytotoxicity in maize (Zea mays). Pseudomonas_Acidovorax_Aniline_Degradation_SynCom Pseudomonas-Acidovorax Aniline-Degradation SynCom BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A two-member Pseudomonas sp./Acidovorax sp. synthetic microbial consortium, RF-PH, assembled from the aniline-degrading strains RF and PH isolated from heavily aniline-contaminated soil in a Dalian chemical industrial park. Pan et al. 2026 identified Pseudomonas and Acidovorax isolates by 16S rRNA sequencing, optimized their inoculation ratio in mineral-salts medium containing aniline, and designated a 3:1 RF:PH mixture as RF-PH after the consortium outperformed either monoculture in aniline shake-flask assays. Pseudomonas_Bacillus_Waxy_Oil_Biodegradation_Consortium Pseudomonas-Bacillus Waxy Oil Biodegradation Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A defined two-member consortium of Pseudomonas aeruginosa PA12 and Bacillus subtilis G1 engineered to biodegrade waxy crude oil. Bacillus improves access to the oil-water interface and supplies metabolic precursors, while Pseudomonas performs deeper oxidation of long-chain alkanes and aromatics. Pseudomonas_Klebsiella_Alcaligenes_FeII_Nitrogen_Removal_SynCom Pseudomonas-Klebsiella-Alcaligenes Fe2+ Nitrogen-Removal SynCom BIOTECHNOLOGY ENGINEERED 3 SIGNIFICANT IRON A defined three-member synthetic bacterial consortium composed of the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. for Fe2+-regulated deep nitrogen removal. The 2026 Environmental Research abstract reports that the Fe2+ treatment increased nitrate-N removal efficiency by 20-30% relative to other iron species and that metagenomic analysis associated Fe2+ with a shift in carbon and nitrogen metabolic networks, including higher dissimilatory nitrate reduction to ammonium pathway abundance and lower denitrification pathway abundance. @@ -336,6 +348,7 @@ RH1_Glyphosate_Streptomyces_Consortium RH1 Glyphosate Streptomyces Consortium BI Rhizorhabdus_Cupriavidus_BDE47_Degradation_SynCom Rhizorhabdus-Cupriavidus BDE-47 Degradation SynCom BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE A defined aerobic two-isolate synthetic consortium pairing Rhizorhabdus wittichii YL-JM2C with the chloroaromatic-degrading strain reported as Cupriavidus necator JMP134 for 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) degradation. YL-JM2C uses the dioxygenase TcsAaAb to initiate BDE-47 conversion to 2,4-dibromophenol and 3,5-dibromocatechol; JMP134 hydroxylates the YL-JM2C dead-end 2,4-dibromophenol intermediate to 3,5-dibromocatechol, which can then enter an ortho-cleavage pathway in either strain. The bottom-up consortium removed BDE-47 from minimal salts medium and real wastewater microcosms. Rhodococcus_Acinetobacter_RAMC_Mixed_Plastic_Upcycling_SynCom Rhodococcus-Acinetobacter RAMC Mixed Plastic Upcycling SynCom BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE A bottom-up, two-member synthetic bacterial consortium, termed RAMC, that couples Rhodococcus jostii strain PET aromatic-carboxylate metabolism with Acinetobacter baylyi ADP1 aliphatic-carboxylate metabolism to consume oxygenated products from post-consumer mixed plastic deconstruction. The platform was optimized across SR:SA starting ratios of 9:1 through 1:9, completely consumed aromatic plus aliphatic model oxygenates that neither monoculture fully depleted, and supported an engineered RAMC-P_9/1 derivative that converted real mixed-plastic effluents into lycopene and microbial lipids. Rhodococcus_Pseudomonas_PPOW_Consortium Rhodococcus-Pseudomonas Plastic Pyrolysis Oil Waste Consortium BIOREMEDIATION ENGINEERED 3 NOT_APPLICABLE A defined three-member synthetic bacterial consortium composed of Rhodococcus opacus DSM 43250, Pseudomonas putida KT2440, and Pseudomonas sp. VLB120 for aerobic degradation of CARBOLIQ-derived plastic pyrolysis oil waste in a 2-nonanone organic-aqueous biphasic system. The consortium was rationally assembled to couple long-chain alkane degradation with aromatic-catabolism and solvent-tolerance functions, and its highest measured activity used an initial R. opacus:P. putida:VLB120 ratio of 1:1:2 at 30 C, 1:5 organic-to-aqueous phase ratio, and 20% v/v PPOW in the organic phase. +Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture SYNTROPHY ENGINEERED 2 INCIDENTAL IRON Defined synthetic bacterial coculture pairing phototrophic nitrogen-fixing Rhodopseudomonas palustris CGA676 with fermentative Escherichia coli PFM2 in an obligate bidirectional carbon-and-nitrogen cross-feeding relationship evolved for 650-800 generations alongside matched monocultures. Beyond engineered carbon (organic acids from glucose fermentation) and nitrogen (ammonium from N2 fixation) exchange, the coculture engages in additional cross-feeding of adenine and iron that represses biosynthesis and scavenging gene expression in the recipient and limits rather than promotes emergent metabolic dependencies. Rhodopseudomonas_Ecoli_CrossFeeding_Coculture Rhodopseudomonas-E. coli Cross-Feeding Coculture BIOTECHNOLOGY ENGINEERED 2 NOT_APPLICABLE A reciprocal cross-feeding coculture pairing N2-fixing Rhodopseudomonas palustris with fermentative Escherichia coli. Rhodopseudomonas_Geobacter_Magnetite_Redox_Coculture Rhodopseudomonas-Geobacter Magnetite Redox Coculture METAL_REDUCTION ENGINEERED 2 PRIMARY IRON A defined laboratory coculture in which the phototrophic Fe(II)-oxidizing bacterium Rhodopseudomonas palustris TIE-1 and the anaerobic Fe(III)-reducing bacterium Geobacter sulfurreducens cycle electrons through magnetite. The system demonstrates that mixed-valence magnetite can act as a recyclable electron donor and electron acceptor, effectively functioning as a naturally occurring biogeochemical battery under changing light and redox conditions. This community is DOE-relevant because mineral-mediated electron flow shapes subsurface elemental cycling and can influence contaminant fate in sediments, aquifers, and engineered remediation settings. Rice_Acid_Soil_Bioinoculant_SynCom Rice Acid Soil Bioinoculant SynCom RHIZOSPHERE ENGINEERED 1 NOT_APPLICABLE A customized rhizosphere-competent bacterial SynCom used as a bioinoculant to improve rice production in acid soils. @@ -432,6 +445,7 @@ Tomato_Oxylipin_SynCom3 Tomato Oxylipin-Protective SynCom3 RHIZOSPHERE ENGINEERE Tribromophenol_Anaerobic_Bioremediation_SynCom Tribromophenol Anaerobic Bioremediation SynCom BIOREMEDIATION ENGINEERED 3 NOT_APPLICABLE A synthetic anaerobic community with Clostridium, Dehalobacter, and Desulfatiglans functions for 2,4,6-tribromophenol mineralization. Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture Trichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture SYNTROPHY ENGINEERED 3 NOT_APPLICABLE A defined anaerobic three-member coculture in which fermentative Trichococcus flocculiformis strain ES5 stimulates the syntrophic butyrate-oxidizing partnership between Syntrophomonas wolfei and Methanospirillum hungatei. The system extends the classic two-member fatty-acid syntrophy model by adding a fermentative bacterium that increases butyrate consumption and methane production and aggregates with the syntrophic partners. It is relevant to DOE anaerobic carbon cycling, wastewater treatment bioreactors, and engineered methanogenic consortia. Trichoderma_Lactate_Platform Trichoderma Lactate Platform for SCFA Production LIGNOCELLULOSE ENGINEERED 3 INCIDENTAL A heterogeneous 3-member consortium for direct conversion of lignocellulose to short-chain fatty acids (SCFAs), specifically butyric acid. The platform consists of Trichoderma reesei Rut-C30 (aerobic fungus producing cellulases), Lactobacillus pentosus (facultative anaerobic lactic acid bacterium), and Clostridium tyrobutyricum (obligate anaerobic butyrate producer). Sequential inoculation creates an oxygen gradient allowing coexistence of all members. T. reesei degrades cellulose to sugars, LAB converts sugars to lactate and creates anaerobic conditions, and C. tyrobutyricum ferments lactate to butyrate, achieving 196 kg butyric acid per metric ton of beechwood. +Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium BIOREMEDIATION ENGINEERED 2 NOT_APPLICABLE Cross-kingdom fungal-bacterial synthetic consortium pairing the atrazine-degrading fungus Trichoderma lentiforme HN154 with rhizosphere Burkholderia isolates (strains Bur-4, Bur-5, and Bur-14) to remediate atrazine-contaminated corn-soybean rotation soil and protect soybean (Glycine max) from residual phytotoxicity. Trichoderma lentiforme HN154 transforms atrazine into hydroxyatrazine and biuret intermediates that stimulate Burkholderia chemotaxis, swarming, and swimming motility; cross-feeding on these intermediates harnesses bacterial atzB, atzC, atzE, and atzF catabolic enzymes to achieve 86.3% atrazine degradation within 168 h while boosting soybean SOD, POD, and CAT antioxidant defenses. Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture Trichoderma-E. coli Cellulosic Isobutanol Coculture LIGNOCELLULOSE ENGINEERED 2 NOT_APPLICABLE A synthetic fungal-bacterial consortium designed for direct conversion of cellulosic biomass to isobutanol. The community divides labor between Trichoderma reesei, which secretes cellulases that hydrolyze lignocellulosic biomass into soluble saccharides, and Escherichia coli, which metabolizes those saccharides into the target biofuel product. The study demonstrated conversion of microcrystalline cellulose and pretreated corn stover to isobutanol, making the system relevant to DOE lignocellulosic biofuel and consolidated bioprocessing goals. Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture Trichoderma-Streptomyces Filamentous Cellulose Coculture LIGNOCELLULOSE ENGINEERED 2 NOT_APPLICABLE A synthetic filamentous coculture pairing the cellulolytic fungus Trichoderma reesei RUT-C30 with the noncellulolytic bacterium Streptomyces coelicolor A3(2). The coculture was designed to use cellulose as the carbon source, making S. coelicolor dependent on hydrolysate sugars released by T. reesei cellulases. The system is DOE-relevant as a controllable model for lignocellulose-oriented coculture bioprocessing, where population dynamics, cellulase formation, and secondary-metabolite/pigment production can be tuned through inoculation ratio and abiotic process parameters. Trichodesmium_Alteromonas_Marine_Consortium Trichodesmium-Alteromonas Marine Consortium PHYTOPLANKTON STABLE 3 SIGNIFICANT IRON A marine cyanobacterial colony consortium centered on the nitrogen-fixing photoautotroph Trichodesmium erythraeum IMS101 and conserved heterotrophic partners, especially Alteromonas macleodii. Multi-omics studies support recurring Trichodesmium-associated bacterial consortia in cultures and natural colonies, with potential interactions involving iron and phosphorus acquisition, vitamin B12 exchange, small-carbon compound catabolism, reactive oxygen detoxification, and coordinated diel resource cycling. @@ -442,6 +456,7 @@ Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm Variovorax-Cryptococcus Vita Viili_Fungus_Bacterium_EPS_SynCom Viili Fungus-Bacterium EPS SynCom BIOTECHNOLOGY ENGINEERED 3 NOT_APPLICABLE A top-down three-strain synthetic microbial consortium from Viili fermented milk, composed of Lactococcus lactis V9, Lacticaseibacillus paracasei V21, and Geotrichum candidum Y1. Hu et al. 2026 used monoculture, co-culture, supernatant-supplementation, metabolomics, amino-acid depletion, amino-acid supplementation, and AI-2 perturbation assays to show that G. candidum supplies lactic-acid bacteria with nitrogen sources including valine, increases AI-2/luxS quorum-sensing activity, and gives the three-member community the highest measured exopolysaccharide concentration among the tested microbial combinations. Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community Waste-Sludge Electro-Fermentation Biofilm-Suspension Community BIOREMEDIATION ENGINEERED 5 NOT_APPLICABLE An engineered waste-activated-sludge electro-fermentation community with spatially differentiated electrode-biofilm and planktonic fractions. The source reports biofilm-associated reductive debromination of 4-bromophenol and suspension-associated acidogenesis for volatile-fatty-acid recovery. The five genera recorded here are enriched functional examples, not an exhaustive inventory of the sludge community. Watermelon_Rhizosphere_Fusarium_SynCom8 Watermelon Rhizosphere Fusarium-Protective SynCom8 RHIZOSPHERE ENGINEERED 2 NOT_APPLICABLE A simplified eight-member watermelon rhizosphere SynCom derived from an initial 16-member grafted-watermelon core community. +Wetland_Lindane_Degrading_Organochlorine_Consortium Wetland Lindane-Degrading Organochlorine Bacterial Consortium BIOREMEDIATION ENGINEERED 5 NOT_APPLICABLE Functional anaerobic organochlorine-degrading bacterial consortia (top-down consortium M and bottom-up consortium Y13) constructed around generalist non-obligate organochlorine-degrading Enterococcus strains (Enterococcus casseliflavus PseS3, R1, R3, R12) alongside organohalide-respiring and fermentative partners (Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) for gamma-hexachlorocyclohexane (lindane) bioremediation in coastal wetland sediment microcosms while suppressing CO2-reduction methanogenesis. Wetland_Oxygen_Sulfate_GHG_Microcosm_Community Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community METHANOGENESIS PERTURBED 3 NOT_APPLICABLE Freshwater wetland soil microbial microcosms incubated under anoxic non-sulfate, anoxic sulfate-addition, oxic non-sulfate, and oxic sulfate-addition conditions to resolve how climate-linked oxygen and sulfate exposures alter methane and carbon dioxide emissions. The study integrated geochemical measurements, proteogenomics, metaproteomics, and stoichiometric modeling to identify altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Sulfate exposure reduced methane production, oxygen shifted greenhouse gas emissions from CH4 toward CO2, and the combined exposure resembled oxygen exposure alone. Wheat_CrownRot_SixStrain_CrossKingdom_SMC Wheat Crown-Rot Six-Strain Cross-Kingdom SMC RHIZOSPHERE ENGINEERED 6 NOT_APPLICABLE A six-strain cross-kingdom wheat-rhizosphere synthetic microbial community that combined Trichoderma harzianum T19, Bacillus subtilis BS-Z15, Bacillus spizizenii PM9, Bacillus rugosus PM16, Bacillus rugosus S32, and Bacillus halotolerans S8 for nonsterile-soil wheat pot assays against Fusarium pseudograminearum Fusarium crown rot. Zhou et al. 2026 assembled the SMC from antagonistic, growth-promoting, and auxiliary wheat-rhizosphere isolates and compared sterile-water, Fusarium-only, SMC-only, and SMC-plus-Fusarium treatments for plant growth, disease severity, resident rhizosphere amplicon profiles, co-occurrence networks, and rhizosphere metabolomics. Wheat_CrownRot_TB_CrossKingdom_SynCom Wheat Crown-Rot TB Cross-Kingdom SynCom RHIZOSPHERE ENGINEERED 2 NOT_APPLICABLE A minimal two-member cross-kingdom wheat-rhizosphere SynCom, named TB by Zhou et al. 2026, that mixed Trichoderma harzianum T19 with Bacillus rugosus PM16 and was soil-drenched onto Fusarium-pseudograminearum-challenged Triticum aestivum cv. Hechun 213 seedlings. The controlled tissue-culture-chamber pot experiment tested sterile-water, Fusarium-only, SynCom-only, and Fusarium-plus-SynCom treatments in non-sterile topsoil; after 45 days the authors scored wheat crown rot, profiled rhizosphere 16S/ITS communities, and measured rhizosphere metabolites. diff --git a/docs/communities/Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom.html b/docs/communities/Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom.html new file mode 100644 index 000000000..f6ddab991 --- /dev/null +++ b/docs/communities/Bacillus_Aspergillus_Green_Waste_Vermicomposting_SynCom.html @@ -0,0 +1,1355 @@ + + + + + + Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom - CommunityMech + + + +
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+
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+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
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Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom

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+ +
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+ Community ID + + CommunityMech:000473 + +
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+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + compost +
+ + ENVO:00002170 + + · HabitatMech ↗ + +
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Synthetic lignocellulose-degrading cross-kingdom microbial consortium (SynCom) composed of Bacillus licheniformis, Bacillus subtilis, Aspergillus nidulans, and Aspergillus rugulosus applied at 5% inoculation during earthworm (Eisenia fetida) co-vermicomposting of high-lignin green waste and cattle manure. The SynCom stimulates lignocellulolytic enzyme and urease activities, enriches carbohydrate esterases, glycosyltransferases, and nitrification gene hao, reduces the C/N ratio, and increases humic substance and nitrate nitrogen content.

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Taxonomy

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TaxonOntology IDFunctional RolesAbundance
+ Bacillus licheniformis + + + NCBITaxon:1402 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "The SynCom was constructed using the three strains isolated in this study together with one laboratory-preserved strain, comprising two bacterial species ( Bacillus licheniformis and Bacillus subtilis ) and two fungal species ( Aspergillus nidulans and Aspergillus rugulosus )."
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    • + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "Finally, three culturable strains with no antagonistic activity against the laboratory-preserved lignin-modifying fungus Aspergillus nidulans were selected ( Yu et al., 2018 ): Bacillus licheniformis and Bacillus subtilis , which exhibited cellulase, LiP, or MnP activities, and Aspergillus rugulosus , which exhibited cellulase and Lac activities."
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    • + +
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+ Bacillus subtilis + + + NCBITaxon:1423 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "The SynCom was constructed using the three strains isolated in this study together with one laboratory-preserved strain, comprising two bacterial species ( Bacillus licheniformis and Bacillus subtilis ) and two fungal species ( Aspergillus nidulans and Aspergillus rugulosus )."
    + +
    • + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "Finally, three culturable strains with no antagonistic activity against the laboratory-preserved lignin-modifying fungus Aspergillus nidulans were selected ( Yu et al., 2018 ): Bacillus licheniformis and Bacillus subtilis , which exhibited cellulase, LiP, or MnP activities, and Aspergillus rugulosus , which exhibited cellulase and Lac activities."
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    • + +
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+ Aspergillus nidulans + + + NCBITaxon:162425 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "The SynCom was constructed using the three strains isolated in this study together with one laboratory-preserved strain, comprising two bacterial species ( Bacillus licheniformis and Bacillus subtilis ) and two fungal species ( Aspergillus nidulans and Aspergillus rugulosus )."
    + +
    • + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "Finally, three culturable strains with no antagonistic activity against the laboratory-preserved lignin-modifying fungus Aspergillus nidulans were selected ( Yu et al., 2018 ): Bacillus licheniformis and Bacillus subtilis , which exhibited cellulase, LiP, or MnP activities, and Aspergillus rugulosus , which exhibited cellulase and Lac activities."
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    • + +
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+ Aspergillus rugulosus + + + NCBITaxon:41736 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + +
+ + 		DOMINANT
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    + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "The SynCom was constructed using the three strains isolated in this study together with one laboratory-preserved strain, comprising two bacterial species ( Bacillus licheniformis and Bacillus subtilis ) and two fungal species ( Aspergillus nidulans and Aspergillus rugulosus )."
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    • + +
  • + + PMID:42780861 + + - SUPPORT (IN_VITRO) + +
    "Finally, three culturable strains with no antagonistic activity against the laboratory-preserved lignin-modifying fungus Aspergillus nidulans were selected ( Yu et al., 2018 ): Bacillus licheniformis and Bacillus subtilis , which exhibited cellulase, LiP, or MnP activities, and Aspergillus rugulosus , which exhibited cellulase and Lac activities."
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Ecological Interactions

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The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

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+ + Ecological interaction network for Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
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+ Syntrophy +
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Cross-Kingdom Fungal-Bacterial Lignocellulose Hydrolysis and Humification

+ SYNTROPHY +
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The four-species cross-kingdom SynCom (Bacillus licheniformis, Bacillus subtilis, Aspergillus nidulans, and Aspergillus rugulosus) stimulates lignocellulose-degrading enzyme and urease activities during green waste co-vermicomposting, reducing the C/N ratio and increasing humic substance content.

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Metabolites: + + lignocellulose + (CHEBI:180683 + · MediaIngredientMech + · CMMMech) + +

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Biological Processes:

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Evidence

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  • +
    + + PMID:42780861 + + - SUPPORT (IN_VITRO) +
    + +
    "Compared with other treatments, 5% SynComs showed the strongest stimulatory effect on lignocellulose-degrading enzyme and urease activities, effectively reduced the C/N ratio, and increased the germination index, humic substance content, nitrate nitrogen content, and overall quality score."
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Coordinated Carbohydrate Esterase Enrichment and Nitrification Enhancement

+ SYNTROPHY +
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Inoculation of the four-species cross-kingdom SynCom enriches carbohydrate esterases, glycosyltransferases, and the nitrification gene hao in the vermicomposting microbiome, enhancing lignocellulose degradation product transformation and nitrate accumulation.

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Metabolites: + + nitrate + (CHEBI:17632 + · MediaIngredientMech + · CMMMech) + +

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Biological Processes:

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Evidence

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  • +
    + + PMID:42780861 + + - SUPPORT (IN_VITRO) +
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    "SynComs further increased the abundances of carbohydrate esterases and glycosyltransferases, as well as the relative abundance of the nitrification gene hao, thereby enhancing the potential for lignocellulose degradation, degradation product transformation, and nitrification."
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Cross-Mech Suite Links

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Explore related entities across the CultureBotAI X-Mech knowledge bases:

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+ + + HabitatMech: compost ↗ + + + + + + TaxonMech: Bacillus licheniformis ↗ + + + TraitMech: Bacillus licheniformis ↗ + + + + TaxonMech: Bacillus subtilis ↗ + + + TraitMech: Bacillus subtilis ↗ + + + + TaxonMech: Aspergillus nidulans ↗ + + + TraitMech: Aspergillus nidulans ↗ + + + + TaxonMech: Aspergillus rugulosus ↗ + + + TraitMech: Aspergillus rugulosus ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7.html b/docs/communities/Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7.html new file mode 100644 index 000000000..a30b93759 --- /dev/null +++ b/docs/communities/Bacillus_Pseudomonas_Chili_Root_Rot_Antagonistic_SynCom_T7.html @@ -0,0 +1,1151 @@ + + + + + + Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot - CommunityMech + + + +
+
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+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
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Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot

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+ Community ID + + CommunityMech:000483 + +
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+ Ecological State + + + ENGINEERED + + +
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+ Environment + + rhizosphere +
+ + ENVO:00005801 + + · HabitatMech ↗ + +
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Synthetic bacterial community (T7 SynCom) constructed from core antagonistic rhizosphere biomarker isolates of Bacillus and Pseudomonas depleted during prolonged continuous cropping of chili pepper (Capsicum annuum). T7 SynCom directly antagonizes the root rot pathogen Fusarium solani, reduces chili root rot incidence, and induces systemic plant resistance by activating MAPK, ethylene, jasmonic acid, and salicylic acid immune signaling pathways.

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Taxonomy

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TaxonOntology IDFunctional RolesAbundance
+ Bacillus — ontology label: Bacillus <firmicutes> + + + NCBITaxon:1386 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
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    + +
  • + + PMID:42693392 + + - SUPPORT (IN_VIVO) + +
    "LEfSe analysis showed that Bacillus and Pseudomonas were the core bacterial biomarkers in chili continuous cropping soil, which were successfully isolated and demonstrated significant antagonistic effects against Fusarium solani."
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+ Pseudomonas + + + NCBITaxon:286 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42693392 + + - SUPPORT (IN_VIVO) + +
    "LEfSe analysis showed that Bacillus and Pseudomonas were the core bacterial biomarkers in chili continuous cropping soil, which were successfully isolated and demonstrated significant antagonistic effects against Fusarium solani."
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Ecological Interactions

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The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

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+ + Ecological interaction network for Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism. + +
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+ Mutualism +
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Cooperative Bacillus-Pseudomonas Suppression of Fusarium solani and Chili Immune Activation

+ MUTUALISM +
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Bacillus and Pseudomonas strains in T7 SynCom cooperate to antagonize the root rot pathogen Fusarium solani and activate MAPK, ethylene, jasmonic acid, and salicylic acid immune signaling pathways in Capsicum annuum to suppress root rot.

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Source Taxon: Bacillus

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Target Taxon: Pseudomonas

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Biological Processes:

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Evidence

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  • +
    + + PMID:42693392 + + - SUPPORT (IN_VIVO) +
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    "Among them, the T7 SynCom exhibited excellent biocontrol efficacy."
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  • +
    + + PMID:42693392 + + - SUPPORT (IN_VIVO) +
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    "It effectively suppressed the pathogen, reduced the incidence of root rot, and enhanced systemic induced resistance by activating the plant immune-associated pathways, including the MAPK signaling pathway, ethylene signaling pathway, and pathways mediated by jasmonic acid and salicylic acid."
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Environmental Factors

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FactorValueUnit
Continuous Cropping Monoculture RegimeProlonged continuous cropping of Capsicum annuumN/A
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  • + + PMID:42693392 + + - SUPPORT (IN_VIVO) + +
    "High-throughput sequencing analysis indicated a marked increase in the abundance of Fusarium pathogens, accompanied by a significant decline in antagonistic bacteria from the genera Bacillus and Pseudomonas."
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Cross-Mech Suite Links

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Explore related entities across the CultureBotAI X-Mech knowledge bases:

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+ + + HabitatMech: rhizosphere ↗ + + + + + + TaxonMech: Bacillus ↗ + + + TraitMech: Bacillus ↗ + + + + TaxonMech: Pseudomonas ↗ + + + TraitMech: Pseudomonas ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture.html b/docs/communities/Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture.html new file mode 100644 index 000000000..21395315e --- /dev/null +++ b/docs/communities/Bifidobacterium_Bacillus_Alginate_Biofilm_Probiotic_Coculture.html @@ -0,0 +1,1124 @@ + + + + + + Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture - CommunityMech + + + +
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Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture

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+ Community ID + + CommunityMech:000478 + +
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+ Environment + + laboratory environment +
+ + ENVO:01001405 + + · HabitatMech ↗ + +
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Engineered probiotic co-culture of oxygen-sensitive anaerobic Bifidobacterium longum DSM20219 and biofilm-forming Bacillus subtilis SOM8 co-encapsulated in sodium alginate hydrogel beads. Bacillus subtilis SOM8 promotes interspecies cell aggregation, extracellular polymeric matrix development, and biofilm formation within the alginate matrix, enhancing B. longum DSM20219 survival by ~3-log CFU/g (>7-log CFU/g) in simulated gastric and intestinal fluids and maintaining >6-log CFU/g over 28 days of aerobic storage.

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Taxonomy

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TaxonOntology IDFunctional RolesAbundance
+ Bacillus subtilis + + + NCBITaxon:1423 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
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  • + + PMID:42372892 + + - SUPPORT (IN_VITRO) + +
    "Here, we developed an alginate-based, biofilm-assisted encapsulation system for the co-culture and co-delivery of Bacillus subtilis SOM8 and Bifidobacterium longum DSM20219."
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+ Bifidobacterium longum + + + NCBITaxon:216816 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
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  • + + PMID:42372892 + + - SUPPORT (IN_VITRO) + +
    "Biofilm-assisted encapsulation improved B. longum DSM20219 viability, maintaining survival above 7-log CFU/g after 2 h in SGF and SIF, representing an approximately 3-log improvement over alginate-only encapsulation."
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Ecological Interactions

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The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

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+ + Ecological interaction network for Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture + Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details. + +
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Biofilm- and Extracellular Matrix-Mediated Stress Protection

+ COMMENSALISM +
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Bacillus subtilis SOM8 and Bifidobacterium longum DSM20219 form a cooperative biofilm and extracellular matrix inside alginate hydrogel beads that shields oxygen-sensitive B. longum from gastric acid, bile salts, and aerobic storage.

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Source Taxon: Bacillus subtilis

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Target Taxon: Bifidobacterium longum

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Biological Processes:

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Evidence

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  • +
    + + PMID:42372892 + + - SUPPORT (IN_VITRO) +
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    "Imaging and time-resolved co-culture analyses suggested that the enhanced protection was associated with biofilm formation, cell aggregation, extracellular matrix development, and dynamic interspecies interactions within the alginate system."
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Environmental Factors

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FactorValueUnit
Simulated Gastrointestinal Fluids and Aerobic Storage2 h in SGF and SIF; 28 days aerobic storageN/A
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  • + + PMID:42372892 + + - SUPPORT (IN_VITRO) + +
    "This strategy enhanced probiotic tolerance to simulated gastric fluids (SGF) and simulated intestinal fluids (SIF), and extended shelf life under aerobic conditions."
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Cross-Mech Suite Links

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Explore related entities across the CultureBotAI X-Mech knowledge bases:

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+ + + HabitatMech: laboratory environment ↗ + + + + + + TaxonMech: Bacillus subtilis ↗ + + + TraitMech: Bacillus subtilis ↗ + + + + TaxonMech: Bifidobacterium longum ↗ + + + TraitMech: Bifidobacterium longum ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom.html b/docs/communities/Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom.html new file mode 100644 index 000000000..2a608d9c5 --- /dev/null +++ b/docs/communities/Black_Soil_Glucose_Activated_Herbicide_Mixture_SynCom.html @@ -0,0 +1,1282 @@ + + + + + + Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000482 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + contaminated soil +
+ + ENVO:00002116 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Simplified four-isolate bacterial synthetic community (SynCom) constructed from keystone taxa—Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter—identified in a natural microbial consortium enriched from herbicide-stressed agricultural black soil in Northeast China. Activated by glucose supplementation that fuels glycolytic and TCA cycle energy supply and environmental acidification, the SynCom co-metabolically degrades a recalcitrant mixture of nicosulfuron (97.27%), mesotrione (68.00%), and atrazine (22.91%) via enriched catabolic genes including atzF (allophanate hydrolase) and gst (glutathione S-transferase).

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Burkholderia + + + NCBITaxon:32008 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41762466 + + - SUPPORT (IN_VITRO) + +
    "Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa."
    + +
    • + +
+
+ Rhodanobacter + + + NCBITaxon:75309 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41762466 + + - SUPPORT (IN_VITRO) + +
    "Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa."
    + +
    • + +
+
+ Achromobacter + + + NCBITaxon:222 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41762466 + + - SUPPORT (IN_VITRO) + +
    "Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
+
+ Taxon +
+
+ Syntrophy +
+
+
+ + +
+
+

Glucose-Driven Co-Metabolic Degradation of Atrazine, Nicosulfuron, and Mesotrione

+ SYNTROPHY +
+

In the presence of glucose, the keystone SynCom taxa (Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter) activate central carbon metabolism (glycolysis and TCA cycle) and express enriched catabolic genes including atzF and gst to co-metabolically degrade mixed nicosulfuron, mesotrione, and atrazine.

+ + + + + + +

Metabolites: + + glucose + (CHEBI:17234 + · MediaIngredientMech + · CMMMech), + + atrazine + (CHEBI:15930 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41762466 + + - SUPPORT (IN_VITRO) +
    + +
    "Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase)."
    + +
    • + +
+ +
+ +
+
+

Synergistic Four-Isolate SynCom Herbicide-Mixture Mineralization

+ SYNTROPHY +
+

The simplified four-isolate SynCom constructed from Burkholderia, Rhodanobacter, and Achromobacter degrades recalcitrant herbicide mixtures more efficiently than either the individual isolates or the parent natural microbial consortium in the glucose-supplemented system.

+ + + + + + +

Metabolites: + + glucose + (CHEBI:17234 + · MediaIngredientMech + · CMMMech) + +

+ + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41762466 + + - SUPPORT (IN_VITRO) +
    + +
    "A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Glucose Co-Substrate Supplementation and Herbicide MixtureGlucose-supplemented mineral salt medium (GSM) with atrazine, nicosulfuron, and mesotrioneN/A
+
    + +
  • + + PMID:41762466 + + - SUPPORT (IN_VITRO) + +
    "Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: contaminated soil ↗ + + + + + + TaxonMech: Burkholderia ↗ + + + TraitMech: Burkholderia ↗ + + + + TaxonMech: Rhodanobacter ↗ + + + TraitMech: Rhodanobacter ↗ + + + + TaxonMech: Achromobacter ↗ + + + TraitMech: Achromobacter ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture.html b/docs/communities/Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture.html new file mode 100644 index 000000000..2fdfca4d6 --- /dev/null +++ b/docs/communities/Clostridium_Acetobutylicum_Ljungdahlii_Isopropanol_Syntrophic_Coculture.html @@ -0,0 +1,1200 @@ + + + + + + Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000480 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + bioreactor +
+ + ENVO:00002123 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

High-cell-density syntrophic bacterial coculture pairing genetically engineered Clostridium acetobutylicum (CACas9 delta-hbd-p95ace02_atoB, lacking 4-C metabolism and overexpressing an acetone-formation pathway) with the acetogen and ketoreductase partner Clostridium ljungdahlii in a 3.6-L perfusion bioreactor. C. acetobutylicum ferments glucose to acetone, CO2, and H2; C. ljungdahlii consumes dissolved H2—relieving the thermodynamic bottleneck of NADH-driven H2 evolution in C. acetobutylicum—and reduces cross-fed acetone to isopropanol at supratheoretical yields in continuous carbon-negative glucose fermentation.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Clostridium acetobutylicum + + + NCBITaxon:1488 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SECONDARY_FERMENTER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41831593 + + - SUPPORT (IN_VITRO) + +
    "CACas9 Δhbd-p95ace02_atoB produces acetone without 4-C metabolites and C. ljungdahlii converts the acetone to isopropanol."
    + +
    • + +
+
+ Clostridium ljungdahlii + + + NCBITaxon:1538 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + + SECONDARY_FERMENTER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41831593 + + - SUPPORT (IN_VITRO) + +
    "To explore the potential of this coculture system to achieve supratheoretical isopropanol yields, we identify NADH-driven hydrogen conversion in CACas9 Δhbd-p95ace02_atoB as the thermodynamically limiting step for acetone production in monocultures and thus isopropanol production in cocultures."
    + +
    • + +
  • + + PMID:41831593 + + - SUPPORT (IN_VITRO) + +
    "We then demonstrate the ability of C. ljungdahlii to mitigate this issue by eliminating detectable hydrogen accumulation in the coculture."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
+
+ Taxon +
+
+ Syntrophy +
+
+
+ + +
+
+

Syntrophic Hydrogen Scavenging and Acetone-to-Isopropanol Cross-Feeding

+ SYNTROPHY +
+

Clostridium acetobutylicum CACas9 delta-hbd-p95ace02_atoB ferments glucose to acetone and H2; Clostridium ljungdahlii scavenges H2 to relieve NADH thermodynamic inhibition of acetone formation and reduces acetone to isopropanol.

+ + +

Source Taxon: Clostridium acetobutylicum

+ + + +

Target Taxon: Clostridium ljungdahlii

+ + + +

Metabolites: + + glucose + (CHEBI:17234 + · MediaIngredientMech + · CMMMech), + + acetone + (CHEBI:15347 + · MediaIngredientMech + · CMMMech), + + dihydrogen + (CHEBI:18276 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41831593 + + - SUPPORT (IN_VITRO) +
    + +
    "CACas9 Δhbd-p95ace02_atoB produces acetone without 4-C metabolites and C. ljungdahlii converts the acetone to isopropanol."
    + +
    • + +
  • +
    + + PMID:41831593 + + - SUPPORT (IN_VITRO) +
    + +
    "We then demonstrate the ability of C. ljungdahlii to mitigate this issue by eliminating detectable hydrogen accumulation in the coculture."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Cell Density and C. ljungdahlii Population Fraction in Perfusion Bioreactor3.6-L continuous perfusion bioreactor with high C. ljungdahlii population fractionN/A
+
    + +
  • + + PMID:41831593 + + - SUPPORT (IN_VITRO) + +
    "Pseudo-perfusion cocultures showed that high cell densities combined with a high population fraction of C. ljungdahlii enable dramatic increases in isopropanol yields beyond the thermodynamic limitation imposed in CACas9 Δhbd-p95ace02_atoB monocultures."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: bioreactor ↗ + + + + + + TaxonMech: Clostridium acetobutylicum ↗ + + + TraitMech: Clostridium acetobutylicum ↗ + + + + TaxonMech: Clostridium ljungdahlii ↗ + + + TraitMech: Clostridium ljungdahlii ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium.html b/docs/communities/Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium.html new file mode 100644 index 000000000..c33a1ff0e --- /dev/null +++ b/docs/communities/Cold_Seep_ANME_SRB_Carbon_Monoxide_Syntrophic_Consortium.html @@ -0,0 +1,1202 @@ + + + + + + Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000475 + +
+ +
+ Ecological State + + + PERTURBED + + +
+ + +
+ Environment + + marine sediment +
+ + ENVO:03000033 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Syntrophic consortium of anaerobic methane-oxidizing archaea (ANME-2b, family Candidatus Methanocomedenaceae / Candidatus Methanomarinus) and sulfate-reducing bacteria (Seep-SRB1g, phylum Thermodesulfobacteriota) from deep-sea methane seep sediments on the Costa Rica margin capable of oxidizing carbon monoxide (CO) in the absence of methane. CO oxidation is coupled syntrophically to dissimilatory sulfate reduction and, under sulfate-free conditions, to CO2 (bicarbonate) reduction to methane by ANME-2b to support cellular maintenance.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Candidatus Methanocomedenaceae + + + NCBITaxon:3386223 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41980960 + + - SUPPORT (IN_VITRO) + +
    "The oxidation of CO was coupled with sulphate-reduction by syntrophic consortia, and, in the absence of sulphate, through CO2 reduction to methane by ANME-2."
    + +
    • + +
+
+ Thermodesulfobacteriota + + + NCBITaxon:200940 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41980960 + + - SUPPORT (IN_VITRO) + +
    "Here, we show that environmental ANME-SRB consortia can oxidize CO in the absence of methane, in anoxic microcosm experiments using a combination of stable isotope geochemical tracers, metatranscriptomics, and single cell activity measurements (FISH-nanoSIMS)."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
+
+ Taxon +
+
+ Syntrophy +
+
+
+ + +
+
+

Syntrophic Carbon Monoxide Oxidation Coupled to Sulfate and Bicarbonate Reduction

+ SYNTROPHY +
+

ANME-2b archaea and Seep-SRB1g sulfate-reducing bacteria oxidize CO to dissolved inorganic carbon (bicarbonate/CO2) coupled to dissimilatory sulfate reduction to hydrogen sulfide via interspecies electron transfer, while ANME-2b also reduces bicarbonate to methane.

+ + +

Source Taxon: Candidatus Methanocomedenaceae

+ + + +

Target Taxon: Thermodesulfobacteriota

+ + + +

Metabolites: + + carbon monoxide + (CHEBI:17245 + · MediaIngredientMech + · CMMMech), + + sulfate + (CHEBI:16189 + · MediaIngredientMech + · CMMMech), + + hydrogencarbonate + (CHEBI:17544 + · MediaIngredientMech + · CMMMech), + + methane + (CHEBI:16183 + · MediaIngredientMech + · CMMMech), + + hydrogen sulfide + (CHEBI:16136 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41980960 + + - SUPPORT (IN_VITRO) +
    + +
    "The oxidation of CO was coupled with sulphate-reduction by syntrophic consortia, and, in the absence of sulphate, through CO2 reduction to methane by ANME-2."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Carbon Monoxide Partial Pressure and Sulfate Availability0.1 to 1.0 bar CO headspace; presence or absence of 5 mM sulfateN/A
+
    + +
  • + + PMID:41980960 + + - SUPPORT (IN_VITRO) + +
    "Carbon monoxide (CO) has been reported in seep environments and represents a thermodynamically favourable alternative electron donor due to its low reduction potential."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: marine sediment ↗ + + + + + + TaxonMech: Candidatus Methanocomedenaceae ↗ + + + TraitMech: Candidatus Methanocomedenaceae ↗ + + + + TaxonMech: Thermodesulfobacteriota ↗ + + + TraitMech: Thermodesulfobacteriota ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom.html b/docs/communities/Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom.html new file mode 100644 index 000000000..2a6adfedc --- /dev/null +++ b/docs/communities/Cucumber_Low_Phosphorus_Cross_Kingdom_Biocontrol_SynCom.html @@ -0,0 +1,1607 @@ + + + + + + Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000477 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + rhizosphere +
+ + ENVO:00005801 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Cross-kingdom synthetic microbial community (13 bacterial and 6 fungal strains) assembled from signature taxa enriched in the low-phosphorus rhizosphere of cucumber (Cucumis sativus): bacterial genera Bacillus, Cupriavidus, Sphingopyxis, and Devosia together with fungal genera Aspergillus and Amesomyces (reported as Amesia). Recruited and sustained by low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the cross-kingdom SynCom engages in mutualistic biofilm and hyphal facilitation and reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85-99%, suppressing cucumber Fusarium wilt even under high-phosphorus conditions.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Bacillus — ontology label: Bacillus <firmicutes> + + + NCBITaxon:1386 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+ Devosia + + + NCBITaxon:46913 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+ Sphingopyxis + + + NCBITaxon:165697 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+ Cupriavidus + + + NCBITaxon:106589 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+ Aspergillus + + + NCBITaxon:5052 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+ Amesomyces + + + NCBITaxon:1934349 + + + · TaxonMech + · TraitMech + + + +
+ + PATHOGEN_ANTAGONIST + + SYNTROPHIC_PARTNER + +
+ + 		ABUNDANT
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Amplicon sequencing analyses reveal that low phosphorus conditions promote microbial community stochastic assembly, enriching beneficial genera (bacterial genera Bacillus, Devosia, Sphingopyxis, Cupriavidus, and fungal genera Aspergillus and Amesia) with dual functions of phosphate solubilization and disease resistance, and enhancing cross-kingdom network robustness."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism, colonization facilitation. + +
+
+ Taxon +
+
+ Mutualism +
+
+ Colonization facilitation +
+
+
+ + +
+
+

Metabolite-Recruited Cross-Kingdom Pathogen Suppression of Fusarium oxysporum

+ MUTUALISM +
+

Combined with low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the 19-strain cross-kingdom SynCom (Bacillus, Devosia, Sphingopyxis, Cupriavidus, Aspergillus, and Amesomyces) reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85% and suppresses cucumber wilt under high-phosphorus conditions.

+ + + + + + +

Metabolites: + + phosphate + (CHEBI:26020 + · MediaIngredientMech + · CMMMech), + + succinic acid + (CHEBI:15741 + · MediaIngredientMech + · CMMMech), + + methionine + (CHEBI:16811 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41882811 + + - SUPPORT (IN_VIVO) +
    + +
    "To validate the functional role of microbes-metabolites interaction, we constructed a synthetic microbial community composed of the signature taxa from the low phosphorus microbiota, which, when combined with low phosphorus metabolites, reduced pathogen abundance by 85% and conferred disease suppression under high phosphorus conditions."
    + +
    • + +
+ +
+ +
+
+

Cross-Kingdom Devosia and Amesomyces Biofilm and Colony Mutualism

+ MUTUALISM +
+

Devosia (strain B2) and Amesomyces (reported as Amesia sp. F7) engage in direct cross-kingdom mutual promotion, concurrently enhancing bacterial biofilm formation and fungal colony diameter in co-culture.

+ + +

Source Taxon: Devosia

+ + + +

Target Taxon: Amesomyces

+ + + + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41882811 + + - SUPPORT (IN_VITRO) +
    + +
    "(i) Mutual promotion (reflected by concurrent enhancement of bacterial biofilm formation and fungal colony diameter) was observed between specific fungal-bacterial pairs, including: Amesia sp. F7 & Devosia sp. B2; Amesia sp. F7 & Bacillus sp. B10; Aspergillus sp. F5 and Bacillus sp. B18."
    + +
    • + +
+ +
+ +
+
+

Unidirectional Cross-Kingdom Facilitation of Cupriavidus by Aspergillus

+ COLONIZATION_FACILITATION +
+

Aspergillus (strains F3 and F5) unidirectionally facilitates the growth and biofilm formation of Cupriavidus (strain B12) in cross-kingdom co-culture assays.

+ + +

Source Taxon: Aspergillus

+ + + +

Target Taxon: Cupriavidus

+ + + + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:41882811 + + - SUPPORT (IN_VITRO) +
    + +
    "(ii) Unidirectional facilitation (where one partner enhanced the growth of the other without a reciprocal benefit) characterized other interactions, including Aspergillus sp. F4 & Bacillus sp. B10; Aspergillus sp. F3 & Cupriavidus sp. B12; Aspergillus sp. F5 & Cupriavidus sp. B12)."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Soil Phosphorus Availability and Low-P Rhizosphere MetabolitesLow phosphorus (500 uM Pi) vs. high phosphorus (2 mM Pi); 100 uM LPDRMsN/A
+
    + +
  • + + PMID:41882811 + + - SUPPORT (IN_VIVO) + +
    "Metabolomics identified low phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine) that recruit beneficial taxa, whereas high phosphorus distinguished rhizosphere metabolites promoted pathogen growth."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: rhizosphere ↗ + + + + + + TaxonMech: Bacillus ↗ + + + TraitMech: Bacillus ↗ + + + + TaxonMech: Devosia ↗ + + + TraitMech: Devosia ↗ + + + + TaxonMech: Sphingopyxis ↗ + + + TraitMech: Sphingopyxis ↗ + + + + TaxonMech: Cupriavidus ↗ + + + TraitMech: Cupriavidus ↗ + + + + TaxonMech: Aspergillus ↗ + + + TraitMech: Aspergillus ↗ + + + + TaxonMech: Amesomyces ↗ + + + TraitMech: Amesomyces ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture.html b/docs/communities/Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture.html new file mode 100644 index 000000000..faf7c431b --- /dev/null +++ b/docs/communities/Delftia_Klebsiella_Light_Driven_Hydrogen_Denitrifying_Coculture.html @@ -0,0 +1,1174 @@ + + + + + + Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000481 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + anaerobic bioreactor +
+ + ENVO:00002124 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Catalyst-free, light-driven defined bacterial co-culture pairing the light-responsive electroactive bio-photosensitizer bacterium Delftia acidovorans YP-3 with hydrogen-producing and nitrate-reducing Klebsiella oxytoca DX-3 for simultaneous wastewater nitrogen removal and biohydrogen recovery. Through direct contact and soluble redox-active mediators that lower electron-transfer resistance and stimulate NADH metabolism, the YP-3/DX-3 co-culture generates 345.52 mL/L H2 in 48 h and achieves 90.25% nitrate removal with minimal nitrite accumulation in synthetic swine wastewater.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Delftia acidovorans + + + NCBITaxon:80866 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42297253 + + - SUPPORT (IN_VITRO) + +
    "Here, a catalyst-free, light-driven co-culture system was developed by pairing the light-responsive electroactive bacterium Delftia acidovorans YP-3 with Klebsiella oxytoca DX-3, a strain that can produce hydrogen and reduce nitrate."
    + +
    • + +
+
+ Klebsiella oxytoca + + + NCBITaxon:571 + + + · TaxonMech + · TraitMech + + + +
+ + ELECTRON_ACCEPTOR + + SECONDARY_FERMENTER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42297253 + + - SUPPORT (IN_VITRO) + +
    "In batch cultures, the YP-3/DX-3 co-culture generated 345.52 mL/L H2 within 48 h and enhanced the removal of nitrate, nitrite, and total nitrogen compared to the DX-3 monoculture."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
+
+ Taxon +
+
+ Syntrophy +
+
+
+ + +
+
+

Light-Driven Interspecies Electron Transfer for Biohydrogen Production and Denitrification

+ SYNTROPHY +
+

Light-responsive electroactive Delftia acidovorans YP-3 transfers electrons via direct cell contact and soluble redox mediators to Klebsiella oxytoca DX-3, enhancing NADH-linked hydrogen production (345.52 mL/L H2) and nitrate/nitrite reduction (90.25% nitrate removal).

+ + +

Source Taxon: Delftia acidovorans

+ + + +

Target Taxon: Klebsiella oxytoca

+ + + +

Metabolites: + + dihydrogen + (CHEBI:18276 + · MediaIngredientMech + · CMMMech), + + nitrate + (CHEBI:17632 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42297253 + + - SUPPORT (IN_VITRO) +
    + +
    "Electrochemical, extracellular polymeric substance, and metabolomic analyses indicated enhanced redox activity, decreased electron-transfer resistance, NADH-related metabolism, and potential interspecies electron transfer via direct contact and soluble redox-active mediators."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Light Illumination and Synthetic Swine Wastewater Nitrate LoadLight-driven catalyst-free regime; synthetic swine wastewaterN/A
+
    + +
  • + + PMID:42297253 + + - SUPPORT (IN_VITRO) + +
    "In a synthetic swine wastewater-fed anaerobic sludge reactor, the co-culture accomplished 90.25 % nitrate removal, minimized nitrite accumulation, and enriched functional groups related to electron transfer, hydrogen production, and nitrogen removal."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: anaerobic bioreactor ↗ + + + + + + TaxonMech: Delftia acidovorans ↗ + + + TraitMech: Delftia acidovorans ↗ + + + + TaxonMech: Klebsiella oxytoca ↗ + + + TraitMech: Klebsiella oxytoca ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium.html b/docs/communities/Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium.html new file mode 100644 index 000000000..adc060e59 --- /dev/null +++ b/docs/communities/Endophytic_SynCom_NS_Brassica_Cadmium_Phytoextraction_Consortium.html @@ -0,0 +1,1415 @@ + + + + + + Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000476 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + contaminated soil +
+ + ENVO:00002116 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Four-strain core endophytic synthetic bacterial community (SynCom-NS)—composed of Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi (Ochrobactrum anthropi) SaOA1, and Novosphingobium lindaniclasticum SaNL1 originally isolated from the hyperaccumulator Sedum alfredii—applied to the high-biomass crop Brassica juncea under cadmium stress. SynCom-NS increases soil Cd bioavailability, upregulates root HMA4 metal transporter expression and glutathione-mediated antioxidant defenses, increases plant fresh weight by 82%, and amplifies shoot Cd accumulation 4.07-fold.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Pseudomonas izuensis + + + NCBITaxon:2684212 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42043130 + + - SUPPORT (IN_VIVO) + +
    "The SynCom-NS consortium, comprising four specific core endophytic bacterial strains Leifsonia shinshuensis , Novosphingobium lindaniclasticum , Ochrobactrum anthropi , and Pseudomonas izuensis , was prepared for inoculation ( Table 1 )"
    + +
    • + +
  • + + PMID:42043130 + + - SUPPORT (IN_VITRO) + +
    "Strain ID Genus and Species ACC Deaminase IAA Production (μg/mL) Cd Resistance (mM) SaPI1 Pseudomonas izuensis + 55.1 4.0 SaLS1 Leifsonia shinshuensis + 150.0 0.5 SaOA1 Ochrobactrum anthropi − 64.2 0.6 SaNL1 Novosphingobium lindaniclasticum − 53.9 2.0"
    + +
    • + +
+
+ Leifsonia shinshuensis + + + NCBITaxon:150026 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42043130 + + - SUPPORT (IN_VIVO) + +
    "The SynCom-NS consortium, comprising four specific core endophytic bacterial strains Leifsonia shinshuensis , Novosphingobium lindaniclasticum , Ochrobactrum anthropi , and Pseudomonas izuensis , was prepared for inoculation ( Table 1 )"
    + +
    • + +
  • + + PMID:42043130 + + - SUPPORT (IN_VITRO) + +
    "Strain ID Genus and Species ACC Deaminase IAA Production (μg/mL) Cd Resistance (mM) SaPI1 Pseudomonas izuensis + 55.1 4.0 SaLS1 Leifsonia shinshuensis + 150.0 0.5 SaOA1 Ochrobactrum anthropi − 64.2 0.6 SaNL1 Novosphingobium lindaniclasticum − 53.9 2.0"
    + +
    • + +
+
+ Brucella anthropi + + + NCBITaxon:529 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42043130 + + - SUPPORT (IN_VIVO) + +
    "The SynCom-NS consortium, comprising four specific core endophytic bacterial strains Leifsonia shinshuensis , Novosphingobium lindaniclasticum , Ochrobactrum anthropi , and Pseudomonas izuensis , was prepared for inoculation ( Table 1 )"
    + +
    • + +
  • + + PMID:42043130 + + - SUPPORT (IN_VITRO) + +
    "Strain ID Genus and Species ACC Deaminase IAA Production (μg/mL) Cd Resistance (mM) SaPI1 Pseudomonas izuensis + 55.1 4.0 SaLS1 Leifsonia shinshuensis + 150.0 0.5 SaOA1 Ochrobactrum anthropi − 64.2 0.6 SaNL1 Novosphingobium lindaniclasticum − 53.9 2.0"
    + +
    • + +
+
+ Novosphingobium lindaniclasticum + + + NCBITaxon:1329895 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42043130 + + - SUPPORT (IN_VIVO) + +
    "The SynCom-NS consortium, comprising four specific core endophytic bacterial strains Leifsonia shinshuensis , Novosphingobium lindaniclasticum , Ochrobactrum anthropi , and Pseudomonas izuensis , was prepared for inoculation ( Table 1 )"
    + +
    • + +
  • + + PMID:42043130 + + - SUPPORT (IN_VITRO) + +
    "Strain ID Genus and Species ACC Deaminase IAA Production (μg/mL) Cd Resistance (mM) SaPI1 Pseudomonas izuensis + 55.1 4.0 SaLS1 Leifsonia shinshuensis + 150.0 0.5 SaOA1 Ochrobactrum anthropi − 64.2 0.6 SaNL1 Novosphingobium lindaniclasticum − 53.9 2.0"
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism, syntrophy. + +
+
+ Taxon +
+
+ Mutualism +
+
+ Syntrophy +
+
+
+ + +
+
+

Microbiome-Driven Cadmium Mobilization, HMA4 Translocation, and Glutathione Detoxification

+ MUTUALISM +
+

Root-zone application of the four-strain SynCom-NS consortium (Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi SaOA1, and Novosphingobium lindaniclasticum SaNL1) induces a >3-fold surge in host glutathione (GSH) and phenylpropanoid defense pathways to scavenge hydrogen peroxide and alleviate cadmium toxicity in Brassica juncea.

+ + + + + + +

Metabolites: + + cadmium(2+) + (CHEBI:48775 + · MediaIngredientMech + · CMMMech), + + glutathione + (CHEBI:16856 + · MediaIngredientMech + · CMMMech), + + hydrogen peroxide + (CHEBI:16240 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42043130 + + - SUPPORT (IN_VIVO) +
    + +
    "Multi-omics analysis demonstrated a systemic modulation of the host's defense machinery, marked by a >3-fold surge in glutathione (GSH) levels and the induction of phenylpropanoid biosynthesis for cell wall reinforcement."
    + +
    • + +
+ +
+ +
+
+

Synergistic Endophytic HMA4 Regulation and Cadmium Translocation

+ SYNTROPHY +
+

The four-strain SynCom-NS consortium mediates tissue-specific regulation of the heavy metal transporter HMA4—upregulating expression in roots and downregulating in shoots—to accelerate root-to-shoot cadmium(2+) translocation and achieve a 4.07-fold increase in shoot Cd phytoextraction.

+ + + + + + +

Metabolites: + + cadmium(2+) + (CHEBI:48775 + · MediaIngredientMech + · CMMMech) + +

+ + + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42043130 + + - SUPPORT (IN_VIVO) +
    + +
    "SynCom-NS application also mediated tissue-specific regulation of the key metal transporter HMA4, upregulating its expression in roots to accelerate long-distance translocation while downregulating it in shoots."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Soil Cadmium Contamination~1.0 mg/kg soil CdN/A
+
    + +
  • + + PMID:42043130 + + - SUPPORT (IN_VIVO) + +
    "Pot experiments revealed that SynCom-NS root-zone application significantly alleviated Cd toxicity, increasing total fresh weight by 82% and chlorophyll content by 33%."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: contaminated soil ↗ + + + + + + TaxonMech: Pseudomonas izuensis ↗ + + + TraitMech: Pseudomonas izuensis ↗ + + + + TaxonMech: Leifsonia shinshuensis ↗ + + + TraitMech: Leifsonia shinshuensis ↗ + + + + TaxonMech: Brucella anthropi ↗ + + + TraitMech: Brucella anthropi ↗ + + + + TaxonMech: Novosphingobium lindaniclasticum ↗ + + + TraitMech: Novosphingobium lindaniclasticum ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Halobacillus_Black_Gram_Halophilic_PGPR_Consortium.html b/docs/communities/Halobacillus_Black_Gram_Halophilic_PGPR_Consortium.html new file mode 100644 index 000000000..1a168d436 --- /dev/null +++ b/docs/communities/Halobacillus_Black_Gram_Halophilic_PGPR_Consortium.html @@ -0,0 +1,1209 @@ + + + + + + Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000472 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + rhizosphere +
+ + ENVO:00005801 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Compatible three-strain halophilic plant growth-promoting bacterial (HPGPB) consortium comprising Halobacillus marinus MKM3, Halobacillus halophilus MKM4, and Halobacillus halophilus MKM11 applied to black gram (Vigna mungo L. varieties VBN8 and VBN11) under 50 and 100 mM NaCl stress. The consortium improves ionic balance, reduces Na+ accumulation and lipid peroxidation, enhances antioxidant enzyme activities, and increases grain yield by up to 38% under saline greenhouse conditions.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Halobacillus marinus MKM3 — ontology label: Halobacillus marinus + + + NCBITaxon:2699466 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42643757 + + - SUPPORT (IN_VIVO) + +
    "The present study evaluated the efficacy of a compatible multi-strain HPGPB consortium comprising MKM3 (Halobacillus marinus), MKM4 (Halobacillus halophilus), and MKM11 (Halobacillus halophilus) in enhancing salinity tolerance in two black gram varieties (VBN8 and VBN11) under greenhouse conditions."
    + +
    • + +
+
+ Halobacillus halophilus MKM4 and MKM11 — ontology label: Halobacillus halophilus + + + NCBITaxon:1570 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42643757 + + - SUPPORT (IN_VIVO) + +
    "The present study evaluated the efficacy of a compatible multi-strain HPGPB consortium comprising MKM3 (Halobacillus marinus), MKM4 (Halobacillus halophilus), and MKM11 (Halobacillus halophilus) in enhancing salinity tolerance in two black gram varieties (VBN8 and VBN11) under greenhouse conditions."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism. + +
+
+ Taxon +
+
+ Mutualism +
+
+
+ + +
+
+

Synergistic Halobacillus Consortium Colonization and Rhizosphere Microbiome Restructuring

+ MUTUALISM +
+

Compatible co-inoculation of Halobacillus marinus MKM3 with Halobacillus halophilus MKM4 and MKM11 restructures the rhizosphere microbial community of Vigna mungo under 50 and 100 mM NaCl stress.

+ + +

Source Taxon: Halobacillus marinus MKM3

+ + + +

Target Taxon: Halobacillus halophilus MKM4 and MKM11

+ + + + + +

Biological Processes:

+ + + + +
+ Downstream Effects: + +
+ → Alleviation of Sodium Toxicity and Enhancement of Black Gram Growth Under Salt Stress +

DIRECTLY IMPLIED: Consortium establishment in the saline rhizosphere supports reduced Na+ uptake and enhanced antioxidant protection in Vigna mungo.

+
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:42643757 + + - SUPPORT (IN_VIVO) +
    + +
    "Rhizosphere metagenomic analysis revealed consortium-associated shifts in microbial community structure under saline conditions."
    + +
    • + +
+ +
+ +
+
+

Alleviation of Sodium Toxicity and Enhancement of Black Gram Growth Under Salt Stress

+ MUTUALISM +
+

Cooperative Halobacillus halophilus (MKM4, MKM11) and Halobacillus marinus (MKM3) activity reduces Na+ accumulation and lipid peroxidation, boosts antioxidant enzyme activity, and increases Vigna mungo biomass and grain yield under salt stress.

+ + +

Source Taxon: Halobacillus halophilus MKM4 and MKM11

+ + + +

Target Taxon: Halobacillus marinus MKM3

+ + + +

Metabolites: + + sodium(1+) + (CHEBI:29101 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42643757 + + - SUPPORT (IN_VIVO) +
    + +
    "Consortium-inoculated plants exhibited improved photosynthetic performance, enhanced nutrient uptake and ionic balance, reduced Na+ accumulation and malondialdehyde content, and increased activities of antioxidant enzymes, indicating enhanced salinity tolerance."
    + +
    • + +
+ +
+ + +
+ + + + + + + + + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: rhizosphere ↗ + + + + + + TaxonMech: Halobacillus marinus MKM3 ↗ + + + TraitMech: Halobacillus marinus MKM3 ↗ + + + + TaxonMech: Halobacillus halophilus MKM4 and MKM11 ↗ + + + TraitMech: Halobacillus halophilus MKM4 and MKM11 ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium.html b/docs/communities/Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium.html new file mode 100644 index 000000000..5213fbd42 --- /dev/null +++ b/docs/communities/Pseudomonas_Achromobacter_Stenotrophomonas_Prometryn_Degrading_Consortium.html @@ -0,0 +1,1266 @@ + + + + + + Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000470 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + contaminated soil +
+ + ENVO:00002116 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Defined 1:1:1 synthetic bacterial consortium composed of Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 isolated from long-term prometryn-contaminated cornfield soil in Harbin, China. The consortium synergistically degrades the methylthio-s-triazine herbicide prometryn (96.87% removal in 12 h in liquid culture and 96.3% removal over 30 days in soil microcosms) and alleviates prometryn phytotoxicity in maize (Zea mays).

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Pseudomonas sp. ZM-1 — ontology label: Pseudomonas + + + NCBITaxon:286 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42795638 + + - SUPPORT (IN_VITRO) + +
    "three prometryn-degrading bacterial strains were isolated from long-term contaminated cornfield soil in Harbin, China, and identified as Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2 and Stenotrophomonas sp. ZM-3"
    + +
    • + +
+
+ Achromobacter sp. ZM-2 — ontology label: Achromobacter + + + NCBITaxon:222 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42795638 + + - SUPPORT (IN_VITRO) + +
    "three prometryn-degrading bacterial strains were isolated from long-term contaminated cornfield soil in Harbin, China, and identified as Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2 and Stenotrophomonas sp. ZM-3"
    + +
    • + +
+
+ Stenotrophomonas sp. ZM-3 — ontology label: Stenotrophomonas + + + NCBITaxon:40323 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42795638 + + - SUPPORT (IN_VITRO) + +
    "three prometryn-degrading bacterial strains were isolated from long-term contaminated cornfield soil in Harbin, China, and identified as Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2 and Stenotrophomonas sp. ZM-3"
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism, syntrophy. + +
+
+ Taxon +
+
+ Mutualism +
+
+ Syntrophy +
+
+
+ + +
+
+

Cooperative Tri-Strain Degradation of Prometryn Herbicide

+ SYNTROPHY +
+

Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 cooperatively degrade prometryn in a 1:1:1 synthetic consortium, achieving 96.8% removal within 15 h in liquid medium and 96.3% removal in soil microcosms.

+ + +

Source Taxon: Pseudomonas sp. ZM-1

+ + + +

Target Taxon: Achromobacter sp. ZM-2

+ + + + + +

Biological Processes:

+ + + + +
+ Downstream Effects: + +
+ → Alleviation of Prometryn Phytotoxicity and Restoration of Maize Growth +

DIRECTLY IMPLIED: Rapid consortium-mediated prometryn removal in soil reduces herbicide exposure and restores maize growth.

+
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:42795638 + + - SUPPORT (IN_VITRO) +
    + +
    "The 1:1:1 synthetic consortium removed 96.8% of prometryn in 15 h, showing markedly superior degradation efficiency compared with single strains, and its 12-h degradation rate reached 96.87% with a half-life of 2.2 h following response surface optimization."
    + +
    • + +
+ +
+ +
+
+

Alleviation of Prometryn Phytotoxicity and Restoration of Maize Growth

+ MUTUALISM +
+

Cooperative prometryn degradation by Achromobacter sp. ZM-2 and Stenotrophomonas sp. ZM-3 in contaminated soil alleviates herbicide phytotoxicity in maize (Zea mays), restoring plant growth to 95-97% of uncontaminated control levels.

+ + +

Source Taxon: Achromobacter sp. ZM-2

+ + + +

Target Taxon: Stenotrophomonas sp. ZM-3

+ + + + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42795638 + + - SUPPORT (IN_VIVO) +
    + +
    "Maize pot experiments confirmed that the consortium significantly alleviated prometryn phytotoxicity at the tested concentration, restoring plant growth parameters to 95-97% of the uncontaminated control."
    + +
    • + +
+ +
+ + +
+ + + + + + + + + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: contaminated soil ↗ + + + + + + TaxonMech: Pseudomonas sp. ZM-1 ↗ + + + TraitMech: Pseudomonas sp. ZM-1 ↗ + + + + TaxonMech: Achromobacter sp. ZM-2 ↗ + + + TraitMech: Achromobacter sp. ZM-2 ↗ + + + + TaxonMech: Stenotrophomonas sp. ZM-3 ↗ + + + TraitMech: Stenotrophomonas sp. ZM-3 ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture.html b/docs/communities/Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture.html new file mode 100644 index 000000000..e78d2b9fa --- /dev/null +++ b/docs/communities/Rhodopseudomonas_Escherichia_Multilayered_Cross_Feeding_Coculture.html @@ -0,0 +1,1277 @@ + + + + + + Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000469 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + laboratory environment +
+ + ENVO:01001405 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Defined synthetic bacterial coculture pairing phototrophic nitrogen-fixing Rhodopseudomonas palustris CGA676 with fermentative Escherichia coli PFM2 in an obligate bidirectional carbon-and-nitrogen cross-feeding relationship evolved for 650-800 generations alongside matched monocultures. Beyond engineered carbon (organic acids from glucose fermentation) and nitrogen (ammonium from N2 fixation) exchange, the coculture engages in additional cross-feeding of adenine and iron that represses biosynthesis and scavenging gene expression in the recipient and limits rather than promotes emergent metabolic dependencies.

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+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Rhodopseudomonas palustris CGA676 — ontology label: Rhodopseudomonas palustris + + + NCBITaxon:1076 + + + · TaxonMech + · TraitMech + + + +
+ + CROSS_FEEDER + + PRIMARY_PRODUCER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42117636 + + - SUPPORT (IN_VITRO) + +
    "Here, we compared mutations that were differentially enriched in bacterial monocultures versus cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli in an obligate cross-feeding relationship based on the exchange of nitrogen and carbon for 650-800 generations."
    + +
    • + +
+
+ Escherichia coli PFM2 — ontology label: Escherichia coli + + + NCBITaxon:562 + + + · TaxonMech + · TraitMech + + + +
+ + CROSS_FEEDER + + PRIMARY_DEGRADER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42117636 + + - SUPPORT (IN_VITRO) + +
    "Here, we compared mutations that were differentially enriched in bacterial monocultures versus cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli in an obligate cross-feeding relationship based on the exchange of nitrogen and carbon for 650-800 generations."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. + +
+
+ Taxon +
+
+ Cross-feeding +
+
+
+ + +
+
+

Obligate Carbon and Nitrogen Cross-Feeding Between Escherichia coli and Rhodopseudomonas palustris

+ CROSS_FEEDING +
+

Escherichia coli ferments glucose into organic acids that serve as carbon source for Rhodopseudomonas palustris, while R. palustris fixes dinitrogen and excretes ammonium as nitrogen source for E. coli across 650-800 generations.

+ + +

Source Taxon: Rhodopseudomonas palustris CGA676

+ + + +

Target Taxon: Escherichia coli PFM2

+ + + +

Metabolites: + + ammonium + (CHEBI:28938 + · MediaIngredientMech + · CMMMech), + + organic acid + (CHEBI:64709 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + +
+ Downstream Effects: + +
+ → Multilayered Iron and Adenine Cross-Feeding Repressing Recipient Gene Cost +

DIRECTLY IMPLIED: Obligate carbon and nitrogen cross-feeding maintains stable coculture coexistence across 650-800 generations, enabling concurrent iron and adenine cross-feeding.

+
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:42117636 + + - SUPPORT (IN_VITRO) +
    + +
    "Here, we compared mutations that were differentially enriched in bacterial monocultures versus cocultures pairing phototrophic Rhodopseudomonas palustris with fermentative Escherichia coli in an obligate cross-feeding relationship based on the exchange of nitrogen and carbon for 650-800 generations."
    + +
    • + +
+ +
+ +
+
+

Multilayered Iron and Adenine Cross-Feeding Repressing Recipient Gene Cost

+ CROSS_FEEDING +
+

In addition to obligate carbon and nitrogen exchange, R. palustris and E. coli engage in secondary cross-feeding of iron and adenine in coculture, repressing iron scavenging and adenine synthesis gene expression and preventing emergent auxotrophies.

+ + +

Source Taxon: Rhodopseudomonas palustris CGA676

+ + + +

Target Taxon: Escherichia coli PFM2

+ + + +

Metabolites: + + iron cation + (CHEBI:24875 + · MediaIngredientMech + · CMMMech), + + purines + (CHEBI:26401 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42117636 + + - SUPPORT (IN_VITRO) +
    + +
    "Contrary to expectations, the emergence of additional dependencies was observed in monoculture, but not in coculture, even though additional layers of cross-feeding involving iron and adenine were present in coculture."
    + +
    • + +
  • +
    + + PMID:42117636 + + - SUPPORT (IN_VITRO) +
    + +
    "Low expression of iron scavenging and adenine synthesis genes in cocultures suggested that cross-feeding repressed expression, thereby lowering gene cost."
    + +
    • + +
+ +
+ + +
+ + + + + + + + + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: laboratory environment ↗ + + + + + + TaxonMech: Rhodopseudomonas palustris CGA676 ↗ + + + TraitMech: Rhodopseudomonas palustris CGA676 ↗ + + + + TaxonMech: Escherichia coli PFM2 ↗ + + + TraitMech: Escherichia coli PFM2 ↗ + + + + + + CMMMech (Critical Minerals & REE) ↗ + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium.html b/docs/communities/Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium.html new file mode 100644 index 000000000..ef9adf7b4 --- /dev/null +++ b/docs/communities/Trichoderma_Burkholderia_Atrazine_Cross_Feeding_Consortium.html @@ -0,0 +1,1157 @@ + + + + + + Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000479 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + contaminated soil +
+ + ENVO:00002116 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Cross-kingdom fungal-bacterial synthetic consortium pairing the atrazine-degrading fungus Trichoderma lentiforme HN154 with rhizosphere Burkholderia isolates (strains Bur-4, Bur-5, and Bur-14) to remediate atrazine-contaminated corn-soybean rotation soil and protect soybean (Glycine max) from residual phytotoxicity. Trichoderma lentiforme HN154 transforms atrazine into hydroxyatrazine and biuret intermediates that stimulate Burkholderia chemotaxis, swarming, and swimming motility; cross-feeding on these intermediates harnesses bacterial atzB, atzC, atzE, and atzF catabolic enzymes to achieve 86.3% atrazine degradation within 168 h while boosting soybean SOD, POD, and CAT antioxidant defenses.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Trichoderma lentiforme + + + NCBITaxon:1567552 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42372060 + + - SUPPORT (IN_VIVO) + +
    "Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h)."
    + +
    • + +
+
+ Burkholderia + + + NCBITaxon:32008 + + + · TaxonMech + · TraitMech + + + +
+ + SECONDARY_FERMENTER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42372060 + + - SUPPORT (IN_VITRO) + +
    "Among 23 rhizosphere isolates, the Burkholderia strains Bur-4, Bur-5, and Bur-14 showed the highest atrazine degradation rates (26.3% - 29.4%) within 72 h."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. + +
+
+ Taxon +
+
+ Cross-feeding +
+
+
+ + +
+
+

Fungal-to-Bacterial Cross-Feeding of Hydroxyatrazine and Biuret Intermediates

+ CROSS_FEEDING +
+

Trichoderma lentiforme HN154 degrades atrazine into hydroxyatrazine and biuret, which act as chemoattractants and cross-fed substrates for Burkholderia strains (Bur-4, Bur-5, Bur-14) carrying atzB/atzC/atzE/atzF, accelerating complete atrazine mineralization to 86.3% within 168 h and enhancing soybean antioxidant enzymes.

+ + +

Source Taxon: Trichoderma lentiforme

+ + + +

Target Taxon: Burkholderia

+ + + +

Metabolites: + + atrazine + (CHEBI:15930 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42372060 + + - SUPPORT (IN_VIVO) +
    + +
    "Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h)."
    + +
    • + +
  • +
    + + PMID:42372060 + + - SUPPORT (IN_VIVO) +
    + +
    "A Trichoderma-Burkholderia synthetic consortium further enhanced remediation by boosting plant antioxidant defenses (SOD, POD, CAT) and reducing oxidative damage (MDA)."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Soil Atrazine Contamination500 mg/kg atrazine in corn-soybean rotation soilN/A
+
    + +
  • + + PMID:42372060 + + - SUPPORT (IN_VIVO) + +
    "By leveraging the atrazine-degrading fungus Trichoderma lentiforme HN154, we achieved an 80.3% removal of atrazine (500 mg/kg) in non-sterilized soils from a corn planting system within 14 days, 22.1% higher degradation than in sterilized soil, while concurrently alleviating phytotoxic symptoms in soybean plants."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: contaminated soil ↗ + + + + + + TaxonMech: Trichoderma lentiforme ↗ + + + TraitMech: Trichoderma lentiforme ↗ + + + + TaxonMech: Burkholderia ↗ + + + TraitMech: Burkholderia ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Wetland_Lindane_Degrading_Organochlorine_Consortium.html b/docs/communities/Wetland_Lindane_Degrading_Organochlorine_Consortium.html new file mode 100644 index 000000000..22f672dfa --- /dev/null +++ b/docs/communities/Wetland_Lindane_Degrading_Organochlorine_Consortium.html @@ -0,0 +1,1385 @@ + + + + + + Wetland Lindane-Degrading Organochlorine Bacterial Consortium - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Wetland Lindane-Degrading Organochlorine Bacterial Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000471 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + wetland area +
+ + ENVO:00000043 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Functional anaerobic organochlorine-degrading bacterial consortia (top-down consortium M and bottom-up consortium Y13) constructed around generalist non-obligate organochlorine-degrading Enterococcus strains (Enterococcus casseliflavus PseS3, R1, R3, R12) alongside organohalide-respiring and fermentative partners (Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) for gamma-hexachlorocyclohexane (lindane) bioremediation in coastal wetland sediment microcosms while suppressing CO2-reduction methanogenesis.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Enterococcus casseliflavus + + + NCBITaxon:37734 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42663479 + + - SUPPORT (IN_VITRO) + +
    "Specifically, Enterococcus avium ATCC 14025 shared an ANI of 98.03 with PseS3 and 98.21 with bin161. Enterococcus thailandicus DSM 21767 exhibited an ANI of 99.35 with R1, 99.31 with R3, and 99.35 with bin381. Similarly, Enterococcus casseliflavus ATCC 49996 shared an ANI of 98.24 with R12 and 98.24 with bin436."
    + +
    • + +
+
+ Sulfurospirillum multivorans + + + NCBITaxon:66821 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		COMMON
+
    + +
  • + + PMID:42663479 + + - SUPPORT (IN_VITRO) + +
    "The consortium comprised the obligate organohalide-respiring bacterium Dehalococcoides mccartyi , supported by the corrinoid-provisioning strains Geobacter lovleyi and Sulfurospirillum multivorans ( 9 , 18 ), the fermentative supplier Petrimonas sulfuriphila PET ( 22 ), and seven isolated γ-HCH-degrading strains, several of which harbor cobalamin synthesis genes ( 23 )."
    + +
    • + +
+
+ Trichlorobacter lovleyi + + + NCBITaxon:313985 + + + · TaxonMech + · TraitMech + + + +
+ + SYNTROPHIC_PARTNER + +
+ + 		COMMON
+
    + +
  • + + PMID:42663479 + + - SUPPORT (IN_VITRO) + +
    "The consortium comprised the obligate organohalide-respiring bacterium Dehalococcoides mccartyi , supported by the corrinoid-provisioning strains Geobacter lovleyi and Sulfurospirillum multivorans ( 9 , 18 ), the fermentative supplier Petrimonas sulfuriphila PET ( 22 ), and seven isolated γ-HCH-degrading strains, several of which harbor cobalamin synthesis genes ( 23 )."
    + +
    • + +
+
+ Petrimonas sulfuriphila + + + NCBITaxon:285070 + + + · TaxonMech + · TraitMech + + + +
+ + SECONDARY_FERMENTER + + SYNTROPHIC_PARTNER + +
+ + 		COMMON
+
    + +
  • + + PMID:42663479 + + - SUPPORT (IN_VITRO) + +
    "The consortium comprised the obligate organohalide-respiring bacterium Dehalococcoides mccartyi , supported by the corrinoid-provisioning strains Geobacter lovleyi and Sulfurospirillum multivorans ( 9 , 18 ), the fermentative supplier Petrimonas sulfuriphila PET ( 22 ), and seven isolated γ-HCH-degrading strains, several of which harbor cobalamin synthesis genes ( 23 )."
    + +
    • + +
+
+ Dehalococcoides mccartyi + + + NCBITaxon:61435 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SYNTROPHIC_PARTNER + +
+ + 		COMMON
+
    + +
  • + + PMID:42663479 + + - SUPPORT (IN_VITRO) + +
    "The consortium comprised the obligate organohalide-respiring bacterium Dehalococcoides mccartyi , supported by the corrinoid-provisioning strains Geobacter lovleyi and Sulfurospirillum multivorans ( 9 , 18 ), the fermentative supplier Petrimonas sulfuriphila PET ( 22 ), and seven isolated γ-HCH-degrading strains, several of which harbor cobalamin synthesis genes ( 23 )."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Wetland Lindane-Degrading Organochlorine Bacterial Consortium + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy. + +
+
+ Taxon +
+
+ Syntrophy +
+
+
+ + +
+
+

Cooperative Organochlorine Dechlorination of Gamma-Hexachlorocyclohexane

+ SYNTROPHY +
+

Inoculated organochlorine-degrading consortia (comprising Enterococcus casseliflavus, Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) cooperatively dechlorinate gamma-hexachlorocyclohexane (lindane) in anoxic wetland sediment microcosms.

+ + + + + + + + +

Biological Processes:

+ + + + +
+ Downstream Effects: + +
+ → Suppression of Carbon Dioxide Reduction Methanogenesis During Lindane Bioremediation +

DIRECTLY IMPLIED: Bioaugmentation with the organochlorine-degrading consortia redirects electron flow toward reductive dechlorination and suppresses CO2-reduction methanogenesis.

+
+ +
+ + + +

Evidence

+
    + +
  • +
    + + PMID:42663479 + + - SUPPORT (IN_VITRO) +
    + +
    "Both consortia demonstrated efficient degradation in sediment microcosms, reducing γ-HCH (C/C₀) to 63.0% (M) and 56.1% (Y13)."
    + +
    • + +
+ +
+ +
+
+

Suppression of Carbon Dioxide Reduction Methanogenesis During Lindane Bioremediation

+ SYNTROPHY +
+

Inoculation of the functional organochlorine-degrading consortia into anoxic wetland sediment microcosms redirects electron flow toward reductive dechlorination and significantly suppresses the CO2-reduction methanogenesis pathway, lowering the CH4/CO2 ratio.

+ + + + + + +

Metabolites: + + methane + (CHEBI:16183 + · MediaIngredientMech + · CMMMech), + + carbon dioxide + (CHEBI:16526 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42663479 + + - SUPPORT (IN_VITRO) +
    + +
    "Simultaneously, functional microbial consortia inoculation significantly suppressed the CO₂ reduction methanogenesis pathway compared with the non-inoculated group (P < 0.05), as evidenced by a marked decline in the CH₄/CO₂ ratio in inoculated groups."
    + +
    • + +
+ +
+ + +
+ + + + + + + + + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: wetland area ↗ + + + + + + TaxonMech: Enterococcus casseliflavus ↗ + + + TraitMech: Enterococcus casseliflavus ↗ + + + + TaxonMech: Sulfurospirillum multivorans ↗ + + + TraitMech: Sulfurospirillum multivorans ↗ + + + + TaxonMech: Trichlorobacter lovleyi ↗ + + + TraitMech: Trichlorobacter lovleyi ↗ + + + + TaxonMech: Petrimonas sulfuriphila ↗ + + + TraitMech: Petrimonas sulfuriphila ↗ + + + + TaxonMech: Dehalococcoides mccartyi ↗ + + + TraitMech: Dehalococcoides mccartyi ↗ + + + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/communities/Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium.html b/docs/communities/Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium.html new file mode 100644 index 000000000..a0758b5d8 --- /dev/null +++ b/docs/communities/Whale_Fall_Vallitalea_Trichloromonas_Chitin_EET_Consortium.html @@ -0,0 +1,1201 @@ + + + + + + Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium - CommunityMech + + + +
+
+
+
+ Home + ← Back to Communities + Text Map + Taxonomic UMAP + Sequence Map + Network + Schema + All Mech projects +
+ +
+

Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium

+
+
+ +
+ +
+
+
+ Community ID + + CommunityMech:000474 + +
+ +
+ Ecological State + + + ENGINEERED + + +
+ + +
+ Environment + + marine sediment +
+ + ENVO:03000033 + + · HabitatMech ↗ + +
+ + +
+
+ + + +
+

Anaerobic deep-sea whale-fall sediment microbial consortium and reconstituted defined co-culture enriched in potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. SHE mimicking iron-reducing conditions. Primary chitin-degrading Vallitalea sp. hydrolyzes insoluble crystalline chitin and ferments oligomers to soluble intermediates (N-acetylglucosamine, glucose, acetate) that are cross-fed to iron-reducing, electrogenic Trichloromonas sp. performing extracellular electron transfer (EET) to electrodes or iron oxides.

+
+ + + + +
+

Taxonomy

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
TaxonOntology IDFunctional RolesAbundance
+ Vallitalea + + + NCBITaxon:1348611 + + + · TaxonMech + · TraitMech + + + +
+ + PRIMARY_DEGRADER + + SECONDARY_FERMENTER + + CROSS_FEEDER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42297039 + + - SUPPORT (IN_VITRO) + +
    "We isolated a chitin-degrading Vallitalea sp. and an iron-reducing, electrogenic Trichloromonas sp., and demonstrated that, when reconstituted in co-culture, they cooperatively degrade chitin via acetate cross-feeding coupled to EET."
    + +
    • + +
+
+ Trichloromonas + + + NCBITaxon:3031666 + + + · TaxonMech + · TraitMech + + + +
+ + SECONDARY_FERMENTER + + SYNTROPHIC_PARTNER + +
+ + 		DOMINANT
+
    + +
  • + + PMID:42297039 + + - SUPPORT (IN_VITRO) + +
    "We isolated a chitin-degrading Vallitalea sp. and an iron-reducing, electrogenic Trichloromonas sp., and demonstrated that, when reconstituted in co-culture, they cooperatively degrade chitin via acetate cross-feeding coupled to EET."
    + +
    • + +
+
+
+
+ +
+

Ecological Interactions

+ + +

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

+ +
+
+ + Ecological interaction network for Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium + Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding. + +
+
+ Taxon +
+
+ Cross-feeding +
+
+
+ + +
+
+

Anaerobic Chitin Hydrolysis and Acetate Cross-Feeding to Electrogenic Respiration

+ CROSS_FEEDING +
+

Vallitalea sp. hydrolyzes insoluble chitin via extracellular chitinases and ferments monomers into acetate, which is cross-fed to electrode- and iron-respiring Trichloromonas sp. to drive anodic current generation and Fe(III) reduction.

+ + +

Source Taxon: Vallitalea

+ + + +

Target Taxon: Trichloromonas

+ + + +

Metabolites: + + chitin + (CHEBI:17029 + · MediaIngredientMech + · CMMMech), + + glucose + (CHEBI:17234 + · MediaIngredientMech + · CMMMech), + + acetate + (CHEBI:30089 + · MediaIngredientMech + · CMMMech), + + iron(3+) + (CHEBI:29034 + · MediaIngredientMech + · CMMMech) + +

+ + + +

Biological Processes:

+ + + + + + +

Evidence

+
    + +
  • +
    + + PMID:42297039 + + - SUPPORT (IN_VITRO) +
    + +
    "We isolated a chitin-degrading Vallitalea sp. and an iron-reducing, electrogenic Trichloromonas sp., and demonstrated that, when reconstituted in co-culture, they cooperatively degrade chitin via acetate cross-feeding coupled to EET."
    + +
    • + +
+ +
+ + +
+ + + + + + + + +
+

Environmental Factors

+
+ + + + + + + + + + + + + + + + + + + + + + +
FactorValueUnit
Crystalline Chitin and Poised Anode (+0.22 V vs. SHE)0.01 g/mL colloidal chitin; +0.22 V vs. SHE poised carbon cloth electrodeN/A
+
    + +
  • + + PMID:42297039 + + - SUPPORT (IN_VITRO) + +
    "Here, we used potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. Standard Hydrogen Electrode, mimicking iron-reducing conditions, to enrich and characterize a chitin-degrading, metal-reducing microbial community from an anoxic deep-sea whale-fall sediment."
    + +
    • + +
+
+
+
+ + + + + + +
+

Cross-Mech Suite Links

+

Explore related entities across the CultureBotAI X-Mech knowledge bases:

+
+ + + HabitatMech: marine sediment ↗ + + + + + + TaxonMech: Vallitalea ↗ + + + TraitMech: Vallitalea ↗ + + + + TaxonMech: Trichloromonas ↗ + + + TraitMech: Trichloromonas ↗ + + + + + + CMMMech (Critical Minerals & REE) ↗ + + + + CultureMech Growth Media ↗ + + + PathwayMech Pathways ↗ + +
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/docs/index.html b/docs/index.html index 623416384..ce47c37a9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -110,11 +110,11 @@

CommunityMech

Microbial community knowledge base — curated, evidence-backed interaction networks.

- 458communities + 473communities 16categories 384-Dtext embeddings 512-Dv3 embeddings @@ -150,7 +150,7 @@

LinkML Schema

Browser index (JS) ↓

Downloads & bulk data

-

Download the full 458-community dataset as structured JSON or tabular TSV, or inspect individual YAML records in kb/communities/.

+

Download the full 473-community dataset as structured JSON or tabular TSV, or inspect individual YAML records in kb/communities/.

View on GitHub →
@@ -167,7 +167,7 @@

GitHub

kg-microbe·METPO
-

Provenance: Schema https://w3id.org/communitymech · Source corpus: kb/communities/ (458 records) · License: BSD-3-Clause

+

Provenance: Schema https://w3id.org/communitymech · Source corpus: kb/communities/ (473 records) · License: BSD-3-Clause

diff --git a/docs/schema.html b/docs/schema.html index 63c0fc689..e454d6d42 100644 --- a/docs/schema.html +++ b/docs/schema.html @@ -101,12 +101,12 @@

Slots & Class Attributes (230)

The single letter before `__` is the rank — d, p, c, o, f, g, s — and it is the way to filter by rank. Required, so it is always there to read: the pattern below constrains the value but says nothing when the key is absent, which is why this slot is the one required attribute here (#414 review). **Filter `d__` out of any coverage figure.** The domain groundings (`d__Bacteria`, `d__Archaea`) are true but carry no information beyond the NCBITaxon id, and counting them as "grounded" moves coverage by about seven percentage points (#393, #403). They are not the whole tautological population: a higher-rank grounding whose GTDB name equals the NCBI name at the same rank says as little — `Actinomycetota` -> `p__Actinomycetota`. Filtering on `is_reclassified: false` above genus rank catches those too. Current counts live in `.claude/skills/ground-taxa-gtdb/SKILL.md` and are pinned by `tests/test_gtdb_support_counts.py`, not written here: pythongen drops attribute descriptions, so a count in this text reaches no generated artifact and nothing would fail when it goes stale.GtdbClassification.gtdb_lineagestringFull GTDB lineage string (domain..species), e.g. "d__Bacteria;p__Bacillota;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;s__Bacillus velezensis".GtdbClassification.gtdb_taxonstringGTDB taxon name (human-readable, spaces preserved), e.g. "Bacillus velezensis".GtdbClassification.is_reclassifiedbooleanTrue when the GTDB name differs from the NCBITaxon name at the rank this block is grounded at. A string comparison, and nothing more, so the name is a poor guide to what it holds. -It said "species name ... (a GTDB reclassification/rename)". Neither half held. Of the 138 blocks currently true, 41 are grounded above species — through genus, family, order, class and phylum — so the rank is wrong for nearly a third of them. And it does not mean GTDB reclassified anything. Partitioning the 138 by why the names differ (#441): +It said "species name ... (a GTDB reclassification/rename)". Neither half held. Of the 141 blocks currently true, 42 are grounded above species — through genus, family, order, class and phylum — so the rank is wrong for nearly a third of them. And it does not mean GTDB reclassified anything. Partitioning the 141 by why the names differ (#441): * 0 dropped strain designations. There were 40 — `Escherichia coli K-12` -> `Escherichia coli` — and #480 removed them: GTDB carries no strain suffixes, so the names differed while the placement did not. `name_differs` now treats that as no difference. -* 32 GTDB polyphyly suffixes — `Bacillota` -> `Bacillota_A`. A split +* 34 GTDB polyphyly suffixes — `Bacillota` -> `Bacillota_A`. A split marker on the same name, not a rename. * 13 that are both at once — `Buchnera aphidicola BCc` -> `Buchnera aphidicola_F`. @@ -115,7 +115,7 @@

Slots & Class Attributes (230)

* 3 rank-appropriate nomenclatural endings on one stem — `Chlorobiota` -> `Chlorobiia`, `Nitrososphaerota` -> `Nitrososphaeria`. -* 87 genuinely different names, and only some of those are GTDB +* 88 genuinely different names, and only some of those are GTDB reclassifications. `Allobosea` -> `Bosea` is an *NCBI* rename: both databases place the organism in the same genus concept, and NCBI moved its label because the bacterial name was a later homonym of @@ -123,7 +123,7 @@

Slots & Class Attributes (230)

`Nitrosotalea devaniterrae` -> `Nitrosotalea devanaterra`, `Methylocystis parvus` -> `Methylocystis parva`. -So 51 of 138 — 37% — are not reclassifications under any reading, and that is a floor: the 87 "genuinely different" include an unknown number of NCBI renames and spelling variants. Filter on this slot to find "the two labels are not identical", which is what it computes. Do not read it as provenance. +So 53 of 141 — 38% — are not reclassifications under any reading, and that is a floor: the 88 "genuinely different" include an unknown number of NCBI renames and spelling variants. Filter on this slot to find "the two labels are not identical", which is what it computes. Do not read it as provenance. #480 narrowed it: dropping the 40 strain-designation cases took the non-reclassification share from 54% to 38% at that time, and the genuinely-different share from 46% to 62%. The current block counts are the ones counted above, not these historical rounded percentages. Polyphyly suffixes are deliberately still reported — `Bacillota` -> `Bacillota_A` is a real GTDB distinction, and #480 records that folding it in here is the arguable middle rather than the obvious next step. An enum (#480 option 3) is where this wants to end up. ONE call site computes it now, `name_differs` (#482). Two used to: `bool(sp and ref and sp != ref)` on the species path, which produced 121 of the then-154, and `top != _clean_label(label)` on the genus-and-higher path. They disagreed — the first had a crosswalk fallback for `ref` and a null-guard returning False where the second returned True, so a missing label read as a name change at genus rank and not at species rank. Counts are pinned by `tests/test_is_reclassified_semantics.py`, which fails when they drift; a count in this text reaches no generated artifact, since pythongen drops attribute descriptions.GtdbClassification.majority_fractionfloatFraction of genomes under the NCBI taxon that map to this GTDB taxon (0.0-1.0), from the kg-microbe NCBI2GTDB table — a confidence for the mapping. 1.0 means an unambiguous 1:1 correspondence.GtdbClassification.mapping_sourcestringProvenance of the mapping: the source table and a content digest of it, e.g. "kg-microbe NCBI2GTDB.tsv.gz sha256:761d5537a7edb4b0 (file mtime 2026-07-25)". The digest is what identifies the input -- an earlier form recorded "GTDB release latest (built <mtime>)", where "latest" was a literal nothing read and the mtime is a filesystem attribute rather than a property of the data, so a block that differs from today's crosswalk could not be told from one that is wrong (#624). Blocks written before that change still carry the old string.GtdbClassification.ncbi_source_idstringThe NCBITaxon id this GTDB classification was mapped from.GtdbClassification.support_genomesintegerNumber of genomes supporting the chosen GTDB taxon — the numerator behind majority_fraction. @@ -157,7 +157,7 @@

Enumerations (26)