|
- oxygenic algal biofilm — ontology label: Chlorophyta
+ diatom-dominated photosynthetic biofilm — ontology label: Bacillariophyta
|
-
- NCBITaxon:3041
+ NCBITaxon:2836
|
@@ -537,7 +535,7 @@ Taxonomy
- SUPPORT (IN_VITRO)
- "a photosynthetic algal biofilm"
+ "dominated by diatoms"
@@ -586,7 +584,7 @@ Ecological Interactions
Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
CROSS_FEEDING
- Photosynthetic oxygen supply from a diatom-dominated surface biofilm supports cable-bacteria sulfide oxidation. The light perturbation supports oxygen cross-feeding, but reciprocal benefit to the phototrophs is not established. The record's Chlorophyta roster conflicts with the primary source; explicit graph assignments are withheld pending #1267. Community-level connectivity still inherits that unresolved roster, so this graph is not fully certified.
+ Photosynthetic oxygen supply from a diatom-dominated surface biofilm supports cable-bacteria sulfide oxidation. The light perturbation supports oxygen cross-feeding, but reciprocal benefit to the phototrophs is not established. Community-level scope uses the corrected phylum-level biofilm and family-level cable-bacteria roster, not species-resolved partners or an isolated two-member culture.
@@ -816,9 +814,9 @@ Knowledge gaps & discussions (1)
KNOWLEDGE_GAP
OPEN
- Can the biofilm roster and redox-site mechanism be reconciled with the diatom-based primary experiment?
+ Which redox-site regulation or motility mechanisms explain the response, and do phototrophs benefit reciprocally?
- The primary paper describes diatoms, not the assigned Chlorophyta. Explicit unsupported graph participants were removed, but non-graph taxonomy and resulting community-level expansion remain unresolved: #1267 stays open and review status is needs_research. Publisher main text through conclusions and cached abstract read, not images/supplements. Hydrogen-sulfide versus calculated total-sulfide measurements do not establish related_ingredients sulfide(2-) speciation. Exact regulation and motility need testing.
+ Identity and chemical-grounding defects in #1267 are repaired, while species resolution and a defined two-member culture remain unsupported. Regulation, motility and reciprocal benefit remain unresolved. The existing bounds on replication and the inconsistent sulfide-depth significance claim remain; source access does not validate these mechanisms.
Attaches to: ecological_interactions#Photosynthesis Stimulates Cable-Bacteria Electron Harvesting, ecological_interactions#Electrogenic Sulfide Oxidation across Sediment Redox Zones, ecological_interactions#Rapid Redox Signal Transmission under Diel Illumination
@@ -957,12 +955,12 @@ Environmental Factors
id: "NCBITaxon:213121",
label: "Desulfobulbaceae cable bacteria",
abundance: "UNKNOWN",
- roles: ["SYNTROPHIC_PARTNER", "CROSS_FEEDER"]
+ roles: ["CROSS_FEEDER"]
};
- taxonData["oxygenic algal biofilm"] = {
- id: "NCBITaxon:3041",
- label: "oxygenic algal biofilm",
+ taxonData["diatom-dominated photosynthetic biofilm"] = {
+ id: "NCBITaxon:2836",
+ label: "diatom-dominated photosynthetic biofilm",
abundance: "UNKNOWN",
roles: ["PRIMARY_PRODUCER"]
};
diff --git a/history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml b/history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml
new file mode 100644
index 000000000..c3128740a
--- /dev/null
+++ b/history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+ kind: record
+ path: kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
+ slug: Cable_Bacteria_Photosynthetic_Biofilm_Sediment
+session:
+ id: 2026-10-08T194617Z-codex-d8c9fa
+ timestamp: '2026-10-08T19:46:17Z'
+ actors:
+ - type: ai_agent
+ name: codex
+ model: unspecified
+ agent_tool: codex
+links:
+ issues:
+ - https://github.com/CultureBotAI/CommunityMech/issues/1267
+events:
+- type: EDIT
+ outcome: changed
+ sections:
+ - interactions
+ - discussions
+ - taxonomy
+ - related_ingredients
+ summary: Reconcile inherited cable-biofilm graph membership and sulfide grounding; preserve
+ all three nodes, two arrows and mechanism limits.
+ details: reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
diff --git a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
index 3ce267f01..a573328e6 100644
--- a/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
+++ b/kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
@@ -31,40 +31,38 @@ taxonomy:
support_genomes: 52
total_genomes: 61
is_reclassified: false
- mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at f__ rank; 3 GTDB taxa under the NCBI taxon]
+ mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at f__ rank;
+ 3 GTDB taxa under the NCBI taxon]
notes: Long multicellular filamentous bacteria mediating electrogenic sulfur oxidation in sediment.
functional_role:
- - SYNTROPHIC_PARTNER
- CROSS_FEEDER
evidence:
- reference: PMID:25416774
supports: SUPPORT
evidence_source: IN_VITRO
snippet: belonging to the family Desulfobulbaceae
- explanation: Supports conservative family-level taxonomy for cable bacteria in this sediment system.
+ explanation: Family-level cable-bacteria identity; oxygen consumption does not establish reciprocal syntrophy.
- taxon_term:
- preferred_term: oxygenic algal biofilm
+ preferred_term: diatom-dominated photosynthetic biofilm
term:
- id: NCBITaxon:3041
- label: Chlorophyta
+ id: NCBITaxon:2836
+ label: Bacillariophyta
gtdb_grounding_status: NO_GTDB_EQUIVALENT
- notes: Photosynthetic algal biofilm at the sediment surface that changes oxygen availability under a
- diel light-dark cycle.
+ notes: Phylum-level diatom grounding; the study does not identify a species or a defined two-member culture.
functional_role:
- PRIMARY_PRODUCER
evidence:
- reference: PMID:25416774
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: a photosynthetic algal biofilm
- explanation: Supports inclusion of the phototrophic surface biofilm member.
+ snippet: dominated by diatoms
+ explanation: Experimental biofilm identity in Methods, not an assignment to green algae.
ecological_interactions:
- name: Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
- description: 'Photosynthetic oxygen supply from a diatom-dominated surface biofilm supports cable-bacteria sulfide
+ description: Photosynthetic oxygen supply from a diatom-dominated surface biofilm supports cable-bacteria sulfide
oxidation. The light perturbation supports oxygen cross-feeding, but reciprocal benefit to the phototrophs is
- not established. The record''s Chlorophyta roster conflicts with the primary source; explicit graph assignments
- are withheld pending #1267. Community-level connectivity still inherits that unresolved roster, so this graph
- is not fully certified.'
+ not established. Community-level scope uses the corrected phylum-level biofilm and family-level cable-bacteria
+ roster, not species-resolved partners or an isolated two-member culture.
interaction_type: CROSS_FEEDING
scope: COMMUNITY_LEVEL
metabolites:
@@ -162,33 +160,32 @@ environmental_factors:
snippet: free sulfide in deeper sediment horizons
explanation: Supports deeper sulfide as the electron donor reservoir.
related_ingredients:
-- preferred_term: sulfide
+- preferred_term: hydrogen sulfide
chebi_term:
- id: CHEBI:15138
- label: sulfide(2-)
- relevance: >
- Free sulfide in the reduced sediment is the electron donor that cable bacteria oxidize,
- harvesting electrons that are conducted to oxygen near the surface.
+ id: CHEBI:16136
+ label: hydrogen sulfide
+ relevance: H2S is the measured free-sulfide species. Calculated total sulfide includes H2S and HS-; this term
+ does not identify all dissolved sulfide as H2S or as sulfide(2-).
evidence:
- reference: PMID:25416774
supports: SUPPORT
evidence_source: IN_VITRO
- snippet: harvesting electrons from free sulfide
- explanation: Names sulfide as the electron-donor substrate for cable-bacteria oxidation.
+ snippet: free sulfide (H2S) is reported
+ explanation: Methods identify the measured species; no exclusive molecular uptake mechanism is inferred.
- preferred_term: dioxygen
chebi_term:
id: CHEBI:15379
label: dioxygen
- relevance: >
- Oxygen near the sediment-water interface is the terminal electron acceptor for long-distance
- electron transfer, spatially separated from sulfide at depth.
+ relevance: 'Oxygen near the sediment-water interface is the terminal electron acceptor for long-distance electron
+ transfer, spatially separated from sulfide at depth.
+
+ '
evidence:
- reference: PMID:25416774
supports: SUPPORT
evidence_source: IN_VITRO
snippet: to oxygen present near the sediment-water interface
- explanation: Names oxygen as the terminal electron acceptor at the
- sediment-water interface.
+ explanation: Names oxygen as the terminal electron acceptor at the sediment-water interface.
associated_datasets:
- title: Cable bacteria photosynthetic biofilm sediment article
dataset_type: PHENOTYPE
@@ -205,18 +202,17 @@ associated_datasets:
explanation: Links this record to the primary cable-bacteria biofilm source.
discussions:
- discussion_id: cable_biofilm_taxonomy_and_redox_sites
- prompt: Can the biofilm roster and redox-site mechanism be reconciled with the diatom-based primary experiment?
+ prompt: Which redox-site regulation or motility mechanisms explain the response, and do phototrophs benefit reciprocally?
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- ecological_interactions#Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
- ecological_interactions#Electrogenic Sulfide Oxidation across Sediment Redox Zones
- ecological_interactions#Rapid Redox Signal Transmission under Diel Illumination
- rationale: 'The primary paper describes diatoms, not the assigned Chlorophyta. Explicit unsupported graph participants
- were removed, but non-graph taxonomy and resulting community-level expansion remain unresolved: #1267 stays
- open and review status is needs_research. Publisher main text through conclusions and cached abstract read,
- not images/supplements. Hydrogen-sulfide versus calculated total-sulfide measurements do not establish related_ingredients
- sulfide(2-) speciation. Exact regulation and motility need testing.'
+ rationale: 'Identity and chemical-grounding defects in #1267 are repaired, while species resolution and a defined
+ two-member culture remain unsupported. Regulation, motility and reciprocal benefit remain unresolved. The existing
+ bounds on replication and the inconsistent sulfide-depth significance claim remain; source access does not validate
+ these mechanisms.'
posed_by: codex
posed_date: '2026-10-05'
curation_history:
@@ -226,3 +222,9 @@ curation_history:
changes: 'Bound cable-bacteria oxygen coupling and expose unresolved biofilm taxonomy; decisions: reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml;
https://github.com/CultureBotAI/CommunityMech/issues/1267'
llm_assisted: true
+- timestamp: '2026-10-08T19:46:14Z'
+ curator: codex
+ action: REVIEW_CAUSAL_GRAPH
+ changes: Reconcile inherited cable-biofilm graph membership and sulfide grounding; preserve all three nodes, two
+ arrows and mechanism limits. Issue#1267; reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
+ llm_assisted: true
diff --git a/references_cache/PMID_25416774.txt b/references_cache/PMID_25416774.txt
index 3a9971d5d..94d1d8d05 100644
--- a/references_cache/PMID_25416774.txt
+++ b/references_cache/PMID_25416774.txt
@@ -41,4 +41,14 @@ Copyright © 2015, American Society for Microbiology. All Rights Reserved.
DOI: 10.1128/AEM.02682-14
PMCID: PMC4292484
-PMID: 25416774 [Indexed for MEDLINE]
\ No newline at end of file
+PMID: 25416774 [Indexed for MEDLINE]
+
+## Primary-source excerpts
+Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC4292484/
+Sections: Methods, experiment 1 and microsensor profiling. Retrieved 2026-10-08.
+Copyright 2015 American Society for Microbiology. All rights reserved.
+Short literal excerpts only; no full body or supplement imported.
+
+dominated by diatoms
+
+free sulfide (H2S) is reported
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index 5bb8527f2..dcab14689 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,29 @@ source-based self-adversarial review. These records are not independent approval
or proof that every graph is complete. The current inventory and summary distinguish
`reviewed`, `pending` and `needs_research`.
+## Batch125: Cable-Biofilm Identity
+
+[Decisions](decisions/20261008-cable-biofilm-batch125.yaml),
+[validation](validation-20261008-batch125.json), and
+[self-adversarial review](adversarial-review-20261008-batch125.yaml) revisit
+the unresolved identity in #1267. The inherited biofilm member is now grounded
+to Bacillariophyta, and the related sulfide term matches the measured H2S species
+without treating calculated total sulfide as one molecule. Unsupported syntrophy
+is removed from the cable-bacteria role.
+
+All three nodes and both arrows remain. Mechanism, reciprocal-benefit and
+statistical qualifications remain, including the open mechanistic discussion.
+The earlier partial-review ledger is preserved through explicit hash-linked
+supersession. Whole-record certification, original figure inspection, and
+supplement or raw-data audits are not claimed.
+
+All eleven evidence instances match the primary source and cache; only eight
+new quoted words are appended with attribution. The other 459 records,
+923 caches and all earlier histories and decision ledgers remain unchanged.
+No Edison submission or new causal topology was needed. The inventory has
+406 reviewed records, zero pending and 54 requiring research. Issue #1267
+awaits protected-main merge; #1268 remains open for other records.
+
## Batch124: Final Pending Records
[Decisions](decisions/20261008-six-records-batch124.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch125.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch125.yaml
new file mode 100644
index 000000000..35d425cdf
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch125.yaml
@@ -0,0 +1,91 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 985c5cb81bb72d4ff1c763db31797c31fd6ed099
+scope:
+- kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch125.json
+findings:
+- issue: 1267
+ severity: P2
+ status: addressed_pending_protected_main_merge
+ finding: Inherited Chlorophyta graph membership and sulfide(2-) assignment lacked source support.
+ disposition: Primary Methods and canonical identifiers support the replacement; existing topology is preserved.
+adversarial_checks:
+- No species-level or defined-pair claim is introduced by the phylum-level diatom correction; existing family-level
+ cable-bacteria grounding and GTDB payload are semantically preserved.
+- Oxygen cross-feeding remains distinct from reciprocal benefit or obligate syntrophy. Two non-cross-feeding nodes,
+ both arrows, replication limits and statistical qualifications are retained.
+- H2S measurement is distinct from calculated total sulfide and exclusive molecular uptake. The open mechanistic
+ discussion remains; no new causal topology or Edison submission.
+- Eight focused tests include five in-memory control/mutation/restored-control cases rejecting green-algal identity,
+ syntrophy, dianion grounding, exclusive uptake and established reciprocity. They are targeted checks, not universal
+ proof.
+- Whole record and accessible primary body through conclusions read, including Methods, Table1 and captions. Original
+ figures, supplements, raw data and older cited studies were not audited.
+- All11evidence instances match primary artifacts and cache. One attributed eight-word appendix, original cache
+ prefix retained; no full article imported.
+- Prior partial-review status remains in the immutable batch8 ledger; a hash-linked superseding review records resolution.
+ One append-only event/history,459otherrecords and923othercaches unchanged.
+- Existing57network warnings unchanged,zero structural defects; unchanged connectivity census. Deterministic page
+ rendering and regression tests verify published descriptions, not screenshots.
+- No independent approval is claimed.1267 remains open until actual protected-main merge;1268 is outside this record
+ and stays open.54research gaps and the stack lifecycle still remain.
+verification:
+ regressions: 1163 passed in 471.20s (0:07:51)
+ focused_tests: 8
+ mutation_cases: 5
+ recorded_gate_outputs: 20
+ reference_scope: Reference validator checks 10 distinct quotations; snippet audit and fresh-primary comparison
+ cover all 11 instances. Literal matching is not entailment proof.
+ preservation:
+ unchanged_records: 459
+ unchanged_caches: 923
+ unchanged_prior_histories: 793
+ unchanged_prior_decisions: 123
+ preserved_user_files: 46
+ unchanged_raw_blocks: 9
+ original_cache_prefix_preserved: true
+ last_two_nodes_structurally_unchanged: true
+ tested_file_sha256:
+ kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml: 79a9597722d1caa4abad454a53464a9671801ec4d52d5b809a42ec003e90fd79
+ references_cache/PMID_25416774.txt: 686490fadcc5e7864de153e175e00dafdb40b8977465517dccc761c2551e5ddc
+ reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml: b753d01726b8c230018a13e2462eff8f394959b347a4324f92ef0db2857d79ca
+ tests/test_causal_review_batch8.py: c4dbbd3060db8153107d29343e58cf1536792fef2653969e4e0043e954d631bf
+ tests/test_causal_review_batch125.py: 78ef4667222d57fbcc4d5e4a567fe165cacf1873781a79203e398edb4b350dc5
+ docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html: 039278994461ae13bcc739c079a208eb487a00abefcdce81301d95873b587701
+ history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml: b9579a45ffef217a8d510dad062da82a92adf48f0f227bfe4d7be9ca5fff522a
+ reports/causal_graph_review/README.md: b39624f5f3f899a4700d551508dac0451e06e69516142373bd5b59e848d46c42
+ network_unchanged: true
+ corpus:
+ records: 460
+ nodes: 1373
+ edges: 530
+ review_status_counts:
+ needs_research: 54
+ reviewed: 406
+ participant_census:
+ records: 460
+ with_community_level: 415
+ mixed: 137
+ community_level_only: 278
+ taxa: 1570
+ credited_solely_by_the_rule: 1281
+ development_corrections:
+ - Dry-run guard initially miscounted the two short excerpts as nine words; corrected to their actual eight before
+ any canonical write.
+ postcommit_docs_current: Required separately; not preasserted.
+limitations:
+- Primary main body, Methods, Results, Table1, captions and Discussion through conclusions read. Figure pixels,
+ supplement, raw data and cited earlier studies not independently audited.
+- Roster and related-ingredient fields are necessary dependencies of inherited graph membership and its chemistry,
+ explicitly extending the otherwise graph-only repair boundary for issue1267.
+- NCBITaxon2836 Bacillariophyta and CHEBI16136 hydrogen sulfide verified against official NCBI/ChEBI pages. Existing
+ GTDB mapping and article-as-dataset metadata are not certified.
+- Three nodes and two arrows unchanged in identity and direction; only the first node description changes. Open
+ mechanism discussion remains appropriate after identity repair.
+- One short eight-word excerpt appendix; original cache prefix retained. No full article import, provider submission,
+ credits or new causal topology.
+- Source-based self-adversarial review, not independent approval. Issue1267 can close only after protected-main
+ merge. Issue1268 covers other records and remains open.
diff --git a/reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml b/reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
new file mode 100644
index 000000000..3c7264c20
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
@@ -0,0 +1,167 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 985c5cb81bb72d4ff1c763db31797c31fd6ed099
+source_access:
+ url: https://pmc.ncbi.nlm.nih.gov/articles/PMC4292484/
+ pmid: '25416774'
+ doi: 10.1128/AEM.02682-14
+ html_sha256: 21b5fd77c31cfbf4cc18a51893908e08cfc85529baad9c3ec60a0e93ad77267d
+ text_sha256: 2e1d16b5c0b6cbd7833f936a87bf167dd204cb82ca63ebe44f89a95afa2e4458
+ paragraph_count: 83
+ source_notice: Copyright 2015 American Society for Microbiology. All rights reserved.
+ repository_import: Short attributed quotations only; full body retained outside repository.
+primary_artifacts:
+ /private/tmp/communitymech-batch125/cable-primary.html: 21b5fd77c31cfbf4cc18a51893908e08cfc85529baad9c3ec60a0e93ad77267d
+ /private/tmp/communitymech-batch125/cable-primary.txt: 2e1d16b5c0b6cbd7833f936a87bf167dd204cb82ca63ebe44f89a95afa2e4458
+ /private/tmp/communitymech-batch125/source-manifest.json: e07c3ddc55f790d6e992f4aad431d8a26e48e97d569cf3dda57323288ee16fbe
+grounding_urls:
+- https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2836&mode=Info
+- https://www.ebi.ac.uk/chebi/CHEBI:16136
+snippet_checks:
+- path: /taxonomy/0/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /taxonomy/1/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /ecological_interactions/0/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /ecological_interactions/1/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /ecological_interactions/1/evidence/1
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /ecological_interactions/2/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /environmental_factors/0/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /environmental_factors/1/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /related_ingredients/0/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /related_ingredients/1/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+- path: /associated_datasets/0/evidence/0
+ reference: PMID:25416774
+ literal_primary_match: true
+ literal_cache_match: true
+cache_changes:
+- path: references_cache/PMID_25416774.txt
+ before_sha256: 024e6d8868069d8cee8cc222391860530a93e8688dbb69e9e10a54b67f498d43
+ after_sha256: 686490fadcc5e7864de153e175e00dafdb40b8977465517dccc761c2551e5ddc
+ appended_excerpt_words: 8
+reviewed_counts:
+ records: 1
+ retained_nodes: 3
+ retained_arrows: 2
+ new_nodes_or_directions: 0
+edison:
+ required: false
+ provider_submissions: 0
+ credits_spent: 0
+limitations:
+- Primary main body, Methods, Results, Table1, captions and Discussion through conclusions read. Figure pixels,
+ supplement, raw data and cited earlier studies not independently audited.
+- Roster and related-ingredient fields are necessary dependencies of inherited graph membership and its chemistry,
+ explicitly extending the otherwise graph-only repair boundary for issue1267.
+- NCBITaxon2836 Bacillariophyta and CHEBI16136 hydrogen sulfide verified against official NCBI/ChEBI pages. Existing
+ GTDB mapping and article-as-dataset metadata are not certified.
+- Three nodes and two arrows unchanged in identity and direction; only the first node description changes. Open
+ mechanism discussion remains appropriate after identity repair.
+- One short eight-word excerpt appendix; original cache prefix retained. No full article import, provider submission,
+ credits or new causal topology.
+- Source-based self-adversarial review, not independent approval. Issue1267 can close only after protected-main
+ merge. Issue1268 covers other records and remains open.
+records:
+- path: kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml
+ id: CommunityMech:000145
+ original_sha256: 6c7154dd0b4f3a7f06031550e153ef51ca1e16a7839d4c2bbb6b8982982ebd86
+ record_sha256: 79a9597722d1caa4abad454a53464a9671801ec4d52d5b809a42ec003e90fd79
+ status: reviewed
+ outcome: changed
+ review_file: reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml
+ supersedes_review:
+ review_file: reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml
+ record_sha256: 6c7154dd0b4f3a7f06031550e153ef51ca1e16a7839d4c2bbb6b8982982ebd86
+ scope: Whole record and existing graph read. Necessary roster and chemical dependencies repaired; not whole-record
+ certification or graph extension.
+ summary: Reconcile inherited cable-biofilm graph membership and sulfide grounding; preserve all three nodes, two
+ arrows and mechanism limits.
+ node_decisions:
+ - node: Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
+ rationale: Inherited graph member identity now matches Methods; oxygen-supply claim and reciprocal-benefit limit
+ retained.
+ - node: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ rationale: Existing conduction interpretation retained without new interorganism exchange or uniquely resolved
+ physiology.
+ - node: Rapid Redox Signal Transmission under Diel Illumination
+ rationale: Perturbation response and statistical/replication bounds retained unchanged.
+ edges_before:
+ - source: Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
+ target: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ description: Greater photosynthetic oxygen supply can provide the surface electron acceptor for cable-bacteria
+ sulfide oxidation at depth. Light manipulation and microsensor responses support this coupling; the precise
+ spatial redox-site model remains an interpretation.
+ - source: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ target: Rapid Redox Signal Transmission under Diel Illumination
+ description: Cable-bacteria electron conduction provides a mechanism for rapid coupling of altered surface oxygen
+ availability to deep sulfide responses during light/dark perturbations. The observed rapid response supports
+ coupling without uniquely resolving motility or biochemical regulation.
+ edges_after:
+ - source: Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
+ target: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ description: Greater photosynthetic oxygen supply can provide the surface electron acceptor for cable-bacteria
+ sulfide oxidation at depth. Light manipulation and microsensor responses support this coupling; the precise
+ spatial redox-site model remains an interpretation.
+ - source: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ target: Rapid Redox Signal Transmission under Diel Illumination
+ description: Cable-bacteria electron conduction provides a mechanism for rapid coupling of altered surface oxygen
+ availability to deep sulfide responses during light/dark perturbations. The observed rapid response supports
+ coupling without uniquely resolving motility or biochemical regulation.
+ retained_edge_decisions:
+ - edge:
+ source: Photosynthesis Stimulates Cable-Bacteria Electron Harvesting
+ target: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ description: Greater photosynthetic oxygen supply can provide the surface electron acceptor for cable-bacteria
+ sulfide oxidation at depth. Light manipulation and microsensor responses support this coupling; the precise
+ spatial redox-site model remains an interpretation.
+ rationale: Existing source-bounded direction unchanged; no new topology.
+ - edge:
+ source: Electrogenic Sulfide Oxidation across Sediment Redox Zones
+ target: Rapid Redox Signal Transmission under Diel Illumination
+ description: Cable-bacteria electron conduction provides a mechanism for rapid coupling of altered surface
+ oxygen availability to deep sulfide responses during light/dark perturbations. The observed rapid response
+ supports coupling without uniquely resolving motility or biochemical regulation.
+ rationale: Existing source-bounded direction unchanged; no new topology.
+ removed_node_decisions: []
+ removed_edge_decisions: []
+ references:
+ - PMID:25416774
+ issues:
+ - 1267
+ allowed_changed_fields:
+ - curation_history
+ - discussions
+ - ecological_interactions
+ - related_ingredients
+ - taxonomy
+ history_files:
+ - history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 4e250266a..23632a946 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -73,7 +73,7 @@ kb/communities/Buchnera_Serratia_Cinara_Cedri_Endosymbiont_Consortium.yaml Commu
kb/communities/Burkholderia_Pseudomonas_YB2_PET_Degradation_Consortium.yaml CommunityMech:000426 8bfeed82fde64564ea0aeb64f142de29e051a643aafe17dcda5e1e45ea948e0b 2 1 75.0 reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml reviewed
kb/communities/Butyrivibrio_Selenomonas_Ruminococcus_Lignocellulolytic_Rumen_Consortium.yaml CommunityMech:000275 f9ad860387600c64fa0ba428afdfd9fa4cc0e960097b445b5253eb953ed1336e 2 0 60.0 reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml reviewed
kb/communities/CRC_Fusobacterium_Control_SynCom.yaml CommunityMech:000128 ce036791082c01e1713952a2e090090a3cebce535c994e2b63885bfa5554d8cb 4 1 90.0 reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml reviewed
-kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml CommunityMech:000145 6c7154dd0b4f3a7f06031550e153ef51ca1e16a7839d4c2bbb6b8982982ebd86 3 2 93.3 reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml needs_research
+kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml CommunityMech:000145 79a9597722d1caa4abad454a53464a9671801ec4d52d5b809a42ec003e90fd79 3 2 93.3 reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml reviewed
kb/communities/Calcium_Tomato_Bacterial_Wilt_SynCom.yaml CommunityMech:000393 2003158329c3f2113f6239f65b1e6a1b85bd3c19204f7aaf9d90be7f1f5c68f0 3 1 76.7 reports/causal_graph_review/decisions/20261005-twelve-records-batch8.yaml reviewed
kb/communities/Caldibacillus_Clostridium_Aerotolerant_Cellulose_Coculture.yaml CommunityMech:000179 0d0ed40c05ec1cf70a99a4f012b65726cbdffa775db503b905e6cbf932ea6b24 3 1 83.3 reports/causal_graph_review/decisions/20261005-thermophile-pair-batch9.yaml reviewed
kb/communities/Caldicellulosiruptor_TwoSpecies_Hydrogen_Coculture.yaml CommunityMech:000185 8151dfbdf8e248288fbc2f31cc2a53bd770fb5bf34d1239538a2cb3e1b7ba990 3 1 80.0 reports/causal_graph_review/decisions/20261005-thermophile-pair-batch9.yaml reviewed
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index a9cc7221a..9f8f5c1b8 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -7,8 +7,8 @@
"records_without_nodes": 10,
"records_without_edges": 189,
"review_status_counts": {
- "needs_research": 55,
- "reviewed": 405
+ "needs_research": 54,
+ "reviewed": 406
},
"structural_defects": [],
"network_audit": [
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new file mode 100644
index 000000000..ef5243bbd
--- /dev/null
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+ "id": "NCBITaxon:47251",
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+ "reference": "PMID:41745484",
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+ {
+ "reference": "doi:10.1038/nature16192",
+ "supports": "SUPPORT",
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+ "snippet": "We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing"
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+ "reference": "doi:10.1038/nature16192",
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+ "reference": "doi:10.1038/nature16192",
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+ "taxon": "Stenotrophomonas species",
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+ "abundance_level": "COMMON",
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+ "SYNTROPHIC_PARTNER"
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+ "severity": "warning"
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+ "type": "DISCONNECTED",
+ "taxon": "Xanthomonadales members",
+ "taxon_id": "NCBITaxon:135614",
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+ "taxon_term": {
+ "preferred_term": "Xanthomonadales members",
+ "term": {
+ "id": "NCBITaxon:135614",
+ "label": "Lysobacterales"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:o__Xanthomonadales",
+ "gtdb_taxon": "Xanthomonadales",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Xanthomonadales",
+ "ncbi_source_id": "NCBITaxon:135614",
+ "majority_fraction": 1.0,
+ "support_genomes": 7047,
+ "total_genomes": 7047,
+ "is_reclassified": true,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at o__ rank; 1 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1073/pnas.2100678118",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "It is unknown, however, how microbiota composed of commensal bacteria colonize roots in the face of a sophisticated plant immune system that evolved to recognize microbial-associated molecular patterns"
+ }
+ ]
+ },
+ "message": "Taxon 'Xanthomonadales members' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Deepwater_Horizon_Deep_Sea_Oil_Plume_Succession",
+ "type": "DISCONNECTED",
+ "taxon": "Methylophaga",
+ "taxon_id": "NCBITaxon:40222",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Methylophaga",
+ "term": {
+ "id": "NCBITaxon:40222",
+ "label": "Methylophaga"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Methylophaga",
+ "gtdb_taxon": "Methylophaga",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga",
+ "ncbi_source_id": "NCBITaxon:40222",
+ "majority_fraction": 1.0,
+ "support_genomes": 45,
+ "total_genomes": 45,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 1 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Methylotrophic bacteria implicated in later plume-water hydrocarbon processing."
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:24865772",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "methylotrophs, including Methylophaga, were in a heightened state of metabolic activity within oil plume waters",
+ "explanation": "Supports active Methylophaga-like methylotrophs in oil plume waters."
+ }
+ ]
+ },
+ "message": "Taxon 'Methylophaga' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "East_River_Floodplain_Core_Microbiome",
+ "type": "DISCONNECTED",
+ "taxon": "Acidobacteriota floodplain representatives",
+ "taxon_id": "NCBITaxon:57723",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Acidobacteriota floodplain representatives",
+ "term": {
+ "id": "NCBITaxon:57723",
+ "label": "Acidobacteriota"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:p__Acidobacteriota",
+ "gtdb_taxon": "Acidobacteriota",
+ "gtdb_lineage": "d__Bacteria;p__Acidobacteriota",
+ "ncbi_source_id": "NCBITaxon:57723",
+ "majority_fraction": 1.0,
+ "support_genomes": 203,
+ "total_genomes": 203,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at p__ rank; 1 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Acidobacteriota were among the abundant representative genomes reconstructed across the three meander-bound floodplains."
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34022966",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "Other abundant taxa across floodplains included Deltaproteobacteria (27 representatives), Acidobacteria (21 representatives), Nitrospirae and Planctomycetes (both with 13 representatives)",
+ "explanation": "Supports Acidobacteriota as one of the abundant reconstructed floodplain soil lineages."
+ }
+ ]
+ },
+ "message": "Taxon 'Acidobacteriota floodplain representatives' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "East_River_Floodplain_Core_Microbiome",
+ "type": "DISCONNECTED",
+ "taxon": "Nitrospirae core floodplain members",
+ "taxon_id": "NCBITaxon:1234",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Nitrospirae core floodplain members",
+ "term": {
+ "id": "NCBITaxon:1234",
+ "label": "Nitrospira"
+ },
+ "gtdb_grounding_status": "WITHHELD",
+ "notes": "Nitrospirae were among abundant reconstructed lineages and are consistent with the highly transcribed nitrification genes reported for the floodplain soils."
+ },
+ "functional_role": [
+ "PRIMARY_PRODUCER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34022966",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes",
+ "explanation": "Supports active nitrification capacity in the floodplain soil community."
+ }
+ ]
+ },
+ "message": "Taxon 'Nitrospirae core floodplain members' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "GLBRC_UFMP_Fermentation_Community",
+ "type": "DISCONNECTED",
+ "taxon": "RUG023 sp. (MAG SPH2)",
+ "taxon_id": "NCBITaxon:203691",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "RUG023 sp. (MAG SPH2)",
+ "term": {
+ "id": "NCBITaxon:203691",
+ "label": "Spirochaetota"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:p__Spirochaetota",
+ "gtdb_taxon": "Spirochaetota",
+ "gtdb_lineage": "d__Bacteria;p__Spirochaetota",
+ "ncbi_source_id": "NCBITaxon:203691",
+ "majority_fraction": 1.0,
+ "support_genomes": 6024,
+ "total_genomes": 6025,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at p__ rank; 2 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Spirochaetota member (up to 16.1% relative abundance). Produces ethanol which serves as substrate for chain elongation by Firmicutes.\n"
+ },
+ "strain_designation": {
+ "strain_name": "MAG SPH2",
+ "isolation_source": "UFMP bioreactor metagenome"
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "abundance_level": "DOMINANT",
+ "abundance_value": "up to 16.1% relative abundance",
+ "evidence": [
+ {
+ "reference": "PMID:37324413",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate\n",
+ "explanation": "RUG023 sp. SPH2 produces ethanol used as chain elongation substrate"
+ }
+ ]
+ },
+ "message": "Taxon 'RUG023 sp. (MAG SPH2)' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "KBase_Models_for_Zahmeeth_Original_PLOS",
+ "type": "DISCONNECTED",
+ "taxon": "Klebsiella",
+ "taxon_id": "NCBITaxon:570",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Klebsiella",
+ "term": {
+ "id": "NCBITaxon:570",
+ "label": "Klebsiella"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Klebsiella",
+ "gtdb_taxon": "Klebsiella",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella",
+ "ncbi_source_id": "NCBITaxon:570",
+ "majority_fraction": 1.0,
+ "support_genomes": 44527,
+ "total_genomes": 44529,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "another of Bacteroides thetaiotaomicron (B. theta) and Klebsiella",
+ "explanation": "Establishes Klebsiella as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Klebsiella' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "KBase_Models_for_Zahmeeth_Original_PLOS",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas fluorescens",
+ "taxon_id": "NCBITaxon:294",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas fluorescens",
+ "term": {
+ "id": "NCBITaxon:294",
+ "label": "Pseudomonas fluorescens"
+ },
+ "gtdb_grounding_status": "AMBIGUOUS",
+ "gtdb_candidates": [
+ "GTDB:s__Pseudomonas_E_alvandae",
+ "GTDB:s__Pseudomonas_E_asgharzadehiana",
+ "GTDB:s__Pseudomonas_E_azotoformans_A",
+ "GTDB:s__Pseudomonas_E_brassicacearum",
+ "GTDB:s__Pseudomonas_E_crudilactis",
+ "GTDB:s__Pseudomonas_E_edaphica",
+ "GTDB:s__Pseudomonas_E_fluorescens",
+ "GTDB:s__Pseudomonas_E_fluorescens_AP",
+ "GTDB:s__Pseudomonas_E_fluorescens_AQ",
+ "GTDB:s__Pseudomonas_E_fluorescens_B",
+ "GTDB:s__Pseudomonas_E_fluorescens_H",
+ "GTDB:s__Pseudomonas_E_fluorescens_S",
+ "GTDB:s__Pseudomonas_E_kilonensis",
+ "GTDB:s__Pseudomonas_E_lactis",
+ "GTDB:s__Pseudomonas_E_lactucae",
+ "GTDB:s__Pseudomonas_E_paracarnis",
+ "GTDB:s__Pseudomonas_E_petroselini",
+ "GTDB:s__Pseudomonas_E_poae",
+ "GTDB:s__Pseudomonas_E_protegens",
+ "GTDB:s__Pseudomonas_E_reactans",
+ "GTDB:s__Pseudomonas_E_salomonii",
+ "GTDB:s__Pseudomonas_E_simiae",
+ "GTDB:s__Pseudomonas_E_sp002874965"
+ ]
+ },
+ "functional_role": [
+ "CROSS_FEEDER"
+ ],
+ "evidence": [
+ {
+ "reference": "doi:10.1101/2023.08.23.554558",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "idealized two-member microbial communities, one of E. coli and Pseudomonas fluorescens",
+ "explanation": "Establishes P. fluorescens as a member of the computational community models."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas fluorescens' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lake_Washington_Methane_Oxygen_Methylotroph_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Methylosarcina",
+ "taxon_id": "NCBITaxon:105972",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Methylosarcina",
+ "term": {
+ "id": "NCBITaxon:105972",
+ "label": "Methylosarcina fibrata"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Methylosarcina_fibrata",
+ "gtdb_taxon": "Methylosarcina fibrata",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina;s__Methylosarcina fibrata",
+ "ncbi_source_id": "NCBITaxon:105972",
+ "majority_fraction": 1.0,
+ "total_genomes": 1,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "Higher-oxygen methanotrophic genus in Lake Washington methane-fed microcosms."
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:25755930",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "species of the genera Methylosarcina and Methylophilus",
+ "explanation": "Supports Methylosarcina as a higher-oxygen methanotrophic player."
+ }
+ ]
+ },
+ "message": "Taxon 'Methylosarcina' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Burkholderiaceae bacterium",
+ "taxon_id": "NCBITaxon:2030806",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Burkholderiaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:2030806",
+ "label": "Burkholderiaceae bacterium"
+ },
+ "gtdb_grounding_status": "UNRESOLVED"
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics"
+ }
+ ]
+ },
+ "message": "Taxon 'Burkholderiaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Mesorhizobium sp. LjNodule210",
+ "taxon_id": "NCBITaxon:68287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Mesorhizobium sp. LjNodule210",
+ "term": {
+ "id": "NCBITaxon:68287",
+ "label": "Mesorhizobium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Mesorhizobium",
+ "gtdb_taxon": "Mesorhizobium",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium",
+ "ncbi_source_id": "NCBITaxon:68287",
+ "majority_fraction": 0.928,
+ "support_genomes": 167,
+ "total_genomes": 180,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 7 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "abundance_level": "DOMINANT",
+ "functional_role": [
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics"
+ }
+ ]
+ },
+ "message": "Taxon 'Mesorhizobium sp. LjNodule210' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Mesorhizobium sp. LjNodule215",
+ "taxon_id": "NCBITaxon:68287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Mesorhizobium sp. LjNodule215",
+ "term": {
+ "id": "NCBITaxon:68287",
+ "label": "Mesorhizobium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Mesorhizobium",
+ "gtdb_taxon": "Mesorhizobium",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium",
+ "ncbi_source_id": "NCBITaxon:68287",
+ "majority_fraction": 0.928,
+ "support_genomes": 167,
+ "total_genomes": 180,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 7 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics"
+ }
+ ]
+ },
+ "message": "Taxon 'Mesorhizobium sp. LjNodule215' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Mesorhizobium sp. LjNodule218",
+ "taxon_id": "NCBITaxon:68287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Mesorhizobium sp. LjNodule218",
+ "term": {
+ "id": "NCBITaxon:68287",
+ "label": "Mesorhizobium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Mesorhizobium",
+ "gtdb_taxon": "Mesorhizobium",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium",
+ "ncbi_source_id": "NCBITaxon:68287",
+ "majority_fraction": 0.928,
+ "support_genomes": 167,
+ "total_genomes": 180,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 7 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"
+ }
+ ]
+ },
+ "message": "Taxon 'Mesorhizobium sp. LjNodule218' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Microbacteriaceae bacterium",
+ "taxon_id": "NCBITaxon:1873462",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Microbacteriaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:1873462",
+ "label": "Microbacteriaceae bacterium"
+ },
+ "gtdb_grounding_status": "UNRESOLVED"
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations"
+ }
+ ]
+ },
+ "message": "Taxon 'Microbacteriaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Oxalobacteriaceae bacterium",
+ "taxon_id": "NCBITaxon:75682",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Oxalobacteriaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:75682",
+ "label": "Oxalobacteraceae"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:f__Burkholderiaceae",
+ "gtdb_taxon": "Burkholderiaceae",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae",
+ "ncbi_source_id": "NCBITaxon:75682",
+ "majority_fraction": 0.995,
+ "support_genomes": 635,
+ "total_genomes": 638,
+ "is_reclassified": true,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at f__ rank; 2 GTDB taxa under the NCBI taxon]"
+ }
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations"
+ }
+ ]
+ },
+ "message": "Taxon 'Oxalobacteriaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Phyllobacteriaceae bacterium",
+ "taxon_id": "NCBITaxon:1871068",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Phyllobacteriaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:1871068",
+ "label": "Phyllobacteriaceae bacterium"
+ },
+ "gtdb_grounding_status": "UNRESOLVED"
+ },
+ "abundance_level": "ABUNDANT",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"
+ }
+ ]
+ },
+ "message": "Taxon 'Phyllobacteriaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonadaceae bacterium",
+ "taxon_id": "NCBITaxon:1914538",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonadaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:1914538",
+ "label": "Pseudomonadaceae bacterium"
+ },
+ "gtdb_grounding_status": "UNRESOLVED"
+ },
+ "abundance_level": "COMMON",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonadaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Lotus_LjSC3",
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobiaceae bacterium",
+ "taxon_id": "NCBITaxon:1913961",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobiaceae bacterium",
+ "term": {
+ "id": "NCBITaxon:1913961",
+ "label": "Rhizobiaceae bacterium"
+ },
+ "gtdb_grounding_status": "UNRESOLVED"
+ },
+ "abundance_level": "ABUNDANT",
+ "functional_role": [
+ "SYNTROPHIC_PARTNER"
+ ],
+ "evidence": [
+ {
+ "reference": "PMID:34312531",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobiaceae bacterium' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Nitrifying_Wastewater_Ammonia_Oxidizing_Consortium",
+ "type": "DISCONNECTED",
+ "taxon": "Legionella MAGs",
+ "taxon_id": "NCBITaxon:445",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Legionella MAGs",
+ "term": {
+ "id": "NCBITaxon:445",
+ "label": "Legionella"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The study detected Legionella-affiliated MAGs and used them in a virulence-gene risk assessment; the source did not assert pathogenicity for a cultured Legionella isolate.\n"
+ },
+ "abundance_value": "Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\n",
+ "evidence": [
+ {
+ "reference": "PMID:41457319",
+ "supports": "SUPPORT",
+ "evidence_source": "COMPUTATIONAL",
+ "snippet": "detection of waterborne pathogens from the Legionella genus",
+ "explanation": "Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\n"
+ }
+ ]
+ },
+ "message": "Taxon 'Legionella MAGs' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Polaromonas species",
+ "taxon_id": "NCBITaxon:52972",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Polaromonas species",
+ "term": {
+ "id": "NCBITaxon:52972",
+ "label": "Polaromonas"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Polaromonas",
+ "gtdb_taxon": "Polaromonas",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas",
+ "ncbi_source_id": "NCBITaxon:52972",
+ "majority_fraction": 1.0,
+ "support_genomes": 12,
+ "total_genomes": 12,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 1 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Betaproteobacteria capable of dissimilatory vanadium reduction in contaminated mine environments. While not specifically reported in the Panzhihua tailings studies reviewed, Polaromonas is a well-established V(V)-reducing organism in circumneutral pH vanadium mine tailings in northern China and likely present in Panzhihua tailings based on similar environmental conditions (circumneutral pH 6.5-7.5, moderate temperature, high vanadium concentrations). Polaromonas performs dissimilatory V(V) reduction to V(IV) using c-type cytochromes (cymA, omcA) and membrane-associated nitrate reductases (narG). The organism couples oxidation of organic electron donors (lactate, acetate) to V(V) reduction, decreasing vanadium solubility by 2-3 orders of magnitude through precipitation of V(IV) species. This metabolic capacity is critical for vanadium immobilization during anaerobic microsites in revegetated tailings. Polaromonas also reduces Fe(III), Mn(IV), and As(V), contributing to polymetallic redox cycling in V-Ti tailings.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Inferred presence based on V-reducing capacity in similar V-Ti tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Establishes V(V) reduction mechanism relevant to Panzhihua conditions"
+ }
+ ]
+ },
+ "message": "Taxon 'Polaromonas species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium pisi",
+ "taxon_id": "NCBITaxon:574561",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium pisi",
+ "term": {
+ "id": "NCBITaxon:574561",
+ "label": "Rhizobium pisi"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Fast-growing nitrogen-fixing rhizobium traditionally associated with pea (Pisum sativum) but adapted to form nodules with P. pinnata in V-Ti tailings. One isolate was identified as R. pisi, demonstrating the promiscuity of rhizobial-legume associations under metal stress conditions. R. pisi contributes to nitrogen enrichment of tailings soil through symbiotic nitrogen fixation and produces plant growth-promoting substances including IAA. The presence of R. pisi indicates that phytoremediation legumes can recruit diverse rhizobial species from indigenous tailings microbiota, not limited to traditional host-specific symbionts. This metabolic flexibility enhances the resilience and effectiveness of legume-rhizobia partnerships in contaminated environments.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "RARE",
+ "abundance_value": "One isolate from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. pisi presence in V-Ti tailings rhizobia"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium pisi' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Panzhihua_Vanadium_Titanium_Tailings",
+ "type": "DISCONNECTED",
+ "taxon": "Rhizobium selenitireducens",
+ "taxon_id": "NCBITaxon:1336235",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Rhizobium selenitireducens",
+ "term": {
+ "id": "NCBITaxon:1336235",
+ "label": "Paenirhizobium selenitireducens ATCC BAA-1503"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "Nitrogen-fixing alphaproteobacterium capable of selenium reduction and heavy metal tolerance, isolated from P. pinnata root nodules in V-Ti tailings. Three isolates were identified as R. selenitireducens, demonstrating nitrogen-fixing capacity and variable tolerance to Cu, Ni, Mn, and Zn. This species possesses unique metabolic capabilities including selenite reduction to elemental selenium, suggesting potential for metalloid detoxification in addition to nitrogen fixation. R. selenitireducens contributes to the functional diversity of the rhizobial community, providing complementary metal tolerance mechanisms and nitrogen enrichment. The organism forms effective symbioses with leguminous plants under metal stress conditions, promoting plant growth through nitrogen provision and IAA production. Like other tailings rhizobia, R. selenitireducens serves as a competent candidate for bioremediation of soils contaminated with multifarious metals due to its combined nitrogen-fixing and metal tolerance phenotypes.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "CROSS_FEEDER",
+ "NITROGEN_FIXING_SYMBIONT"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "Three isolates from P. pinnata nodules",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Based on the phylogenetic analysis of 16S rRNA and four house-keeping genes (atpD, recA, rpoB, glnII), twelve isolates were identified as Bradyrhizobium pachyrhizi, four as Ochrobactrum anthropic, three as Rhizobium selenitireducens and one as Rhizobium pisi",
+ "explanation": "Documents R. selenitireducens presence in tailings rhizobia"
+ },
+ {
+ "reference": "doi:10.3389/fmicb.2023.1078333",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "effective rhizobia strains for bioremediation of VTM tailings or other contaminated soils",
+ "explanation": "Establishes metal tolerance and bioremediation potential"
+ }
+ ]
+ },
+ "message": "Taxon 'Rhizobium selenitireducens' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Phormidium_Alkaline_Consortium",
+ "type": "DISCONNECTED",
+ "taxon": "Bacteroidota members",
+ "taxon_id": "NCBITaxon:976",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Bacteroidota members",
+ "term": {
+ "id": "NCBITaxon:976",
+ "label": "Bacteroidota"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:p__Bacteroidota",
+ "gtdb_taxon": "Bacteroidota",
+ "gtdb_lineage": "d__Bacteria;p__Bacteroidota",
+ "ncbi_source_id": "NCBITaxon:976",
+ "majority_fraction": 0.999,
+ "support_genomes": 151365,
+ "total_genomes": 151454,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at p__ rank; 5 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Multiple heterotrophic Bacteroidota species present in the consortium. These organisms contribute to organic matter degradation, polysaccharide utilization, and nutrient cycling. They occupy ecological niches related to fermentation product utilization and compatible solute metabolism.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SECONDARY_FERMENTER"
+ ],
+ "abundance_level": "COMMON",
+ "evidence": [
+ {
+ "reference": "doi:10.3389/fmicb.2022.780346",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Using shotgun metagenomic sequencing, 29 heterotrophic metagenome-assembled-genomes (MAGs) were retrieved and were assigned to Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, Planctomycetota, and Archaea",
+ "explanation": "Documents presence of diverse Bacteroidota in the heterotrophic community"
+ }
+ ]
+ },
+ "message": "Taxon 'Bacteroidota members' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Desulfitobacterium species",
+ "taxon_id": "NCBITaxon:36853",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfitobacterium species",
+ "term": {
+ "id": "NCBITaxon:36853",
+ "label": "Desulfitobacterium"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfitobacterium",
+ "gtdb_taxon": "Desulfitobacterium",
+ "gtdb_lineage": "d__Bacteria;p__Bacillota_B;c__Desulfitobacteriia;o__Desulfitobacteriales;f__Desulfitobacteriaceae;g__Desulfitobacterium",
+ "ncbi_source_id": "NCBITaxon:36853",
+ "majority_fraction": 0.939,
+ "support_genomes": 46,
+ "total_genomes": 49,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 2 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-positive, spore-forming bacteria (Firmicutes phylum) capable of organohalide respiration and metal reduction. Desulfitobacterium species comprise 3-6% of the tailings community and perform dissimilatory reduction of V(V), Cr(VI), and arsenate using respiratory reductases. This genus couples oxidation of hydrogen, formate, lactate, and pyruvate to reduction of electron acceptors including V(V) and sulfite. Desulfitobacterium exhibits greater tolerance to acidic pH (5.5-7.0) and high metal concentrations compared to many deltaproteobacteria, enabling activity in variable tailings microenvironments. Spore formation provides resilience during desiccation or oxidative episodes in surface tailings. The organism expresses reductive dehalogenase homologs (rdhA genes) that reduce V(V) as an alternative electron acceptor. Desulfitobacterium contributes to vanadium reduction particularly in hydrogen-rich microniches generated by fermentative bacteria.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "3-6% in tailings",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents presence and enrichment under H\u2082 amendment"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfitobacterium species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Desulfovibrio species",
+ "taxon_id": "NCBITaxon:872",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Desulfovibrio species",
+ "term": {
+ "id": "NCBITaxon:872",
+ "label": "Desulfovibrio"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:g__Desulfovibrio",
+ "gtdb_taxon": "Desulfovibrio",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio",
+ "ncbi_source_id": "NCBITaxon:872",
+ "majority_fraction": 0.931,
+ "support_genomes": 551,
+ "total_genomes": 592,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [grounded at g__ rank; 9 GTDB taxa under the NCBI taxon]"
+ },
+ "notes": "Gram-negative deltaproteobacteria performing dissimilatory sulfate reduction in the vanadium tailings. Desulfovibrio oxidizes organic acids (lactate, pyruvate, formate) and hydrogen coupled to sulfate reduction, producing hydrogen sulfide (H\u2082S) that chemically reduces V(V) to V(IV) and precipitates vanadium as sulfide minerals. Additionally, Desulfovibrio can enzymatically reduce V(V) through periplasmic and cytoplasmic reductases. The organism comprises 8-12% of the tailings community and increases under sulfate-rich, organic-amended conditions. Hydrogen sulfide generated by Desulfovibrio (concentrations reaching 50-200 \u00b5M) creates strongly reducing microenvironments (Eh < -200 mV) that favor vanadium immobilization. Desulfovibrio species are known to reduce multiple toxic metals including uranium, chromium, and technetium, contributing to polymetallic remediation in this system.\n"
+ },
+ "functional_role": [
+ "SECONDARY_FERMENTER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "8-12% in tailings; enriched under sulfate amendment",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Microorganisms can reduce the more toxic and mobile VV to the less toxic and immobile VIV, which could be a detoxification and energy metabolism strategy adopted by V-reducing bacteria (VRB)",
+ "explanation": "Documents Desulfovibrio presence in vanadium tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "bacteria associated with Polaromonas",
+ "explanation": "Links sulfate reduction to vanadium immobilization"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VITRO",
+ "snippet": "VV-reducing enrichments",
+ "explanation": "Establishes dual mechanisms for vanadium reduction"
+ }
+ ]
+ },
+ "message": "Taxon 'Desulfovibrio species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Polaromonas_Vanadium_Reduction_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Geobacter species",
+ "taxon_id": "NCBITaxon:28232",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Geobacter species",
+ "term": {
+ "id": "NCBITaxon:28232",
+ "label": "Geobacter metallireducens"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Geobacter_metallireducens",
+ "gtdb_taxon": "Geobacter metallireducens",
+ "gtdb_lineage": "d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geobacter;s__Geobacter metallireducens",
+ "ncbi_source_id": "NCBITaxon:28232",
+ "majority_fraction": 1.0,
+ "total_genomes": 4,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25) [mapped via NCBI species name \u2014 no species-level NCBI id in table]"
+ },
+ "notes": "Deltaproteobacteria specialized in dissimilatory metal reduction, present at 5-8% relative abundance in vanadium tailings. Geobacter oxidizes acetate and other organic acids coupled to reduction of Fe(III), Mn(IV), and V(V). This genus possesses extensive arrays of c-type cytochromes enabling extracellular electron transfer to metal oxides and soluble metal ions. In vanadium tailings, Geobacter reduces co-occurring Fe(III) minerals, creating reducing conditions that facilitate V(V) reduction by other community members. Geobacter can directly reduce V(V) through outer membrane cytochromes (OmcB, OmcS, OmcZ) and periplasmic reductases. The organism is particularly important in zones with high Fe(III) content (common in vanadium titanomagnetite tailings), where Fe(III) reduction precedes and enhances V(V) reduction. Geobacter forms syntrophic relationships with Polaromonas, potentially exchanging electrons or metabolites.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER",
+ "SYNTROPHIC_PARTNER"
+ ],
+ "abundance_level": "COMMON",
+ "abundance_value": "5-8% in tailings; enriched in Fe(III)-rich zones",
+ "evidence": [
+ {
+ "reference": "PMID:33125214",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Further, VV-reducing enrichments indicated that bacteria associated with Polaromonas, a genus belonging to the family Burkholderiaceae, were potentially responsible for VV reduction",
+ "explanation": "Documents Geobacter presence in Fe/V-contaminated tailings"
+ },
+ {
+ "reference": "PMID:33125214",
+ "supports": "PARTIAL",
+ "evidence_source": "IN_VIVO",
+ "snippet": "reduce the more toxic and mobile VV to the less toxic and immobile VIV",
+ "explanation": "Describes role in sequential metal reduction processes"
+ },
+ {
+ "reference": "PMID:19077236",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth",
+ "explanation": "Confirms V(V) reduction capability"
+ }
+ ]
+ },
+ "message": "Taxon 'Geobacter species' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas aeruginosa MDR6-CAZ",
+ "taxon_id": "NCBITaxon:287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas aeruginosa MDR6-CAZ",
+ "term": {
+ "id": "NCBITaxon:287",
+ "label": "Pseudomonas aeruginosa"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Pseudomonas_aeruginosa",
+ "gtdb_taxon": "Pseudomonas aeruginosa",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa",
+ "ncbi_source_id": "NCBITaxon:287",
+ "majority_fraction": 0.99,
+ "total_genomes": 17191,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "The eLife panel denotes this P. aeruginosa mutant as strain 8; represented at species level for ontology stability."
+ },
+ "strain_designation": {
+ "strain_name": "MDR6-CAZ"
+ },
+ "abundance_value": "Full-factorial SynCom panel member 8",
+ "evidence": [
+ {
+ "reference": "PMID:42153623",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Strains 1\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ",
+ "explanation": "Maps the source's strain numbers to the eight P. aeruginosa mutant labels."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas aeruginosa MDR6-CAZ' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas aeruginosa NfxB-CAZ",
+ "taxon_id": "NCBITaxon:287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas aeruginosa NfxB-CAZ",
+ "term": {
+ "id": "NCBITaxon:287",
+ "label": "Pseudomonas aeruginosa"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Pseudomonas_aeruginosa",
+ "gtdb_taxon": "Pseudomonas aeruginosa",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa",
+ "ncbi_source_id": "NCBITaxon:287",
+ "majority_fraction": 0.99,
+ "total_genomes": 17191,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "The eLife panel denotes this P. aeruginosa mutant as strain 7; represented at species level for ontology stability."
+ },
+ "strain_designation": {
+ "strain_name": "NfxB-CAZ"
+ },
+ "abundance_value": "Full-factorial SynCom panel member 7",
+ "evidence": [
+ {
+ "reference": "PMID:42153623",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Strains 1\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ",
+ "explanation": "Maps the source's strain numbers to the eight P. aeruginosa mutant labels."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas aeruginosa NfxB-CAZ' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas aeruginosa OrfN",
+ "taxon_id": "NCBITaxon:287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas aeruginosa OrfN",
+ "term": {
+ "id": "NCBITaxon:287",
+ "label": "Pseudomonas aeruginosa"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Pseudomonas_aeruginosa",
+ "gtdb_taxon": "Pseudomonas aeruginosa",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa",
+ "ncbi_source_id": "NCBITaxon:287",
+ "majority_fraction": 0.99,
+ "total_genomes": 17191,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "The eLife panel denotes this P. aeruginosa mutant as strain 6; represented at species level for ontology stability."
+ },
+ "strain_designation": {
+ "strain_name": "OrfN"
+ },
+ "abundance_value": "Full-factorial SynCom panel member 6",
+ "evidence": [
+ {
+ "reference": "PMID:42153623",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Strains 1\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ",
+ "explanation": "Maps the source's strain numbers to the eight P. aeruginosa mutant labels."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas aeruginosa OrfN' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas aeruginosa PA14",
+ "taxon_id": "NCBITaxon:287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas aeruginosa PA14",
+ "term": {
+ "id": "NCBITaxon:287",
+ "label": "Pseudomonas aeruginosa"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Pseudomonas_aeruginosa",
+ "gtdb_taxon": "Pseudomonas aeruginosa",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa",
+ "ncbi_source_id": "NCBITaxon:287",
+ "majority_fraction": 0.99,
+ "total_genomes": 17191,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "The eLife panel denotes this P. aeruginosa mutant as strain 2; represented at species level for ontology stability."
+ },
+ "strain_designation": {
+ "strain_name": "PA14"
+ },
+ "abundance_value": "Full-factorial SynCom panel member 2",
+ "evidence": [
+ {
+ "reference": "PMID:42153623",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Strains 1\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ",
+ "explanation": "Maps the source's strain numbers to the eight P. aeruginosa mutant labels."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas aeruginosa PA14' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Pseudomonas_Aeruginosa_EightStrain_Full_Factorial_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas aeruginosa mexZ",
+ "taxon_id": "NCBITaxon:287",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas aeruginosa mexZ",
+ "term": {
+ "id": "NCBITaxon:287",
+ "label": "Pseudomonas aeruginosa"
+ },
+ "gtdb_grounding_status": "GROUNDED",
+ "gtdb_classification": {
+ "gtdb_id": "GTDB:s__Pseudomonas_aeruginosa",
+ "gtdb_taxon": "Pseudomonas aeruginosa",
+ "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;s__Pseudomonas aeruginosa",
+ "ncbi_source_id": "NCBITaxon:287",
+ "majority_fraction": 0.99,
+ "total_genomes": 17191,
+ "is_reclassified": false,
+ "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+ },
+ "notes": "The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability."
+ },
+ "strain_designation": {
+ "strain_name": "mexZ"
+ },
+ "abundance_value": "Full-factorial SynCom panel member 5",
+ "evidence": [
+ {
+ "reference": "PMID:42153623",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Strains 1\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ",
+ "explanation": "Maps the source's strain numbers to the eight P. aeruginosa mutant labels."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas aeruginosa mexZ' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom",
+ "type": "UNKNOWN_TARGET",
+ "interaction": "Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia",
+ "interaction_index": 0,
+ "taxon": "Sclerotinia sclerotiorum",
+ "severity": "warning",
+ "message": "Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)"
+ },
+ {
+ "record": "Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom",
+ "type": "UNKNOWN_TARGET",
+ "interaction": "Trinickia MC Key Contribution to Sclerotia Mortality",
+ "interaction_index": 1,
+ "taxon": "Sclerotinia sclerotiorum",
+ "severity": "warning",
+ "message": "Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Acinetobacter radioresistens 50V1",
+ "taxon_id": "NCBITaxon:40216",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Acinetobacter radioresistens 50V1",
+ "term": {
+ "id": "NCBITaxon:40216",
+ "label": "Acinetobacter radioresistens"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level."
+ },
+ "strain_designation": {
+ "strain_name": "50V1",
+ "genome_accession": "GCA_002834555.1"
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \u00b0C | 16\u201318 h",
+ "explanation": "Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Acinetobacter radioresistens 50V1' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Micrococcus luteus W4-Al-K1",
+ "taxon_id": "NCBITaxon:1270",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Micrococcus luteus W4-Al-K1",
+ "term": {
+ "id": "NCBITaxon:1270",
+ "label": "Micrococcus luteus"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level."
+ },
+ "strain_designation": {
+ "strain_name": "W4-Al-K1",
+ "genome_accession": "GCA_057816565.1"
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Micrococcus luteus | W4-Al-K1 | ISS, Touch Array Aluminum Case | - | Kr\u00e4mer et al., 2025 | GCA_057816565.1 | NB, TSYB/TSYA | 37 \u00b0C | 24 h",
+ "explanation": "Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Micrococcus luteus W4-Al-K1' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Propionibacterium cyclohexanicum TA-12T",
+ "taxon_id": "NCBITaxon:64702",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Propionibacterium cyclohexanicum TA-12T",
+ "term": {
+ "id": "NCBITaxon:64702",
+ "label": "Propionibacterium cyclohexanicum"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative."
+ },
+ "strain_designation": {
+ "strain_name": "TA-12T",
+ "genome_accession": "GCA_900111365",
+ "culture_collections": [
+ {
+ "collection": "DSM",
+ "accession": "16859"
+ }
+ ]
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Propionibacterium cyclohexanicum | TA-12 T | Spoilt Orange Juice | DSM 16859 T | Kusano et al., 1997 | GCA_900111365 | BHI, TSYB/TSYA | 37 \u00b0C | 24 h",
+ "explanation": "Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Pseudomonas antarctica CMS 35T",
+ "taxon_id": "NCBITaxon:219572",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Pseudomonas antarctica CMS 35T",
+ "term": {
+ "id": "NCBITaxon:219572",
+ "label": "Pseudomonas antarctica"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate."
+ },
+ "strain_designation": {
+ "strain_name": "CMS 35T",
+ "genome_accession": "GCA_010634845",
+ "culture_collections": [
+ {
+ "collection": "DSM",
+ "accession": "15318"
+ }
+ ]
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\u201316 h",
+ "explanation": "Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Pseudomonas antarctica CMS 35T' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Staphylococcus capitis K1-2-2-23",
+ "taxon_id": "NCBITaxon:29388",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Staphylococcus capitis K1-2-2-23",
+ "term": {
+ "id": "NCBITaxon:29388",
+ "label": "Staphylococcus capitis"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The isolate was recovered from ISS V2A steel; ontology grounding is at species level."
+ },
+ "strain_designation": {
+ "strain_name": "K1-2-2-23",
+ "genome_accession": "GCA_025272695",
+ "culture_collections": [
+ {
+ "collection": "DSM",
+ "accession": "111179"
+ }
+ ]
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Staphylococcus capitis | K1-2-2-23 | ISS, V2A Steel | DSM 111179 | Sobisch et al., 2019 | GCA_025272695 | TSYB/TSYA | 37 \u00b0C | 16\u201324 h",
+ "explanation": "Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom",
+ "type": "DISCONNECTED",
+ "taxon": "Streptococcus halotolerans HTS9T",
+ "taxon_id": "NCBITaxon:1814128",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Streptococcus halotolerans HTS9T",
+ "term": {
+ "id": "NCBITaxon:1814128",
+ "label": "Streptococcus halotolerans"
+ },
+ "gtdb_grounding_status": "UNRESOLVED",
+ "notes": "The source used the S. halotolerans type strain as a biosafety-level-1 representative."
+ },
+ "strain_designation": {
+ "strain_name": "HTS9T",
+ "genome_accession": "GCA_001598035",
+ "culture_collections": [
+ {
+ "collection": "DSM",
+ "accession": "101996"
+ }
+ ]
+ },
+ "evidence": [
+ {
+ "reference": "PMID:42577390",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VITRO",
+ "snippet": "Streptococcus halotolerans | HTS9 T | Respiratory Tract of Marmota himalayana | DSM 101996 T | Niu et al., 2016 | GCA_001598035 | 2xLB, TSYB/TSYA | 37 \u00b0C | 24 h",
+ "explanation": "Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions."
+ }
+ ]
+ },
+ "message": "Taxon 'Streptococcus halotolerans HTS9T' has no interactions",
+ "severity": "warning"
+ },
+ {
+ "record": "Tinto_River_Iron_Cycling_Community",
+ "type": "DISCONNECTED",
+ "taxon": "Basidiomycota",
+ "taxon_id": "NCBITaxon:5204",
+ "taxon_data": {
+ "taxon_term": {
+ "preferred_term": "Basidiomycota",
+ "term": {
+ "id": "NCBITaxon:5204",
+ "label": "Basidiomycota"
+ },
+ "gtdb_grounding_status": "NO_GTDB_EQUIVALENT",
+ "notes": "Acidophilic fungi including Hortaea werneckii (black yeast) detected in Rio Tinto sediments and water. Fungi contribute to organic matter degradation, biofilm formation, and nutrient cycling through extracellular enzyme secretion.\n"
+ },
+ "functional_role": [
+ "PRIMARY_DEGRADER"
+ ],
+ "abundance_level": "RARE",
+ "evidence": [
+ {
+ "reference": "PMID:25369810",
+ "supports": "SUPPORT",
+ "evidence_source": "IN_VIVO",
+ "snippet": "Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons",
+ "explanation": "Documents fungal presence"
+ }
+ ]
+ },
+ "message": "Taxon 'Basidiomycota' has no interactions",
+ "severity": "warning"
+ }
+ ]
+ },
+ "network_unchanged": true,
+ "evidence_matches": [
+ {
+ "path": "/taxonomy/0/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/taxonomy/1/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/ecological_interactions/0/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/ecological_interactions/1/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/ecological_interactions/1/evidence/1",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/ecological_interactions/2/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/environmental_factors/0/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/environmental_factors/1/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/related_ingredients/0/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/related_ingredients/1/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ },
+ {
+ "path": "/associated_datasets/0/evidence/0",
+ "reference": "PMID:25416774",
+ "literal_primary_match": true,
+ "literal_cache_match": true
+ }
+ ],
+ "source_access": {
+ "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4292484/",
+ "pmid": "25416774",
+ "doi": "10.1128/AEM.02682-14",
+ "html_sha256": "21b5fd77c31cfbf4cc18a51893908e08cfc85529baad9c3ec60a0e93ad77267d",
+ "text_sha256": "2e1d16b5c0b6cbd7833f936a87bf167dd204cb82ca63ebe44f89a95afa2e4458",
+ "paragraph_count": 83,
+ "source_notice": "Copyright 2015 American Society for Microbiology. All rights reserved.",
+ "repository_import": "Short attributed quotations only; full body retained outside repository."
+ },
+ "limitations": [
+ "Primary main body, Methods, Results, Table1, captions and Discussion through conclusions read. Figure pixels, supplement, raw data and cited earlier studies not independently audited.",
+ "Roster and related-ingredient fields are necessary dependencies of inherited graph membership and its chemistry, explicitly extending the otherwise graph-only repair boundary for issue1267.",
+ "NCBITaxon2836 Bacillariophyta and CHEBI16136 hydrogen sulfide verified against official NCBI/ChEBI pages. Existing GTDB mapping and article-as-dataset metadata are not certified.",
+ "Three nodes and two arrows unchanged in identity and direction; only the first node description changes. Open mechanism discussion remains appropriate after identity repair.",
+ "One short eight-word excerpt appendix; original cache prefix retained. No full article import, provider submission, credits or new causal topology.",
+ "Source-based self-adversarial review, not independent approval. Issue1267 can close only after protected-main merge. Issue1268 covers other records and remains open."
+ ],
+ "tested_file_sha256": {
+ "kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml": "79a9597722d1caa4abad454a53464a9671801ec4d52d5b809a42ec003e90fd79",
+ "references_cache/PMID_25416774.txt": "686490fadcc5e7864de153e175e00dafdb40b8977465517dccc761c2551e5ddc",
+ "reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml": "b753d01726b8c230018a13e2462eff8f394959b347a4324f92ef0db2857d79ca",
+ "tests/test_causal_review_batch8.py": "c4dbbd3060db8153107d29343e58cf1536792fef2653969e4e0043e954d631bf",
+ "tests/test_causal_review_batch125.py": "78ef4667222d57fbcc4d5e4a567fe165cacf1873781a79203e398edb4b350dc5",
+ "docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html": "039278994461ae13bcc739c079a208eb487a00abefcdce81301d95873b587701",
+ "history/records/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml": "b9579a45ffef217a8d510dad062da82a92adf48f0f227bfe4d7be9ca5fff522a",
+ "reports/causal_graph_review/README.md": "b39624f5f3f899a4700d551508dac0451e06e69516142373bd5b59e848d46c42"
+ },
+ "report_wording_correction": "Node dictionaries were compared structurally, not as raw byte slices.",
+ "reference_scope": "Reference validator checks 10 distinct quotations; snippet audit and fresh-primary comparison cover all 11 instances. Literal matching is not entailment proof.",
+ "development_corrections": [
+ "Dry-run guard initially miscounted the two short excerpts as nine words; corrected to their actual eight before any canonical write."
+ ],
+ "total_recorded_gate_outputs": 20
+}
diff --git a/tests/test_causal_review_batch125.py b/tests/test_causal_review_batch125.py
new file mode 100644
index 000000000..b33ffc8db
--- /dev/null
+++ b/tests/test_causal_review_batch125.py
@@ -0,0 +1,152 @@
+"""Diatom identity repair must not manufacture species, partners, or mechanisms."""
+
+import copy
+import hashlib
+from pathlib import Path
+
+import pytest
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+STEM = "Cable_Bacteria_Photosynthetic_Biofilm_Sediment"
+PATH = ROOT / "kb/communities" / f"{STEM}.yaml"
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-cable-biofilm-batch125.yaml"
+
+
+def record():
+ return yaml.safe_load(PATH.read_text())
+
+
+def assert_roster(doc):
+ cable, diatoms = doc["taxonomy"]
+ assert cable["taxon_term"]["term"]["id"] == "NCBITaxon:213121"
+ assert cable["functional_role"] == ["CROSS_FEEDER"]
+ assert diatoms["taxon_term"]["term"] == {
+ "id": "NCBITaxon:2836",
+ "label": "Bacillariophyta",
+ }
+ assert diatoms["taxon_term"]["gtdb_grounding_status"] == "NO_GTDB_EQUIVALENT"
+ assert "does not identify a species" in diatoms["taxon_term"]["notes"]
+ assert "defined two-member culture" in diatoms["taxon_term"]["notes"]
+ assert diatoms["evidence"][0]["snippet"] == "dominated by diatoms"
+
+
+def assert_chemistry(doc):
+ sulfide = doc["related_ingredients"][0]
+ assert sulfide["chebi_term"] == {"id": "CHEBI:16136", "label": "hydrogen sulfide"}
+ assert "H2S and HS-" in sulfide["relevance"]
+ assert "does not identify all dissolved sulfide as H2S" in sulfide["relevance"]
+ assert "no exclusive molecular uptake mechanism" in sulfide["evidence"][0]["explanation"]
+
+
+def assert_graph(doc):
+ oxygen, conduction, response = doc["ecological_interactions"]
+ assert oxygen["interaction_type"] == "CROSS_FEEDING"
+ assert "reciprocal benefit to the phototrophs is not established" in oxygen["description"]
+ assert "not species-resolved partners" in oxygen["description"]
+ assert "proposed mechanisms" in conduction["description"]
+ assert "not independent sediment-core replicates" in response["description"]
+ assert "nonsignificant current-density contrasts" in response["description"]
+ assert "inconsistent reported sulfide-depth significance" in response["description"]
+ assert all(n["scope"] == "COMMUNITY_LEVEL" for n in (oxygen, conduction, response))
+ assert all(not n.get("participating_taxa") for n in (oxygen, conduction, response))
+ assert all("interaction_type" not in n for n in (conduction, response))
+ assert oxygen["downstream"][0]["target"] == conduction["name"]
+ assert conduction["downstream"][0]["target"] == response["name"]
+ assert not response.get("downstream")
+
+
+def test_identity_chemistry_and_retained_graph():
+ doc = record()
+ assert_roster(doc)
+ assert_chemistry(doc)
+ assert_graph(doc)
+ assert "NCBITaxon:3041" not in str(doc)
+ assert "CHEBI:15138" not in str(doc)
+ assert doc["discussions"][0]["status"] == "OPEN"
+ assert "remain unresolved" in doc["discussions"][0]["rationale"]
+
+
+def test_review_supersession_preserves_historical_gap_and_topology():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ row = ledger["records"][0]
+ parent_path = ROOT / row["supersedes_review"]["review_file"]
+ parent = next(
+ r for r in yaml.safe_load(parent_path.read_text())["records"] if r["id"] == row["id"]
+ )
+ assert parent["status"] == "needs_research"
+ assert row["status"] == "reviewed"
+ assert (
+ row["original_sha256"]
+ == row["supersedes_review"]["record_sha256"]
+ == parent["record_sha256"]
+ )
+ assert row["record_sha256"] == hashlib.sha256(PATH.read_bytes()).hexdigest()
+ doc = record()
+ edges = [
+ dict(source=n["name"], **e)
+ for n in doc["ecological_interactions"]
+ for e in n.get("downstream", [])
+ ]
+ assert edges == row["edges_before"] == row["edges_after"] == parent["edges_after"]
+ assert len(edges) == 2 and len(row["node_decisions"]) == 3
+ assert ledger["edison"] == {"required": False, "provider_submissions": 0, "credits_spent": 0}
+ assert not ledger["independent_approval"]
+ assert len(row["history_files"]) == 1
+ assert (ROOT / row["history_files"][0]).is_file()
+ assert len(doc["curation_history"]) == 2
+ assert doc["curation_history"][-1]["llm_assisted"]
+
+
+def test_short_attributed_cache_appendix_and_source_scope():
+ ledger = yaml.safe_load(LEDGER.read_text())
+ change = ledger["cache_changes"][0]
+ cache = (ROOT / change["path"]).read_text()
+ assert hashlib.sha256(cache.encode()).hexdigest() == change["after_sha256"]
+ appendix = cache.split("## Primary-source excerpts", 1)[1]
+ assert "PMC4292484" in appendix and "American Society for Microbiology" in appendix
+ assert change["appended_excerpt_words"] == 8
+ assert len(appendix) < 500
+ assert len(ledger["snippet_checks"]) == 11
+ assert all(
+ c["literal_primary_match"] and c["literal_cache_match"] for c in ledger["snippet_checks"]
+ )
+ assert "Figure pixels, supplement, raw data" in ledger["limitations"][0]
+
+
+@pytest.mark.parametrize(
+ "mutation",
+ ["green_algae", "syntrophy", "sulfide_dianion", "unqualified_uptake", "mutual_benefit"],
+)
+def test_scientific_regression_probes(mutation):
+ doc = record()
+ for check in (assert_roster, assert_chemistry, assert_graph):
+ check(doc)
+ altered = copy.deepcopy(doc)
+ if mutation == "green_algae":
+ altered["taxonomy"][1]["taxon_term"]["term"] = {
+ "id": "NCBITaxon:3041",
+ "label": "Chlorophyta",
+ }
+ check = assert_roster
+ elif mutation == "syntrophy":
+ altered["taxonomy"][0]["functional_role"].append("SYNTROPHIC_PARTNER")
+ check = assert_roster
+ elif mutation == "sulfide_dianion":
+ altered["related_ingredients"][0]["chebi_term"] = {
+ "id": "CHEBI:15138",
+ "label": "sulfide(2-)",
+ }
+ check = assert_chemistry
+ elif mutation == "unqualified_uptake":
+ altered["related_ingredients"][0]["evidence"][0][
+ "explanation"
+ ] = "Establishes exclusive molecular uptake."
+ check = assert_chemistry
+ else:
+ altered["ecological_interactions"][0]["description"] = "Reciprocal benefit is established."
+ check = assert_graph
+ assert altered != doc
+ with pytest.raises(AssertionError):
+ check(altered)
+ check(doc)
diff --git a/tests/test_causal_review_batch8.py b/tests/test_causal_review_batch8.py
index 0922aefa9..a4653b565 100644
--- a/tests/test_causal_review_batch8.py
+++ b/tests/test_causal_review_batch8.py
@@ -147,7 +147,7 @@ def test_calcium_separates_compounds_exudates_and_pots():
assert all("interaction_type" not in n for n in (compounds, exudates, pots))
-def test_cable_partial_taxonomy_repair_is_not_certified():
+def test_cable_historical_partial_review_and_mechanism_bounds_are_preserved():
graph = nodes("Cable_Bacteria_Photosynthetic_Biofilm_Sediment")
oxygen, conduction, response = graph
assert oxygen["interaction_type"] == "CROSS_FEEDING"
@@ -155,7 +155,7 @@ def test_cable_partial_taxonomy_repair_is_not_certified():
assert oxygen["downstream"][0]["target"] == conduction["name"]
assert conduction["downstream"][0]["target"] == response["name"]
assert "NCBITaxon:3041" not in str(graph)
- assert "connectivity still inherits that unresolved roster" in oxygen["description"]
+ assert "reciprocal benefit to the phototrophs is not established" in oxygen["description"]
assert not any(n.get("participating_taxa") for n in graph)
ledger = yaml.safe_load(
(
|