realmarcin · Oct 8, 2026
diff --git a/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html b/docs/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.html
@@ -474,8 +474,6 @@ <h2>Taxonomy</h2>
 
                             <div class="roles-list">
 
-                                <span class="role-badge">SYNTROPHIC_PARTNER</span>
-
                                 <span class="role-badge">CROSS_FEEDER</span>
 
                             </div>
@@ -506,12 +504,12 @@ <h2>Taxonomy</h2>
 
                     <tr>
                         <td>
-                            <strong>oxygenic algal biofilm<span class="ontology-label"> — ontology label: Chlorophyta</span></strong>
+                            <strong>diatom-dominated photosynthetic biofilm<span class="ontology-label"> — ontology label: Bacillariophyta</span></strong>
                         </td>
                         <td>
-                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3041"
+                            <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2836"
                                class="term-link" target="_blank" rel="noopener noreferrer">
-                                NCBITaxon:3041
+                                NCBITaxon:2836
                             </a>
                         </td>
                         <td>
@@ -537,7 +535,7 @@ <h2>Taxonomy</h2>
 
                                     - SUPPORT (IN_VITRO)
 
-                                    <div class="snippet">"a photosynthetic algal biofilm"</div>
+                                    <div class="snippet">"dominated by diatoms"</div>
 
                                 </li>
 
@@ -586,7 +584,7 @@ <h2>Ecological Interactions</h2>
                     <h3>Photosynthesis Stimulates Cable-Bacteria Electron Harvesting</h3>
                     <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-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&#39;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.</p>
+                <p class="prewrap interaction-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. 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.</p>
 
 
 
@@ -816,9 +814,9 @@ <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
                 <h3>
                     <span class="role-badge">KNOWLEDGE_GAP</span>
                     <span class="role-badge">OPEN</span>
-                    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?
                 </h3>
-                <p class="prewrap">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.</p>
+                <p class="prewrap">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.</p>
 
                 <p class="muted small">Attaches to: <code>ecological_interactions#Photosynthesis Stimulates Cable-Bacteria Electron Harvesting</code>, <code>ecological_interactions#Electrogenic Sulfide Oxidation across Sediment Redox Zones</code>, <code>ecological_interactions#Rapid Redox Signal Transmission under Diel Illumination</code></p>
 
@@ -957,12 +955,12 @@ <h2>Environmental Factors</h2>
             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/...cords/Cable_Bacteria_Photosynthetic_Biofilm_Sediment/2026-10-08T194617Z-codex-d8c9fa.yaml b/...cords/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
@@ -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
@@ -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]
+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
@@ -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),