diff --git a/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html b/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
index 66780aa26..569f568c5 100644
--- a/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
+++ b/docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
@@ -585,17 +585,12 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Dehalococcoides-Pelobacter Acetylene TCE Coculture</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy, colonization facilitation).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
                         <span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
                     </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
                              aria-hidden="true" data-symbol="symbolTriangle"
@@ -603,8 +598,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolPlus"
-                             data-color="#edab12"></svg> Colonization facilitation
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -615,7 +610,7 @@ <h2>Ecological Interactions</h2>
                     <h3>Acetylene-Fueled Dechlorinating Coculture</h3>
                     <span class="interaction-type">SYNTROPHY</span>
                 </div>
-                <p class="prewrap interaction-description">Pelobacter strain SFB93 enables a defined coculture in which acetylene is supplied as electron donor and carbon source while D. mccartyi strain 195 uses TCE as the electron acceptor for reductive dechlorination.</p>
+                <p class="prewrap interaction-description">SFB93 fermentation allows acetylene to supply electron donor and carbon for the defined strain-195 coculture through hydrogen and acetate provision. Strain 195 reductively dechlorinates TCE, predominantly to vinyl chloride under the reported conditions. The BAV1 coculture and the ANAS enrichment are separate systems.</p>
 
 
                 <p><strong>Source Taxon:</strong> Pelobacter strain SFB93</p>
@@ -658,8 +653,7 @@ <h3>Acetylene-Fueled Dechlorinating Coculture</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> D. mccartyi Reductive Dechlorination
-                        <p class="prewrap causal-description">Pelobacter fermentation lets acetylene serve as the reduced substrate that fuels D. mccartyi organohalide respiration of TCE in the defined coculture.
-</p>
+                        <p class="prewrap causal-description">SFB93 acetylene fermentation supplies hydrogen and acetate that support strain-195 TCE dechlorination and growth. This positive nutritional coupling is distinct from removal of an initially inhibitory acetylene exposure; it does not assign BAV1 vinyl-chloride respiration to strain 195.</p>
                     </div>
 
                 </div>
@@ -702,17 +696,14 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>D. mccartyi Reductive Dechlorination</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">D. mccartyi strain 195 performs reductive dechlorination of TCE in the coculture; transcriptomic observations indicate that reductive dehalogenase genes such as tceA were monitored during acetylene inhibition.</p>
+                <p class="prewrap interaction-description">Strain 195 performs hydrogen-dependent reductive dechlorination of TCE in the coculture, predominantly producing vinyl chloride. This is the recipient phenotype, not nutrient transfer back to SFB93. In separate acetylene-inhibited strain-195 assays, unchanged tceA transcript abundance does not establish induction-mediated rescue or identify the inhibited enzyme.</p>
 
 
                 <p><strong>Source Taxon:</strong> Dehalococcoides mccartyi strain 195</p>
 
 
 
-                <p><strong>Target Taxon:</strong> Pelobacter strain SFB93</p>
-
 
 
                 <p><strong>Metabolites:</strong>
@@ -766,7 +757,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/28075122/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28075122</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"genes encoding for reductive dehalogenases"</div>
@@ -780,15 +771,16 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>SFB93-Mediated Relief of Acetylene Inhibition</h3>
-                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
                 </div>
-                <p class="prewrap interaction-description">Addition of the acetylene-fermenting SFB93 partner removed acetylene inhibition of reductive dechlorination and methanogenesis in the ANAS enrichment, supporting the functional relevance of pairing acetylene metabolism with dechlorinating organisms.</p>
+                <p class="prewrap interaction-description">Adding SFB93 to acetylene-inhibited strain-195 cultures consumed acetylene and restored TCE reductive dechlorination in the primary study. This exact-pair rescue is distinct from the separate ANAS enrichment and its condition-dependent methanogenesis response; it is detoxification support, not demonstrated colonization facilitation.</p>
 
 
                 <p><strong>Source Taxon:</strong> Pelobacter strain SFB93</p>
 
 
 
+                <p><strong>Target Taxon:</strong> Dehalococcoides mccartyi strain 195</p>
+
 
 
                 <p><strong>Metabolites:</strong>
@@ -819,8 +811,7 @@ <h3>SFB93-Mediated Relief of Acetylene Inhibition</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> D. mccartyi Reductive Dechlorination
-                        <p class="prewrap causal-description">Acetylene fermentation by SFB93 relieves acetylene inhibition of organohalide respiration, allowing D. mccartyi to resume reductive dechlorination in acetylene-fed cultures.
-</p>
+                        <p class="prewrap causal-description">SFB93 consumption of inhibitory acetylene permits strain 195 to resume TCE reductive dechlorination, as tested by delayed partner addition in the primary Results and Figure 2 caption. The local abstract rescue phrase concerns ANAS and alone does not establish this exact-pair result; ANAS methanogenesis is not transferred to this arrow.</p>
                     </div>
 
                 </div>
@@ -836,7 +827,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/28075122/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28075122</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"inhibition was removed by adding Pelobacter SFB93"</div>
@@ -903,6 +894,25 @@ <h2>Associated Datasets</h2>
             </div>
         </section>
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which acetylene-sensitive processes limit strain-195 recovery after SFB93 addition?
+                </h3>
+                <p class="prewrap">The whole primary main body and six figure captions were read. Figure 2 reports exact strain-195 rescue after delayed SFB93 addition; the cached abstract rescue sentence instead concerns ANAS. Unchanged tceA transcription does not identify the inhibited enzyme. Distinguish the nutritional coculture, inhibited-isolate rescue and ANAS methanogenesis assays. Exact-pair body evidence is not locally snippet-verifiable. Existing non-graph evidence debt remains under #765; the curated Syntrophotalea grounding is unchanged. No figure images, Table 1 or supplements were inspected.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Acetylene-Fueled Dechlorinating Coculture</code>, <code>ecological_interactions#D. mccartyi Reductive Dechlorination</code>, <code>ecological_interactions#SFB93-Mediated Relief of Acetylene Inhibition</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1332,7 +1342,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1367,16 +1377,11 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
-            var tgtKey = "Pelobacter strain SFB93";
-            if (taxonNodeIds[tgtKey]) {
-                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
-            }
-
         })();
 
         (function() {
             var intId = "interaction:2";
-            var intType = "COLONIZATION_FACILITATION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1409,6 +1414,11 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var tgtKey = "Dehalococcoides mccartyi strain 195";
+            if (taxonNodeIds[tgtKey]) {
+                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
+            }
+
         })();
 
 
diff --git a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
index 3c44dcded..573cb4052 100644
--- a/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
+++ b/docs/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.html
@@ -563,17 +563,12 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy, colonization facilitation).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
                         <span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
                     </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
                              aria-hidden="true" data-symbol="symbolTriangle"
@@ -581,8 +576,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolPlus"
-                             data-color="#edab12"></svg> Colonization facilitation
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -593,7 +588,7 @@ <h2>Ecological Interactions</h2>
                     <h3>Butyrate Fermentation Supporting TCE Dechlorination</h3>
                     <span class="interaction-type">SYNTROPHY</span>
                 </div>
-                <p class="prewrap interaction-description">S. wolfei ferments butyrate in the coculture, producing hydrogen and acetate; D. mccartyi 195 consumes hydrogen for reductive dechlorination of TCE, keeping hydrogen low enough to make syntrophic butyrate oxidation favorable.</p>
+                <p class="prewrap interaction-description">S. wolfei ferments butyrate to provide hydrogen and acetate while strain 195 consumes hydrogen for TCE reductive dechlorination, supporting favorable fermentative energetics. This positive coupling concerns the butyrate-fed, externally cobalamin-supplemented coculture; crotonate comparisons and donor-limited threshold assays are distinct conditions.</p>
 
 
                 <p><strong>Source Taxon:</strong> Syntrophomonas wolfei</p>
@@ -650,8 +645,7 @@ <h3>Butyrate Fermentation Supporting TCE Dechlorination</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Reductive Dechlorination by Dehalococcoides
-                        <p class="prewrap causal-description">Hydrogen produced during syntrophic butyrate oxidation by S. wolfei supplies the electron donor D. mccartyi 195 uses for TCE dechlorination; the coupling is demonstrated by nanomolar aqueous H2 during dechlorination and the strain-195 minimum H2 threshold.
-</p>
+                        <p class="prewrap causal-description">Hydrogen from S. wolfei butyrate oxidation supplies the electron donor for strain-195 TCE dechlorination, while recipient consumption maintains a favorable hydrogen sink. The separate donor-limited minimum-threshold assay is not the routine culture concentration. Later residual butyrate consumption and cometabolic vinyl-chloride conversion do not establish continued growth after the growth-supporting acceptors are depleted.</p>
                     </div>
 
                 </div>
@@ -694,17 +688,14 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Reductive Dechlorination by Dehalococcoides</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">D. mccartyi 195 uses hydrogen supplied by S. wolfei as electron donor and TCE as electron acceptor, producing less chlorinated ethene products including ethene under the tested coculture conditions.</p>
+                <p class="prewrap interaction-description">Strain 195 uses hydrogen for reductive dechlorination of TCE and cis-DCE toward vinyl chloride in the coculture. Subsequent vinyl-chloride-to-ethene conversion is cometabolic, not demonstrated growth-coupled vinyl-chloride respiration. This recipient phenotype is not nutrient transfer from strain 195 to S. wolfei.</p>
 
 
                 <p><strong>Source Taxon:</strong> Dehalococcoides mccartyi 195</p>
 
 
 
-                <p><strong>Target Taxon:</strong> Syntrophomonas wolfei</p>
-
 
 
                 <p><strong>Metabolites:</strong>
@@ -793,16 +784,19 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Aggregation-Enhanced Hydrogen Flux</h3>
-                    <span class="interaction-type">COLONIZATION_FACILITATION</span>
                 </div>
-                <p class="prewrap interaction-description">The coculture forms cell aggregates that reduce interspecies distances and support the hydrogen flux required for observed TCE dechlorination rates.</p>
+                <p class="prewrap interaction-description">SEM directly observed joint cell aggregates during syntrophic growth. PARTIAL - a Fick diffusion model predicts that shorter interspecies distances support the hydrogen flux needed for the measured dechlorination rate. The model and microscopy do not selectively demonstrate aggregation necessity, one-way colonization facilitation or conductive electron transfer.</p>
 
 
-                <p><strong>Source Taxon:</strong> Syntrophomonas wolfei</p>
 
 
+                <p><strong>Participating Taxa:</strong>
 
-                <p><strong>Target Taxon:</strong> Dehalococcoides mccartyi 195</p>
+                    Dehalococcoides mccartyi 195,
+
+                    Syntrophomonas wolfei
+
+                </p>
 
 
 
@@ -834,8 +828,7 @@ <h3>Aggregation-Enhanced Hydrogen Flux</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Reductive Dechlorination by Dehalococcoides
-                        <p class="prewrap causal-description">Cell aggregation shortens the interspecies distance and sustains the hydrogen flux required for the observed TCE dechlorination rates (supported by the reported need for aggregation; lower-confidence than the direct H2-threshold edge).
-</p>
+                        <p class="prewrap causal-description">PARTIAL - aggregation could shorten diffusion distances and thereby support hydrogen delivery to strain 195 at the measured dechlorination rate. This mechanistic contribution is inferred from the diffusion model together with observed aggregates, not from selective disruption and rescue of aggregation.</p>
                     </div>
 
                 </div>
@@ -864,7 +857,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/25576615/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:25576615</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
                         <div class="snippet">"demonstrated the need for aggregation"</div>
@@ -931,6 +924,25 @@ <h2>Associated Datasets</h2>
             </div>
         </section>
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Do aggregation and carbon-monoxide removal causally explain the coculture advantage?
+                </h3>
+                <p class="prewrap">The 2015 primary body supports observed aggregates and modeled hydrogen diffusion, without selective aggregation disruption. It also reports CO consumption in S. wolfei assays and lower coculture CO, proposing supplementary energy and toxicity relief; a selective exact-pair CO-removal/rescue contribution remains unresolved. New CO structure awaits one-community Edison research and primary-source assessment under #1392; this record remains needs_research. A dry run prepared the prompt, but no provider job was submitted. In the 2016 follow-up, exact-Dhc qRT-PCR is distinct from protein/complex assays with M. hungatei; induction is not genetic necessity. No figure images or supplement files were inspected.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Butyrate Fermentation Supporting TCE Dechlorination</code>, <code>ecological_interactions#Reductive Dechlorination by Dehalococcoides</code>, <code>ecological_interactions#Aggregation-Enhanced Hydrogen Flux</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1390,7 +1402,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1429,16 +1441,11 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
-            var tgtKey = "Syntrophomonas wolfei";
-            if (taxonNodeIds[tgtKey]) {
-                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
-            }
-
         })();
 
         (function() {
             var intId = "interaction:2";
-            var intType = "COLONIZATION_FACILITATION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1464,17 +1471,20 @@ <h4 style="color: var(--text);">Evidence</h4>
             });
 
 
-            var srcKey = "Syntrophomonas wolfei";
-            if (taxonNodeIds[srcKey]) {
-                links.push({ source: taxonNodeIds[srcKey], target: intId });
-            }
 
 
+            var participantKeys = [
 
-            var tgtKey = "Dehalococcoides mccartyi 195";
-            if (taxonNodeIds[tgtKey]) {
-                links.push({ source: intId, target: taxonNodeIds[tgtKey] });
-            }
+                "Dehalococcoides mccartyi 195",
+
+                "Syntrophomonas wolfei"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
 
         })();
 
diff --git a/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html b/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
index 83a7fa94a..928b44216 100644
--- a/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
+++ b/docs/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.html
@@ -518,17 +518,12 @@ <h2>Ecological Interactions</h2>
                 <div class="network-tooltip" id="network-tooltip" role="status" aria-live="polite"></div>
                 <svg id="network-svg" role="img" aria-labelledby="network-svg-title network-svg-desc">
                     <title id="network-svg-title">Ecological interaction network for Dehalococcoides mccartyi CWV2 Dechlorinating Consortium</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
                         <span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
                     </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolTriangle"
-                             data-color="#7f30cf"></svg> Syntrophy
-                    </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
                              aria-hidden="true" data-symbol="symbolTriangle2"
@@ -542,7 +537,7 @@ <h2>Ecological Interactions</h2>
                 <div class="interaction-header">
                     <h3>BC600 Biochar-Consortium Coupling</h3>
                 </div>
-                <p class="prewrap interaction-description">The remediation strategy combined Zizania latifolia husk biochar produced at 600 degrees C with a native microbial consortium enriched in D. mccartyi CWV2 to treat TCE-contaminated groundwater.</p>
+                <p class="prewrap interaction-description">The strategy amends a native Dhc-containing groundwater consortium with Zizania latifolia husk biochar produced at 600 degrees C. The author-uploaded proof distinguishes consortium D345 from CWV2; the graph does not treat the isolate and the complete community as identical.</p>
 
 
 
@@ -566,7 +561,7 @@ <h3>BC600 Biochar-Consortium Coupling</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> BC600 Colonization and Activity Enhancement
-                        <p class="prewrap causal-description">Coupling BC600 to the native dechlorinating consortium lets the biochar combine adsorption with enhanced microbial colonization and activity.</p>
+                        <p class="prewrap causal-description">BC600 amendment supplies sorptive surfaces and is associated with enhanced microbial colonization and activity in the tested consortium. Amendment effects depend on dose and inoculum conditions; this does not establish that adsorption itself is biological dechlorination.</p>
                     </div>
 
                 </div>
@@ -597,7 +592,7 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>BC600 Colonization and Activity Enhancement</h3>
                 </div>
-                <p class="prewrap interaction-description">BC600 provided the strongest adsorptive support in the study and increased microbial colonization and activity in the dechlorinating consortium.</p>
+                <p class="prewrap interaction-description">BC600 was selected for adsorption performance and practical cost considerations and was associated with enhanced microbial colonization and activity. The proof reports slightly greater sorption for BC700, so BC600 is not asserted to have the strongest adsorption. Sorption and biological transformation remain distinct processes.</p>
 
 
 
@@ -621,7 +616,7 @@ <h3>BC600 Colonization and Activity Enhancement</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Biochar-Accelerated TCE Degradation
-                        <p class="prewrap causal-description">Biochar-associated colonization and activity were linked to faster TCE degradation.</p>
+                        <p class="prewrap causal-description">PARTIAL - biochar-associated microbial colonization and activity could contribute to faster TCE transformation, alongside sorption and bioavailability effects. The amendment comparison does not selectively isolate colonization as the causal mediator, and TCE disappearance through adsorption is not itself degradation.</p>
                     </div>
 
                 </div>
@@ -637,7 +632,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/41442978/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41442978</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"Biochar (BC600) demonstrated optimal adsorption while enhancing microbial colonization and activity"</div>
@@ -652,7 +647,7 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>Biochar-Accelerated TCE Degradation</h3>
                 </div>
-                <p class="prewrap interaction-description">BC600 amendment accelerated trichloroethene removal by the native D. mccartyi CWV2-enriched consortium.</p>
+                <p class="prewrap interaction-description">BC600 amendment accelerated TCE transformation in the tested native-consortium experiments. Removal includes a sorption contribution and must not be equated wholesale with biological degradation. Dose and inoculum comparisons differ; faster TCE transformation alone does not imply lower vinyl-chloride accumulation.</p>
 
 
 
@@ -673,16 +668,6 @@ <h3>Biochar-Accelerated TCE Degradation</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Vinyl Chloride Accumulation Mitigation
-                        <p class="prewrap causal-description">Accelerated TCE degradation was part of the BC600 response that also limited accumulation of the carcinogenic intermediate vinyl chloride.</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -709,7 +694,7 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>Vinyl Chloride Accumulation Mitigation</h3>
                 </div>
-                <p class="prewrap interaction-description">Complete vinyl chloride dechlorination by the CWV2-containing consortium, assisted by BC600, mitigated accumulation of the toxic TCE intermediate.</p>
+                <p class="prewrap interaction-description">A separate high-inoculum BC600 experiment reported lower peak vinyl-chloride accumulation, consistent with support for downstream dechlorination. In lower-inoculum comparisons, biochar could instead increase vinyl chloride while unamended controls retained TCE. CWV2 vinyl-chloride-to-ethene capability and the consortium amendment outcome are related but distinct observations.</p>
 
 
 
@@ -772,9 +757,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Hydrogen- and Electroactive-Guild Dechlorination Stability</h3>
-                    <span class="interaction-type">SYNTROPHY</span>
                 </div>
-                <p class="prewrap interaction-description">Biochar promoted unnamed syntrophic hydrogen producers and electroactive bacteria in the native consortium, a community shift associated with long-term dechlorination stability.</p>
+                <p class="prewrap interaction-description">Community profiling associated biochar with relative-abundance shifts among putative hydrogen-producing and electroactive guilds. HYPOTHESIZED - those guilds could support dechlorination through reducing-equivalent supply. Relative profiles do not demonstrate hydrogen or electron flux, direct interspecies electron transfer, selective guild necessity or long-term field stability.</p>
 
 
 
@@ -806,7 +790,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/41442978/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41442978</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"Microbial community analysis further indicated that biochar promoted syntrophic hydrogen producers and electroactive bacteria, ensuring long-term dechlorination stability."</div>
@@ -822,6 +806,25 @@ <h4>Evidence</h4>
 
         <!-- Associated Datasets -->
 
+        <section id="discussions">
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which biochar effects and community members causally mediate condition-specific dechlorination?
+                </h3>
+                <p class="prewrap">The published abstract and complete author-uploaded uncorrected-proof body were read, not the complete final published body. Colonization, sorption, bioavailability and putative guild activity were not selectively separated. Faster TCE transformation and lower peak VC are not a demonstrated directed causal sequence and differ by inoculum condition. Proof units and concentrations are inconsistent between methods, results and captions, so none are normalized here. Figure captions and Table 1 text were read, not figure images or supplements. Consortium D345/CWV2 identity, named-member and metadata claims remain open under #1391; no new taxa or compensating arrows are invented.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#BC600 Biochar-Consortium Coupling</code>, <code>ecological_interactions#BC600 Colonization and Activity Enhancement</code>, <code>ecological_interactions#Biochar-Accelerated TCE Degradation</code>, <code>ecological_interactions#Vinyl Chloride Accumulation Mitigation</code>, <code>ecological_interactions#Hydrogen- and Electroactive-Guild Dechlorination Stability</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1085,7 +1088,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:4";
-            var intType = "SYNTROPHY";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
diff --git a/history/records/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture/2026-10-06T061823Z-codex-d74031.yaml b/history/records/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture/2026-10-06T061823Z-codex-d74031.yaml
new file mode 100644
index 000000000..e0fa97abe
--- /dev/null
+++ b/history/records/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture/2026-10-06T061823Z-codex-d74031.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
+  slug: Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture
+session:
+  id: 2026-10-06T061823Z-codex-d74031
+  timestamp: '2026-10-06T06:18:23Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1388
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain positive acetylene-fed nutritional support, separating the exact pair from
+    BAV1 and ANAS.; Represent recipient dechlorination without reverse cross-feeding or induction-mediated
+    rescue.; Retain directly observed exact-pair acetylene rescue, exposing the abstract-only
+    snippet limitation and removing the colonization label.
+  details: Source-bounded graph correction; no new nodes/arrows. reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
diff --git a/history/records/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture/2026-10-06T061823Z-codex-91ce0c.yaml b/history/records/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture/2026-10-06T061823Z-codex-91ce0c.yaml
new file mode 100644
index 000000000..8d960dfb2
--- /dev/null
+++ b/history/records/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture/2026-10-06T061823Z-codex-91ce0c.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
+  slug: Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture
+session:
+  id: 2026-10-06T061823Z-codex-91ce0c
+  timestamp: '2026-10-06T06:18:23Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1389
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain positive butyrate-fed hydrogen support with assay, cofactor and late-stage
+    growth limits.; Represent recipient dechlorination without reverse transfer or growth-coupled
+    vinyl-chloride respiration.; Keep joint aggregates and their conditional diffusion-model
+    contribution while leaving new CO structure pending.
+  details: Source-bounded graph correction; no new nodes/arrows. reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
diff --git a/history/records/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium/2026-10-06T061824Z-codex-ea8b4f.yaml b/history/records/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium/2026-10-06T061824Z-codex-ea8b4f.yaml
new file mode 100644
index 000000000..a9923a951
--- /dev/null
+++ b/history/records/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium/2026-10-06T061824Z-codex-ea8b4f.yaml
@@ -0,0 +1,28 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
+  slug: Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium
+session:
+  id: 2026-10-06T061824Z-codex-ea8b4f
+  timestamp: '2026-10-06T06:18:24Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1390
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain the biochar amendment with consortium/isolate scope explicit.; Retain activity
+    enhancement with adsorption and mediation uncertainty.; Retain the TCE outcome but remove
+    the unsupported causal arrow to lower VC.; Retain the condition-specific lower-VC observation
+    without generalizing across inocula.; Retain measured composition and hypothesized guild
+    contribution without demonstrated flux or stability.
+  details: Source-bounded graph correction; no new nodes/arrows. reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
diff --git a/kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml b/kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
index 79b898a33..a2facafce 100644
--- a/kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
+++ b/kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
@@ -116,9 +116,9 @@ taxonomy:
     explanation: Supports SFB93 as the organism added to relieve acetylene inhibition in the dechlorinating consortium.
 ecological_interactions:
 - name: Acetylene-Fueled Dechlorinating Coculture
-  description: Pelobacter strain SFB93 enables a defined coculture in which acetylene is
-    supplied as electron donor and carbon source while D. mccartyi strain 195 uses
-    TCE as the electron acceptor for reductive dechlorination.
+  description: SFB93 fermentation allows acetylene to supply electron donor and carbon for the defined strain-195
+    coculture through hydrogen and acetate provision. Strain 195 reductively dechlorinates TCE, predominantly to
+    vinyl chloride under the reported conditions. The BAV1 coculture and the ANAS enrichment are separate systems.
   interaction_type: SYNTROPHY
   scope: PAIRWISE
   source_taxon:
@@ -147,10 +147,9 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: D. mccartyi Reductive Dechlorination
-    description: >
-      Pelobacter fermentation lets acetylene serve as the reduced substrate that
-      fuels D. mccartyi organohalide respiration of TCE in the defined
-      coculture.
+    description: SFB93 acetylene fermentation supplies hydrogen and acetate that support strain-195 TCE dechlorination
+      and growth. This positive nutritional coupling is distinct from removal of an initially inhibitory acetylene
+      exposure; it does not assign BAV1 vinyl-chloride respiration to strain 195.
   evidence:
   - reference: PMID:28075122
     supports: SUPPORT
@@ -161,23 +160,19 @@ ecological_interactions:
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: TCE or cis-DCE served as the electron acceptor
-    explanation: Supports chlorinated ethenes as electron acceptors in the defined cocultures.
+    explanation: The abstract covers TCE or cis-DCE across different cocultures. The strain-195 experiment uses
+      TCE; the substrate and product results of BAV1 are not pooled into this pair.
 - name: D. mccartyi Reductive Dechlorination
-  description: D. mccartyi strain 195 performs reductive dechlorination of TCE in the coculture;
-    transcriptomic observations indicate that reductive dehalogenase genes such as
-    tceA were monitored during acetylene inhibition.
-  interaction_type: CROSS_FEEDING
+  description: Strain 195 performs hydrogen-dependent reductive dechlorination of TCE in the coculture, predominantly
+    producing vinyl chloride. This is the recipient phenotype, not nutrient transfer back to SFB93. In separate
+    acetylene-inhibited strain-195 assays, unchanged tceA transcript abundance does not establish induction-mediated
+    rescue or identify the inhibited enzyme.
   scope: PAIRWISE
   source_taxon:
     preferred_term: Dehalococcoides mccartyi strain 195
     term:
       id: NCBITaxon:243164
       label: Dehalococcoides mccartyi 195
-  target_taxon:
-    preferred_term: Pelobacter strain SFB93
-    term:
-      id: NCBITaxon:18
-      label: Pelobacter
   metabolites:
   - preferred_term: trichloroethene
     term:
@@ -200,16 +195,18 @@ ecological_interactions:
     snippet: reductive dechlorination of TCE by Dehalococcoides mccartyi
     explanation: Supports D. mccartyi as the TCE reductive dechlorinator.
   - reference: PMID:28075122
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: genes encoding for reductive dehalogenases
-    explanation: Supports the reductive dehalogenase mechanism monitored during the experiment.
+    explanation: The complete abstract says reductive-dehalogenase transcripts such as tceA were not affected during
+      inhibition. This snippet identifies monitored genes, not induced activity or a mechanism of rescue; the transcript
+      assay is distinct from the coculture outcome.
 - name: SFB93-Mediated Relief of Acetylene Inhibition
-  description: Addition of the acetylene-fermenting SFB93 partner removed acetylene inhibition
-    of reductive dechlorination and methanogenesis in the ANAS enrichment, supporting
-    the functional relevance of pairing acetylene metabolism with dechlorinating organisms.
-  interaction_type: COLONIZATION_FACILITATION
-  scope: COMMUNITY_LEVEL
+  description: Adding SFB93 to acetylene-inhibited strain-195 cultures consumed acetylene and restored TCE reductive
+    dechlorination in the primary study. This exact-pair rescue is distinct from the separate ANAS enrichment and
+    its condition-dependent methanogenesis response; it is detoxification support, not demonstrated colonization
+    facilitation.
+  scope: PAIRWISE
   source_taxon:
     preferred_term: Pelobacter strain SFB93
     term:
@@ -227,16 +224,23 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: D. mccartyi Reductive Dechlorination
-    description: >
-      Acetylene fermentation by SFB93 relieves acetylene inhibition of
-      organohalide respiration, allowing D. mccartyi to resume reductive
-      dechlorination in acetylene-fed cultures.
+    description: SFB93 consumption of inhibitory acetylene permits strain 195 to resume TCE reductive dechlorination,
+      as tested by delayed partner addition in the primary Results and Figure 2 caption. The local abstract rescue
+      phrase concerns ANAS and alone does not establish this exact-pair result; ANAS methanogenesis is not transferred
+      to this arrow.
   evidence:
   - reference: PMID:28075122
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: inhibition was removed by adding Pelobacter SFB93
-    explanation: Supports SFB93 as a functional partner that can relieve acetylene inhibition.
+    explanation: This cached abstract phrase refers to ANAS, not the defined pair. Primary Results and Figure 2
+      caption separately report recovery after SFB93 addition to acetylene-inhibited strain 195. Exact-pair support
+      depends on that externally read body; no paywalled body is restored to the cache.
+  target_taxon:
+    preferred_term: Dehalococcoides mccartyi strain 195
+    term:
+      id: NCBITaxon:243164
+      label: Dehalococcoides mccartyi 195
 cultivation_setup:
 - cultivation_mode: BATCH
   system_type: SERUM_BOTTLE
@@ -436,7 +440,31 @@ curation_history:
 - timestamp: '2026-09-13T00:56:49Z'
   curator: codex
   action: RECONCILE_PAYWALLED_EVIDENCE_REMOVAL
-  changes: "Reapplied PR #766's 10 unsupported evidence removals onto current main, preserving its newer
-    interaction curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in
-    #765."
+  changes: 'Reapplied PR #766''s 10 unsupported evidence removals onto current main, preserving its newer interaction
+    curation; retained abstract-supported evidence. Re-evidencing debt remains tracked in #765.'
+  llm_assisted: true
+- timestamp: '2026-10-06T06:18:22Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain positive acetylene-fed nutritional support, separating the exact pair from BAV1 and ANAS.; Represent
+    recipient dechlorination without reverse cross-feeding or induction-mediated rescue.; Retain directly observed
+    exact-pair acetylene rescue, exposing the abstract-only snippet limitation and removing the colonization label.
+    Issue #1388; reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml'
   llm_assisted: true
+discussions:
+- discussion_id: sfb93_exact_pair_rescue_scope
+  prompt: Which acetylene-sensitive processes limit strain-195 recovery after SFB93 addition?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Acetylene-Fueled Dechlorinating Coculture
+  - ecological_interactions#D. mccartyi Reductive Dechlorination
+  - ecological_interactions#SFB93-Mediated Relief of Acetylene Inhibition
+  rationale: 'The whole primary main body and six figure captions were read. Figure 2 reports exact strain-195 rescue
+    after delayed SFB93 addition; the cached abstract rescue sentence instead concerns ANAS. Unchanged tceA transcription
+    does not identify the inhibited enzyme. Distinguish the nutritional coculture, inhibited-isolate rescue and
+    ANAS methanogenesis assays. Exact-pair body evidence is not locally snippet-verifiable. Existing non-graph evidence
+    debt remains under #765; the curated Syntrophotalea grounding is unchanged. No figure images, Table 1 or supplements
+    were inspected.'
+  posed_by: codex
+  posed_date: '2026-10-06'
diff --git a/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml b/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
index 0202e9267..258d651d0 100644
--- a/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
+++ b/kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
@@ -107,9 +107,10 @@ taxonomy:
     explanation: Supports S. wolfei as the bacterial syntrophic partner in the coculture.
 ecological_interactions:
 - name: Butyrate Fermentation Supporting TCE Dechlorination
-  description: S. wolfei ferments butyrate in the coculture, producing hydrogen and acetate;
-    D. mccartyi 195 consumes hydrogen for reductive dechlorination of TCE, keeping
-    hydrogen low enough to make syntrophic butyrate oxidation favorable.
+  description: S. wolfei ferments butyrate to provide hydrogen and acetate while strain 195 consumes hydrogen for
+    TCE reductive dechlorination, supporting favorable fermentative energetics. This positive coupling concerns
+    the butyrate-fed, externally cobalamin-supplemented coculture; crotonate comparisons and donor-limited threshold
+    assays are distinct conditions.
   interaction_type: SYNTROPHY
   scope: PAIRWISE
   source_taxon:
@@ -150,11 +151,10 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: Reductive Dechlorination by Dehalococcoides
-    description: >
-      Hydrogen produced during syntrophic butyrate oxidation by S. wolfei
-      supplies the electron donor D. mccartyi 195 uses for TCE dechlorination;
-      the coupling is demonstrated by nanomolar aqueous H2 during dechlorination
-      and the strain-195 minimum H2 threshold.
+    description: Hydrogen from S. wolfei butyrate oxidation supplies the electron donor for strain-195 TCE dechlorination,
+      while recipient consumption maintains a favorable hydrogen sink. The separate donor-limited minimum-threshold
+      assay is not the routine culture concentration. Later residual butyrate consumption and cometabolic vinyl-chloride
+      conversion do not establish continued growth after the growth-supporting acceptors are depleted.
   evidence:
   - reference: PMID:25576615
     supports: SUPPORT
@@ -167,21 +167,15 @@ ecological_interactions:
     snippet: Aqueous H2 concentrations ranged from 24 to 180 nM
     explanation: Supports low hydrogen transfer as a measured feature of the syntrophic coculture.
 - name: Reductive Dechlorination by Dehalococcoides
-  description: D. mccartyi 195 uses hydrogen supplied by S. wolfei as electron donor and
-    TCE as electron acceptor, producing less chlorinated ethene products including ethene
-    under the tested coculture conditions.
-  interaction_type: CROSS_FEEDING
+  description: Strain 195 uses hydrogen for reductive dechlorination of TCE and cis-DCE toward vinyl chloride in
+    the coculture. Subsequent vinyl-chloride-to-ethene conversion is cometabolic, not demonstrated growth-coupled
+    vinyl-chloride respiration. This recipient phenotype is not nutrient transfer from strain 195 to S. wolfei.
   scope: PAIRWISE
   source_taxon:
     preferred_term: Dehalococcoides mccartyi 195
     term:
       id: NCBITaxon:243164
       label: Dehalococcoides mccartyi 195
-  target_taxon:
-    preferred_term: Syntrophomonas wolfei
-    term:
-      id: NCBITaxon:863
-      label: Syntrophomonas wolfei
   metabolites:
   - preferred_term: trichloroethene
     term:
@@ -210,7 +204,8 @@ ecological_interactions:
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: the minimum H2 threshold value for TCE dechlorination by strain 195
-    explanation: Supports hydrogen-dependent TCE dechlorination by strain 195 in the coculture.
+    explanation: Supports a separately measured donor-limited hydrogen threshold, not the routine concentration
+      during the growth experiment or a reverse transfer mechanism.
   - reference: PMID:25576615
     supports: SUPPORT
     evidence_source: IN_VITRO
@@ -220,22 +215,14 @@ ecological_interactions:
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: reductive dechlorination of trichloroethene (TCE)
-    explanation: Supports reductive dechlorination as the central strain 195 phenotype measured in the related exact-composition study.
+    explanation: Supports reductive dechlorination as the central strain 195 phenotype measured in the related exact-composition
+      study.
 - name: Aggregation-Enhanced Hydrogen Flux
-  description: The coculture forms cell aggregates that reduce interspecies distances and
-    support the hydrogen flux required for observed TCE dechlorination rates.
-  interaction_type: COLONIZATION_FACILITATION
-  scope: PAIRWISE
-  source_taxon:
-    preferred_term: Syntrophomonas wolfei
-    term:
-      id: NCBITaxon:863
-      label: Syntrophomonas wolfei
-  target_taxon:
-    preferred_term: Dehalococcoides mccartyi 195
-    term:
-      id: NCBITaxon:243164
-      label: Dehalococcoides mccartyi 195
+  description: SEM directly observed joint cell aggregates during syntrophic growth. PARTIAL - a Fick diffusion
+    model predicts that shorter interspecies distances support the hydrogen flux needed for the measured dechlorination
+    rate. The model and microscopy do not selectively demonstrate aggregation necessity, one-way colonization facilitation
+    or conductive electron transfer.
+  scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: dihydrogen
     term:
@@ -248,11 +235,9 @@ ecological_interactions:
       label: biological process involved in interspecies interaction between organisms
   downstream:
   - target: Reductive Dechlorination by Dehalococcoides
-    description: >
-      Cell aggregation shortens the interspecies distance and sustains the
-      hydrogen flux required for the observed TCE dechlorination rates
-      (supported by the reported need for aggregation; lower-confidence than the
-      direct H2-threshold edge).
+    description: PARTIAL - aggregation could shorten diffusion distances and thereby support hydrogen delivery to
+      strain 195 at the measured dechlorination rate. This mechanistic contribution is inferred from the diffusion
+      model together with observed aggregates, not from selective disruption and rescue of aggregation.
   evidence:
   - reference: PMID:25576615
     supports: SUPPORT
@@ -260,10 +245,21 @@ ecological_interactions:
     snippet: Cell aggregates during syntrophic growth were observed
     explanation: Supports aggregate formation during coculture growth.
   - reference: PMID:25576615
-    supports: SUPPORT
-    evidence_source: IN_VITRO
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
     snippet: demonstrated the need for aggregation
-    explanation: Supports the interpretation that close physical association enables hydrogen flux.
+    explanation: The abstract bases this interpretation on distances predicted using Fick diffusion. It is modeled
+      flux support, not an experimental perturbation proving aggregation necessary; the separate SEM evidence is
+      IN_VITRO.
+  participating_taxa:
+  - preferred_term: Dehalococcoides mccartyi 195
+    term:
+      id: NCBITaxon:243164
+      label: Dehalococcoides mccartyi 195
+  - preferred_term: Syntrophomonas wolfei
+    term:
+      id: NCBITaxon:863
+      label: Syntrophomonas wolfei
 environmental_factors:
 - name: TCE electron acceptor
   value: trichloroethene
@@ -509,3 +505,30 @@ metal_relevance: NOT_APPLICABLE
 metal_notes: >
   No metal or rare earth element processing role is curated for this chlorinated-solvent
   bioremediation coculture.
+discussions:
+- discussion_id: syntrophomonas_aggregation_and_co_limits
+  prompt: Do aggregation and carbon-monoxide removal causally explain the coculture advantage?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Butyrate Fermentation Supporting TCE Dechlorination
+  - ecological_interactions#Reductive Dechlorination by Dehalococcoides
+  - ecological_interactions#Aggregation-Enhanced Hydrogen Flux
+  rationale: 'The 2015 primary body supports observed aggregates and modeled hydrogen diffusion, without selective
+    aggregation disruption. It also reports CO consumption in S. wolfei assays and lower coculture CO, proposing
+    supplementary energy and toxicity relief; a selective exact-pair CO-removal/rescue contribution remains unresolved.
+    New CO structure awaits one-community Edison research and primary-source assessment under #1392; this record
+    remains needs_research. A dry run prepared the prompt, but no provider job was submitted. In the 2016 follow-up,
+    exact-Dhc qRT-PCR is distinct from protein/complex assays with M. hungatei; induction is not genetic necessity.
+    No figure images or supplement files were inspected.'
+  posed_by: codex
+  posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T06:18:23Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain positive butyrate-fed hydrogen support with assay, cofactor and late-stage growth limits.; Represent
+    recipient dechlorination without reverse transfer or growth-coupled vinyl-chloride respiration.; Keep joint
+    aggregates and their conditional diffusion-model contribution while leaving new CO structure pending. Issue
+    #1389; reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml b/kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
index 8fd7dd640..dfd6d0ab0 100644
--- a/kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
+++ b/kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
@@ -46,9 +46,9 @@ taxonomy:
     explanation: Identifies D. mccartyi strain CWV2 as the keystone dechlorinating member.
 ecological_interactions:
 - name: BC600 Biochar-Consortium Coupling
-  description: The remediation strategy combined Zizania latifolia husk biochar
-    produced at 600 degrees C with a native microbial consortium enriched in
-    D. mccartyi CWV2 to treat TCE-contaminated groundwater.
+  description: The strategy amends a native Dhc-containing groundwater consortium with Zizania latifolia husk biochar
+    produced at 600 degrees C. The author-uploaded proof distinguishes consortium D345 from CWV2; the graph does
+    not treat the isolate and the complete community as identical.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: trichloroethene
@@ -57,21 +57,20 @@ ecological_interactions:
       label: trichloroethene
   downstream:
   - target: BC600 Colonization and Activity Enhancement
-    description: Coupling BC600 to the native dechlorinating consortium lets the
-      biochar combine adsorption with enhanced microbial colonization and
-      activity.
+    description: BC600 amendment supplies sorptive surfaces and is associated with enhanced microbial colonization
+      and activity in the tested consortium. Amendment effects depend on dose and inoculum conditions; this does
+      not establish that adsorption itself is biological dechlorination.
   evidence:
   - reference: PMID:41442978
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: integrates biochar derived from Zizania latifolia (water
-      bamboo) husks with a native microbial consortium
-    explanation: Supports amendment of the native D. mccartyi-containing
-      consortium with Zizania-derived biochar.
+    snippet: integrates biochar derived from Zizania latifolia (water bamboo) husks with a native microbial consortium
+    explanation: Supports amendment of the native D. mccartyi-containing consortium with Zizania-derived biochar.
 - name: BC600 Colonization and Activity Enhancement
-  description: BC600 provided the strongest adsorptive support in the study and
-    increased microbial colonization and activity in the dechlorinating
-    consortium.
+  description: BC600 was selected for adsorption performance and practical cost considerations and was associated
+    with enhanced microbial colonization and activity. The proof reports slightly greater sorption for BC700, so
+    BC600 is not asserted to have the strongest adsorption. Sorption and biological transformation remain distinct
+    processes.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: trichloroethene
@@ -80,19 +79,20 @@ ecological_interactions:
       label: trichloroethene
   downstream:
   - target: Biochar-Accelerated TCE Degradation
-    description: Biochar-associated colonization and activity were linked to
-      faster TCE degradation.
+    description: PARTIAL - biochar-associated microbial colonization and activity could contribute to faster TCE
+      transformation, alongside sorption and bioavailability effects. The amendment comparison does not selectively
+      isolate colonization as the causal mediator, and TCE disappearance through adsorption is not itself degradation.
   evidence:
   - reference: PMID:41442978
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
-    snippet: Biochar (BC600) demonstrated optimal adsorption while enhancing
-      microbial colonization and activity
-    explanation: Supports BC600 adsorption plus microbial colonization and
-      activity enhancement in the consortium.
+    snippet: Biochar (BC600) demonstrated optimal adsorption while enhancing microbial colonization and activity
+    explanation: The abstract supports adsorption and enhanced colonization/activity. Its optimal wording does not
+      establish that BC600 sorption exceeds BC700 or selectively isolate colonization from adsorption as the mediator.
 - name: Biochar-Accelerated TCE Degradation
-  description: BC600 amendment accelerated trichloroethene removal by the native
-    D. mccartyi CWV2-enriched consortium.
+  description: BC600 amendment accelerated TCE transformation in the tested native-consortium experiments. Removal
+    includes a sorption contribution and must not be equated wholesale with biological degradation. Dose and inoculum
+    comparisons differ; faster TCE transformation alone does not imply lower vinyl-chloride accumulation.
   scope: COMMUNITY_LEVEL
   target_taxon:
     preferred_term: Dehalococcoides mccartyi strain CWV2
@@ -104,20 +104,18 @@ ecological_interactions:
     term:
       id: CHEBI:16602
       label: trichloroethene
-  downstream:
-  - target: Vinyl Chloride Accumulation Mitigation
-    description: Accelerated TCE degradation was part of the BC600 response that
-      also limited accumulation of the carcinogenic intermediate vinyl chloride.
   evidence:
   - reference: PMID:41442978
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: leading to accelerated TCE degradation
-    explanation: Supports faster TCE degradation after BC600 amendment.
+    explanation: Supports the reported amendment-associated degradation outcome, not a general causal arrow from
+      faster TCE loss to lower vinyl chloride across all assay conditions.
 - name: Vinyl Chloride Accumulation Mitigation
-  description: Complete vinyl chloride dechlorination by the CWV2-containing
-    consortium, assisted by BC600, mitigated accumulation of the toxic TCE
-    intermediate.
+  description: A separate high-inoculum BC600 experiment reported lower peak vinyl-chloride accumulation, consistent
+    with support for downstream dechlorination. In lower-inoculum comparisons, biochar could instead increase vinyl
+    chloride while unamended controls retained TCE. CWV2 vinyl-chloride-to-ethene capability and the consortium
+    amendment outcome are related but distinct observations.
   scope: COMMUNITY_LEVEL
   target_taxon:
     preferred_term: Dehalococcoides mccartyi strain CWV2
@@ -137,20 +135,19 @@ ecological_interactions:
   - reference: PMID:41442978
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: a strain capable of completely dechlorinating VC to non-toxic
-      ethene
+    snippet: a strain capable of completely dechlorinating VC to non-toxic ethene
     explanation: Supports VC-to-ethene dechlorination by D. mccartyi CWV2.
   - reference: PMID:41442978
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: 50 % reduction of VC accumulation
-    explanation: Supports the decrease in vinyl chloride accumulation under the
-      biochar-assisted strategy.
+    explanation: The abstract reports a reduction greater than 50 percent. The author-uploaded proof places this
+      in a separate high-inoculum experiment; it is not a universal effect at every dose, inoculum or time point.
 - name: Hydrogen- and Electroactive-Guild Dechlorination Stability
-  description: Biochar promoted unnamed syntrophic hydrogen producers and
-    electroactive bacteria in the native consortium, a community shift
-    associated with long-term dechlorination stability.
-  interaction_type: SYNTROPHY
+  description: Community profiling associated biochar with relative-abundance shifts among putative hydrogen-producing
+    and electroactive guilds. HYPOTHESIZED - those guilds could support dechlorination through reducing-equivalent
+    supply. Relative profiles do not demonstrate hydrogen or electron flux, direct interspecies electron transfer,
+    selective guild necessity or long-term field stability.
   scope: COMMUNITY_LEVEL
   target_taxon:
     preferred_term: Dehalococcoides mccartyi strain CWV2
@@ -164,12 +161,13 @@ ecological_interactions:
       label: dihydrogen
   evidence:
   - reference: PMID:41442978
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
-    snippet: Microbial community analysis further indicated that biochar promoted syntrophic
-      hydrogen producers and electroactive bacteria, ensuring long-term dechlorination stability.
-    explanation: Supports promotion of syntrophic hydrogen-producing and
-      electroactive guilds in the stable biochar-amended consortium.
+    snippet: Microbial community analysis further indicated that biochar promoted syntrophic hydrogen producers
+      and electroactive bacteria, ensuring long-term dechlorination stability.
+    explanation: Supports community-composition observations and the authors' proposed interpretation. Relative
+      abundance is not measured reducing-equivalent flux or a selective guild perturbation, and field persistence
+      requires separate validation.
 growth_media:
 - name: "biochar-amended TCE groundwater enrichment (unspecified medium)"
   inoculum_source: "native TCE-contaminated groundwater consortium enriched in Dehalococcoides mccartyi strain CWV2"
@@ -184,7 +182,34 @@ curation_history:
 - timestamp: '2026-10-02T06:15:13Z'
   curator: codex
   action: REVIEW_CAUSAL_GRAPH
-  changes: Removed the vinyl-chloride mitigation to hydrogen/electroactive guild
-    stability edge because it pointed from a measured lower-VC endpoint to a
-    biochar-associated community-structure explanation.
+  changes: Removed the vinyl-chloride mitigation to hydrogen/electroactive guild stability edge because it pointed
+    from a measured lower-VC endpoint to a biochar-associated community-structure explanation.
+  llm_assisted: true
+- timestamp: '2026-10-06T06:18:23Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Retain the biochar amendment with consortium/isolate scope explicit.; Retain activity enhancement with
+    adsorption and mediation uncertainty.; Retain the TCE outcome but remove the unsupported causal arrow to lower
+    VC.; Retain the condition-specific lower-VC observation without generalizing across inocula.; Retain measured
+    composition and hypothesized guild contribution without demonstrated flux or stability. Issue #1390; reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml'
   llm_assisted: true
+discussions:
+- discussion_id: cwv2_biochar_mediation_and_condition_limits
+  prompt: Which biochar effects and community members causally mediate condition-specific dechlorination?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#BC600 Biochar-Consortium Coupling
+  - ecological_interactions#BC600 Colonization and Activity Enhancement
+  - ecological_interactions#Biochar-Accelerated TCE Degradation
+  - ecological_interactions#Vinyl Chloride Accumulation Mitigation
+  - ecological_interactions#Hydrogen- and Electroactive-Guild Dechlorination Stability
+  rationale: 'The published abstract and complete author-uploaded uncorrected-proof body were read, not the complete
+    final published body. Colonization, sorption, bioavailability and putative guild activity were not selectively
+    separated. Faster TCE transformation and lower peak VC are not a demonstrated directed causal sequence and differ
+    by inoculum condition. Proof units and concentrations are inconsistent between methods, results and captions,
+    so none are normalized here. Figure captions and Table 1 text were read, not figure images or supplements. Consortium
+    D345/CWV2 identity, named-member and metadata claims remain open under #1391; no new taxa or compensating arrows
+    are invented.'
+  posed_by: codex
+  posed_date: '2026-10-06'
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch31.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch31.yaml
new file mode 100644
index 000000000..c4041001c
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch31.yaml
@@ -0,0 +1,156 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5988d5ace91b79ad27e118720378e5fa58763949
+scope:
+- kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
+- kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
+- kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch31.json
+findings:
+- issue: 1388
+  severity: P2
+  status: addressed_in_this_change
+  finding: Recipient activity was reverse transfer, and the relief node pooled ANAS with strain 195 under
+    a colonization label.
+  disposition: Preserve three nodes/two arrows; source-only recipient, exact-pair primary-body rescue
+    and explicitly PARTIAL abstract evidence. Do not restore a copyrighted body or alter the GTDB pin.
+- issue: 1389
+  severity: P2
+  status: addressed_in_this_change
+  finding: Recipient activity was reverse transfer and joint aggregates/modeling were presented as demonstrated
+    directional colonization.
+  disposition: Preserve three nodes/two arrows with canonical joint participants, separate SEM and computational
+    evidence, and qualified aggregation mediation. Existing-structure repairs do not finish the CO question.
+- issue: 1390
+  severity: P2
+  status: addressed_in_this_change
+  finding: Common biochar outcomes were linked causally and guild composition was overinterpreted as functional
+    flux/stability.
+  disposition: Preserve five nodes/two arrows; remove only TCE outcome to VC outcome. Expose inoculum
+    dependence, sorption-versus-transformation limits and hypothesized guild mechanism.
+- issue: 1391
+  severity: P2
+  status: open_nongraph_followup
+  finding: D345/CWV2 identity, only-named-organism prose and proof-condition inconsistencies need separate
+    metadata curation.
+  disposition: Non-graph raw blocks preserved, not certified; final published body not accessed.
+- issue: 1392
+  severity: P2
+  status: open_graph_research
+  finding: Possible CO scavenging support is missing from the graph and requires new-structure assessment.
+  disposition: Keep the record needs_research. One-community dry run only; no provider job/charge. Specific
+    spend/transmission authorization and primary-source assessment remain required.
+- issue: 765
+  severity: P3
+  status: existing_open_nongraph_followup
+  finding: Pelobacter non-graph evidence debt after copyrighted-text removal predates this batch.
+  disposition: Reuse the existing issue, preserve metadata and caches; a snippet MATCH does not resolve
+    unsupported metadata blocks.
+adversarial_checks:
+- Actual record diffs read against the primary-source access recorded in the ledger. All eleven nodes
+  retained, six arrows retained, one unsupported common-intervention outcome arrow removed. No replacement
+  connectivity or new structure invented.
+- Pelobacter nutritional support remains positive. Exact strain-195 rescue is in primary Results/Figure
+  2, while the cached rescue phrase concerns ANAS and is PARTIAL. ANAS methanogenesis and BAV1 complete
+  dechlorination are not imported. Unchanged tceA expression is not induction-mediated rescue.
+- Both source-only PAIRWISE entries use the established recipient-process convention, not self-edges or
+  reverse nutrient exchange. The curated Pelobacter/Syntrophotalea GTDB pin is unchanged.
+- Syntrophomonas butyrate-fed support, crotonate comparisons, cobalamin supplementation and donor-limited
+  threshold assays remain distinct. Late VC cometabolism is not growth-coupled respiration. SEM aggregates
+  and diffusion predictions have different evidence classifications; necessity was not selectively perturbed.
+- 'CO consumption observations and proposed benefit are not silently added to the fermentation node. Open
+  #1392 and needs_research status retain the missing-structure obligation. The Edison dry run made no
+  provider job or charge; a failed LiteLLM pricing-map request is disclosed.'
+- The 2016 exact-Dhc expression assay is distinguished from M. hungatei protein/complex experiments. Induction
+  does not establish gene necessity or cell-specific flux.
+- CWV2/D345 proof-only body access is explicit. Biochar sorption is not biological transformation; BC600
+  is not claimed to sorb most. Lower-VC high-inoculum and higher-VC lower-inoculum comparisons are not
+  conflated. Community profiles do not demonstrate DIET, flux, guild necessity or long-term field persistence.
+- No final published CWV2 body, figure images or supplement files were inspected. Proof unit/concentration
+  inconsistencies are not normalized. Existing non-graph metadata is not certified by graph correction.
+- Three guarded writes, llm-assisted events and append-only histories. Prior history entries preserved
+  semantically; all non-graph raw blocks, 457 other records and 920 caches unchanged. No article body/PDF
+  committed.
+- Exact participant registry changes only 174 to 175 users. Measured connectivity and all 31 baseline
+  network warnings unchanged; no algorithms or numeric bounds altered.
+- Repeat rendering deterministic, exact descriptions checked across all 456 pages. No browser screenshot
+  QA claimed. All three reference-validator commands performed zero checks despite exit 0; this is no-op,
+  not validation. Actual independent snippet counts and source review are separate; textual matching is
+  not scientific support.
+- 'Deduplication covers 717 all-state issue titles/bodies, broader synonyms and ignored/hidden scoped
+  local files, not every issue comment. Metadata #765/#1391 and research #1392 remain open.'
+verification:
+  combined_regressions: 354 passed in 182.27s (0:03:02)
+  new_regression_tests: 6
+  schema_strict_terms_history: passed; commands and raw results retained
+  snippet_counts_by_record:
+    kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml:
+      MATCH: 18
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml:
+      MATCH: 31
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml:
+      MATCH: 8
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+  network: Zero structural errors; all 31 baseline warnings unchanged, expected warning exit retained.
+  black_ruff_diff: passed
+  tested_file_sha256:
+    reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml: 3ae6fd42367e69f8ffe653271b91ef4cabc271b302f7f729d6d1204a1d7e7b88
+    tests/test_causal_review_batch31.py: eaae0577db25325acb3151834e0e15f9a7662ef5f01b0ffb6fe440a222e295da
+    tests/test_participating_taxa.py: 06833a684b7e82be1ed33ef8bfc1088c879f95d532ac5b624564a99a5e83397f
+    kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml: ab28a71ff971a76db7e6bc3989a24ff65fbf03b0eb1177ae70c85fab1d04c813
+    kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml: b0c182ee42aa14442f77f15b8a8ada5172fbbd989f8175c399af7f83877b6dd2
+    kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml: 252f1bd100591910deeb53b0de75130e7f38995f3de7a10aca6466f3f16e2c66
+  post_commit_docs_current: Separate publication gate; not yet claimed by this pre-commit record.
+  protected_ci_and_merge: Require exact-head protected main checks and queue; not asserted here.
+participant_census:
+  connectivity_before:
+    community_level_only: 264
+    credited_solely_by_the_rule: 1220
+    mixed: 124
+    records: 460
+    taxa: 1496
+    with_community_level: 388
+  connectivity_after:
+    community_level_only: 264
+    credited_solely_by_the_rule: 1220
+    mixed: 124
+    records: 460
+    taxa: 1496
+    with_community_level: 388
+  exact_change: 174 -> 175 users; only the Syntrophomonas/Dhc195 coculture added
+  numeric_bounds_changed: false
+corpus:
+  records: 460
+  nodes: 1470
+  edges: 704
+  review_status_counts:
+    needs_research: 5
+    pending: 318
+    reviewed: 137
+limitations:
+- Two completed graph reviews; the third has repaired existing structure but remains needs_research for
+  possible CO structure. All eleven nodes retained; six arrows retained and one unsupported arrow removed.
+  No new nodes/arrows or paid Edison job.
+- Primary-source access differs by study. The CWV2 body is an author-uploaded uncorrected proof, not the
+  final published body. No figure images or supplement files inspected.
+- No new article body/PDF is committed. All caches and non-graph raw blocks preserved. Exact-pair Pelobacter
+  rescue depends on externally read body text, not its ANAS abstract snippet. Textual MATCH is not scientific
+  validation.
+- Source-only PAIRWISE entries follow the existing intrinsic-recipient convention, not self-edges or reverse
+  exchange. Self-adversarial review is not independent approval, protected CI success or full-corpus completion.
diff --git a/reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml b/reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
new file mode 100644
index 000000000..10954b68b
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
@@ -0,0 +1,309 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5988d5ace91b79ad27e118720378e5fa58763949
+issues:
+- 1388
+- 1389
+- 1390
+open_nongraph_followups:
+- 765
+- 1391
+open_graph_research:
+- 1392
+issue_deduplication:
+  all_state_issue_titles_bodies: 717
+  ignored_hidden_local_files_included: true
+  comments_exhaustive: false
+  relevant_broader_issues_read:
+  - 1305
+  - 1245
+  - 1236
+  - 900
+  - 883
+  - 765
+  - 754
+  - 561
+  - 389
+  - 384
+  - 383
+  finding: No duplicate exact graph defect in searched titles/bodies or scoped local review records. Existing Pelobacter
+    non-graph evidence debt is reused, not duplicated.
+reference_cache_original_hashes:
+  references_cache/PMID_28075122.md: 9ff2ad42fd8c164b8779258503d2f08241e105d3b5f35b684f7508be4c9dfb48
+  references_cache/PMID_25576615.md: 3a02cd4c98774aee7e14e54cee4f54b87fd60188d31e1135386d057115a42fde
+  references_cache/doi_DOI:10.3389_fmicb.2016.01795.json: 4e06cb6bd7a6928d99d5b0ea408d3863854873aa20050b05029f94d8a758c8f7
+  references_cache/PMID_41442978.md: 76ca3d2056b40c34172ddda2b46e4106a9115f3a9a187b5520e6911239e67e38
+  references_cache/PMID_24015929.md: 5a8edfdf6d765c4eb0e041310e03ca88fb53a96c64f2d36383ed22f773f4ff49
+  references_cache/doi_10.3389_fmicb.2016.01795.md: 9bfa7cce73e10ae4946b239c265c4e7039b6880190833fc076b2052889f457c9
+edison:
+  status: dry_run_only_no_provider_job_or_charge
+  community: CommunityMech:000183
+  prompt_characters: 11572
+  prompt_sha256: 40cfa051650b6f7062774e8dddcd740db72e3f5415817324f4676c3de22b9e26
+  limitation: Specific spend/transmission authorization is pending. LiteLLM attempted a remote pricing-map fetch,
+    which failed DNS and used its fallback; no provider job was submitted.
+limitations:
+- Two completed graph reviews; the third has repaired existing structure but remains needs_research for possible
+  CO structure. All eleven nodes retained; six arrows retained and one unsupported arrow removed. No new nodes/arrows
+  or paid Edison job.
+- Primary-source access differs by study. The CWV2 body is an author-uploaded uncorrected proof, not the final published
+  body. No figure images or supplement files inspected.
+- No new article body/PDF is committed. All caches and non-graph raw blocks preserved. Exact-pair Pelobacter rescue
+  depends on externally read body text, not its ANAS abstract snippet. Textual MATCH is not scientific validation.
+- Source-only PAIRWISE entries follow the existing intrinsic-recipient convention, not self-edges or reverse exchange.
+  Self-adversarial review is not independent approval, protected CI success or full-corpus completion.
+records:
+- path: kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml
+  id: CommunityMech:000184
+  original_sha256: cb7e15cd85069763298df062a42ba1f54497fc8db00edd004215590b2a0a8aca
+  record_sha256: ab28a71ff971a76db7e6bc3989a24ff65fbf03b0eb1177ae70c85fab1d04c813
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
+  scope: Whole record and every original node/arrow reviewed at the documented source-access scope; non-graph fields
+    preserved, not certified. New CO structure remains pending only for the Syntrophomonas record.
+  summary: Retain positive acetylene-fed nutritional support, separating the exact pair from BAV1 and ANAS.; Represent
+    recipient dechlorination without reverse cross-feeding or induction-mediated rescue.; Retain directly observed
+    exact-pair acetylene rescue, exposing the abstract-only snippet limitation and removing the colonization label.
+  renamed_nodes: {}
+  node_decisions:
+  - node: Acetylene-Fueled Dechlorinating Coculture
+    rationale: Retain positive acetylene-fed nutritional support, separating the exact pair from BAV1 and ANAS.
+  - node: D. mccartyi Reductive Dechlorination
+    rationale: Represent recipient dechlorination without reverse cross-feeding or induction-mediated rescue.
+  - node: SFB93-Mediated Relief of Acetylene Inhibition
+    rationale: Retain directly observed exact-pair acetylene rescue, exposing the abstract-only snippet limitation
+      and removing the colonization label.
+  removed_node_decisions: []
+  edges_before:
+  - source: Acetylene-Fueled Dechlorinating Coculture
+    target: D. mccartyi Reductive Dechlorination
+    description: 'Pelobacter fermentation lets acetylene serve as the reduced substrate that fuels D. mccartyi organohalide
+      respiration of TCE in the defined coculture.
+
+      '
+  - source: SFB93-Mediated Relief of Acetylene Inhibition
+    target: D. mccartyi Reductive Dechlorination
+    description: 'Acetylene fermentation by SFB93 relieves acetylene inhibition of organohalide respiration, allowing
+      D. mccartyi to resume reductive dechlorination in acetylene-fed cultures.
+
+      '
+  edges_after:
+  - source: Acetylene-Fueled Dechlorinating Coculture
+    target: D. mccartyi Reductive Dechlorination
+    description: SFB93 acetylene fermentation supplies hydrogen and acetate that support strain-195 TCE dechlorination
+      and growth. This positive nutritional coupling is distinct from removal of an initially inhibitory acetylene
+      exposure; it does not assign BAV1 vinyl-chloride respiration to strain 195.
+  - source: SFB93-Mediated Relief of Acetylene Inhibition
+    target: D. mccartyi Reductive Dechlorination
+    description: SFB93 consumption of inhibitory acetylene permits strain 195 to resume TCE reductive dechlorination,
+      as tested by delayed partner addition in the primary Results and Figure 2 caption. The local abstract rescue
+      phrase concerns ANAS and alone does not establish this exact-pair result; ANAS methanogenesis is not transferred
+      to this arrow.
+  retained_edge_decisions:
+  - source: Acetylene-Fueled Dechlorinating Coculture
+    target: D. mccartyi Reductive Dechlorination
+    rationale: SFB93 acetylene fermentation supplies hydrogen and acetate that support strain-195 TCE dechlorination
+      and growth. This positive nutritional coupling is distinct from removal of an initially inhibitory acetylene
+      exposure; it does not assign BAV1 vinyl-chloride respiration to strain 195.
+  - source: SFB93-Mediated Relief of Acetylene Inhibition
+    target: D. mccartyi Reductive Dechlorination
+    rationale: SFB93 consumption of inhibitory acetylene permits strain 195 to resume TCE reductive dechlorination,
+      as tested by delayed partner addition in the primary Results and Figure 2 caption. The local abstract rescue
+      phrase concerns ANAS and alone does not establish this exact-pair result; ANAS methanogenesis is not transferred
+      to this arrow.
+  removed_edge_decisions: []
+  references:
+  - PMID:28075122
+  issues:
+  - 1388
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture/2026-10-06T061823Z-codex-d74031.yaml
+  source_review:
+    PMID:28075122:
+      url: https://escholarship.org/content/qt9nt8k5g2/qt9nt8k5g2.pdf
+      scope: 'Complete cached abstract and complete primary main body: Methods, Results, Discussion and Figures
+        1-6 captions. Exact strain-195 rescue in Results/Figure 2 differs from ANAS abstract wording. No figure
+        images, Table 1 or supplements inspected. Local cache remains abstract-only; no full article added.'
+- path: kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml
+  id: CommunityMech:000183
+  original_sha256: 3c229074814142c66fa8a5a8624c7bf3dbdebc243dfea7eebee3d1840a88f52a
+  record_sha256: b0c182ee42aa14442f77f15b8a8ada5172fbbd989f8175c399af7f83877b6dd2
+  status: needs_research
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
+  scope: Whole record and every original node/arrow reviewed at the documented source-access scope; non-graph fields
+    preserved, not certified. New CO structure remains pending only for the Syntrophomonas record.
+  summary: Retain positive butyrate-fed hydrogen support with assay, cofactor and late-stage growth limits.; Represent
+    recipient dechlorination without reverse transfer or growth-coupled vinyl-chloride respiration.; Keep joint
+    aggregates and their conditional diffusion-model contribution while leaving new CO structure pending.
+  renamed_nodes: {}
+  node_decisions:
+  - node: Butyrate Fermentation Supporting TCE Dechlorination
+    rationale: Retain positive butyrate-fed hydrogen support with assay, cofactor and late-stage growth limits.
+  - node: Reductive Dechlorination by Dehalococcoides
+    rationale: Represent recipient dechlorination without reverse transfer or growth-coupled vinyl-chloride respiration.
+  - node: Aggregation-Enhanced Hydrogen Flux
+    rationale: Keep joint aggregates and their conditional diffusion-model contribution while leaving new CO structure
+      pending.
+  removed_node_decisions: []
+  edges_before:
+  - source: Butyrate Fermentation Supporting TCE Dechlorination
+    target: Reductive Dechlorination by Dehalococcoides
+    description: 'Hydrogen produced during syntrophic butyrate oxidation by S. wolfei supplies the electron donor
+      D. mccartyi 195 uses for TCE dechlorination; the coupling is demonstrated by nanomolar aqueous H2 during dechlorination
+      and the strain-195 minimum H2 threshold.
+
+      '
+  - source: Aggregation-Enhanced Hydrogen Flux
+    target: Reductive Dechlorination by Dehalococcoides
+    description: 'Cell aggregation shortens the interspecies distance and sustains the hydrogen flux required for
+      the observed TCE dechlorination rates (supported by the reported need for aggregation; lower-confidence than
+      the direct H2-threshold edge).
+
+      '
+  edges_after:
+  - source: Butyrate Fermentation Supporting TCE Dechlorination
+    target: Reductive Dechlorination by Dehalococcoides
+    description: Hydrogen from S. wolfei butyrate oxidation supplies the electron donor for strain-195 TCE dechlorination,
+      while recipient consumption maintains a favorable hydrogen sink. The separate donor-limited minimum-threshold
+      assay is not the routine culture concentration. Later residual butyrate consumption and cometabolic vinyl-chloride
+      conversion do not establish continued growth after the growth-supporting acceptors are depleted.
+  - source: Aggregation-Enhanced Hydrogen Flux
+    target: Reductive Dechlorination by Dehalococcoides
+    description: PARTIAL - aggregation could shorten diffusion distances and thereby support hydrogen delivery to
+      strain 195 at the measured dechlorination rate. This mechanistic contribution is inferred from the diffusion
+      model together with observed aggregates, not from selective disruption and rescue of aggregation.
+  retained_edge_decisions:
+  - source: Butyrate Fermentation Supporting TCE Dechlorination
+    target: Reductive Dechlorination by Dehalococcoides
+    rationale: Hydrogen from S. wolfei butyrate oxidation supplies the electron donor for strain-195 TCE dechlorination,
+      while recipient consumption maintains a favorable hydrogen sink. The separate donor-limited minimum-threshold
+      assay is not the routine culture concentration. Later residual butyrate consumption and cometabolic vinyl-chloride
+      conversion do not establish continued growth after the growth-supporting acceptors are depleted.
+  - source: Aggregation-Enhanced Hydrogen Flux
+    target: Reductive Dechlorination by Dehalococcoides
+    rationale: PARTIAL - aggregation could shorten diffusion distances and thereby support hydrogen delivery to
+      strain 195 at the measured dechlorination rate. This mechanistic contribution is inferred from the diffusion
+      model together with observed aggregates, not from selective disruption and rescue of aggregation.
+  removed_edge_decisions: []
+  references:
+  - PMID:25576615
+  - PMID:24015929
+  - doi:10.3389/fmicb.2016.01795
+  issues:
+  - 1389
+  - 1392
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture/2026-10-06T061823Z-codex-91ce0c.yaml
+  source_review:
+    PMID:25576615:
+      url: https://journals.asm.org/doi/10.1128/AEM.03464-14
+      scope: Complete cached abstract and complete primary main body, Tables 1-4 text and Figures 1-4 captions.
+        SEM observation and Fick model distinguished; CO mechanism remains pending. No visual figure inspection
+        or supplements.
+    PMID:24015929:
+      url: https://pubmed.ncbi.nlm.nih.gov/24015929/
+      scope: Complete cached primary abstract only. Exact-pair isotope-fractionation context, not a new mechanism.
+        No full body, figure images or supplements inspected.
+    doi:10.3389/fmicb.2016.01795:
+      url: https://doi.org/10.3389/fmicb.2016.01795
+      scope: Complete existing cached open-access main body, Tables 1-2 text, Figures 1-3 captions and supplementary-caption
+        summaries S1-S3. Despite abstract_only front matter, this existing cache contains OA full text. No figure
+        images or supplement files inspected. Protein/complex assays use M. hungatei; exact-Dhc evidence is qRT-PCR.
+        Cache unchanged.
+- path: kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml
+  id: CommunityMech:000301
+  original_sha256: 481d1d0cd521dbf852b91a98589b5f79c6735732afa88bc39c67e73f0e2a93d2
+  record_sha256: 252f1bd100591910deeb53b0de75130e7f38995f3de7a10aca6466f3f16e2c66
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml
+  scope: Whole record and every original node/arrow reviewed at the documented source-access scope; non-graph fields
+    preserved, not certified. New CO structure remains pending only for the Syntrophomonas record.
+  summary: Retain the biochar amendment with consortium/isolate scope explicit.; Retain activity enhancement with
+    adsorption and mediation uncertainty.; Retain the TCE outcome but remove the unsupported causal arrow to lower
+    VC.; Retain the condition-specific lower-VC observation without generalizing across inocula.; Retain measured
+    composition and hypothesized guild contribution without demonstrated flux or stability.
+  renamed_nodes: {}
+  node_decisions:
+  - node: BC600 Biochar-Consortium Coupling
+    rationale: Retain the biochar amendment with consortium/isolate scope explicit.
+  - node: BC600 Colonization and Activity Enhancement
+    rationale: Retain activity enhancement with adsorption and mediation uncertainty.
+  - node: Biochar-Accelerated TCE Degradation
+    rationale: Retain the TCE outcome but remove the unsupported causal arrow to lower VC.
+  - node: Vinyl Chloride Accumulation Mitigation
+    rationale: Retain the condition-specific lower-VC observation without generalizing across inocula.
+  - node: Hydrogen- and Electroactive-Guild Dechlorination Stability
+    rationale: Retain measured composition and hypothesized guild contribution without demonstrated flux or stability.
+  removed_node_decisions: []
+  edges_before:
+  - source: BC600 Biochar-Consortium Coupling
+    target: BC600 Colonization and Activity Enhancement
+    description: Coupling BC600 to the native dechlorinating consortium lets the biochar combine adsorption with
+      enhanced microbial colonization and activity.
+  - source: BC600 Colonization and Activity Enhancement
+    target: Biochar-Accelerated TCE Degradation
+    description: Biochar-associated colonization and activity were linked to faster TCE degradation.
+  - source: Biochar-Accelerated TCE Degradation
+    target: Vinyl Chloride Accumulation Mitigation
+    description: Accelerated TCE degradation was part of the BC600 response that also limited accumulation of the
+      carcinogenic intermediate vinyl chloride.
+  edges_after:
+  - source: BC600 Biochar-Consortium Coupling
+    target: BC600 Colonization and Activity Enhancement
+    description: BC600 amendment supplies sorptive surfaces and is associated with enhanced microbial colonization
+      and activity in the tested consortium. Amendment effects depend on dose and inoculum conditions; this does
+      not establish that adsorption itself is biological dechlorination.
+  - source: BC600 Colonization and Activity Enhancement
+    target: Biochar-Accelerated TCE Degradation
+    description: PARTIAL - biochar-associated microbial colonization and activity could contribute to faster TCE
+      transformation, alongside sorption and bioavailability effects. The amendment comparison does not selectively
+      isolate colonization as the causal mediator, and TCE disappearance through adsorption is not itself degradation.
+  retained_edge_decisions:
+  - source: BC600 Biochar-Consortium Coupling
+    target: BC600 Colonization and Activity Enhancement
+    rationale: BC600 amendment supplies sorptive surfaces and is associated with enhanced microbial colonization
+      and activity in the tested consortium. Amendment effects depend on dose and inoculum conditions; this does
+      not establish that adsorption itself is biological dechlorination.
+  - source: BC600 Colonization and Activity Enhancement
+    target: Biochar-Accelerated TCE Degradation
+    rationale: PARTIAL - biochar-associated microbial colonization and activity could contribute to faster TCE transformation,
+      alongside sorption and bioavailability effects. The amendment comparison does not selectively isolate colonization
+      as the causal mediator, and TCE disappearance through adsorption is not itself degradation.
+  removed_edge_decisions:
+  - source: Biochar-Accelerated TCE Degradation
+    target: Vinyl Chloride Accumulation Mitigation
+    rationale: Common amendment-associated endpoints with condition-dependent direction; faster TCE transformation
+      is not demonstrated to cause lower VC.
+  references:
+  - PMID:41442978
+  issues:
+  - 1390
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium/2026-10-06T061824Z-codex-ea8b4f.yaml
+  source_review:
+    PMID:41442978:
+      url: https://doi.org/10.1016/j.jenvman.2025.128362
+      alternate_url: https://www.researchgate.net/publication/398909775_Biochar-assisted_detoxification_of_groundwater_trichloroethene_Mitigating_vinyl_chloride_accumulation_and_environmental_risks_via_Dehalococcoides_mccartyi-containing_consortium
+      scope: Complete cached published abstract and publisher-indexed highlights/introduction. Complete author-uploaded
+        UNCORRECTED PROOF main body, Table 1 text and Figures 1-7 captions; uploaded by Che-Wei Lu on 2025-12-24.
+        Final published full body not accessed (publisher 403). No figure images or supplements. Inconsistent proof
+        units and concentrations are not normalized.
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 4c7aef3c2..be2414b1c 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -140,9 +140,9 @@ kb/communities/Defined_ThreeStrain_Organic_Nitrogen_Nitrifying_Community.yaml	Co
 kb/communities/Dehalococcoides_Desulfovibrio_Lactate_TCE_Syntrophy.yaml	CommunityMech:000199	bc9eebbdf57b937cc87c72ee439f404bb7ab51b99b2f06e2f11fd240a454c629	3	2	93.3	reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml	reviewed
 kb/communities/Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml	CommunityMech:000200	2d771dc7df594f59d55d100bdf4e7ed6bbc571dfea0a4e37a774583e831910dc	4	3	95.0	reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml	reviewed
 kb/communities/Dehalococcoides_Methanosarcina_DMB_Cobalamin_Coculture.yaml	CommunityMech:000209	fbf9a3612c04d172cd46cc210b069e03e627b5dcec722682651abfe6e0e6afb7	3	2	93.3	reports/causal_graph_review/decisions/20261006-three-records-batch30.yaml	reviewed
-kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml	CommunityMech:000184	cb7e15cd85069763298df062a42ba1f54497fc8db00edd004215590b2a0a8aca	3	2	100.0		pending
-kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml	CommunityMech:000183	3c229074814142c66fa8a5a8624c7bf3dbdebc243dfea7eebee3d1840a88f52a	3	2	100.0		pending
-kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml	CommunityMech:000301	481d1d0cd521dbf852b91a98589b5f79c6735732afa88bc39c67e73f0e2a93d2	5	3	100.0		pending
+kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml	CommunityMech:000184	ab28a71ff971a76db7e6bc3989a24ff65fbf03b0eb1177ae70c85fab1d04c813	3	2	93.3	reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml	reviewed
+kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml	CommunityMech:000183	b0c182ee42aa14442f77f15b8a8ada5172fbbd989f8175c399af7f83877b6dd2	3	2	93.3	reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml	needs_research
+kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml	CommunityMech:000301	252f1bd100591910deeb53b0de75130e7f38995f3de7a10aca6466f3f16e2c66	5	2	100.0	reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml	reviewed
 kb/communities/Desert_Tomato_Salt_Stress_SynCom5.yaml	CommunityMech:000096	059843349f77b97c255132bcffd43a5ec9384106e6333bdaad61459145cbc68f	4	2	100.0		pending
 kb/communities/Desulfovibrio_Methanococcus_Syntrophy.yaml	CommunityMech:000023	c896fa44995236f5fa5b2834153ff53f170f71148c9836655d3e180057370819	3	3	100.0		pending
 kb/communities/Desulfovibrio_Methanosarcina_Lactate_Syntrophy.yaml	CommunityMech:000150	6e76d6fbc3fa58ef83662bc8476217cbb2b84c8cb7d6d12c18512fe6276619fa	3	2	100.0		pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 4c4f57929..ac2dfdd0b 100644
--- a/reports/causal_graph_review/summary.json
+++ b/reports/causal_graph_review/summary.json
@@ -3,13 +3,13 @@
   "semantic_review_rule": "Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.",
   "records": 460,
   "nodes": 1470,
-  "edges": 705,
+  "edges": 704,
   "records_without_nodes": 8,
   "records_without_edges": 143,
   "review_status_counts": {
-    "needs_research": 4,
-    "pending": 321,
-    "reviewed": 135
+    "needs_research": 5,
+    "pending": 318,
+    "reviewed": 137
   },
   "structural_defects": [],
   "network_audit": [
diff --git a/reports/causal_graph_review/validation-20261006-batch31.json b/reports/causal_graph_review/validation-20261006-batch31.json
new file mode 100644
index 000000000..0ed844519
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch31.json
@@ -0,0 +1,679 @@
+{
+  "base_commit": "5988d5ace91b79ad27e118720378e5fa58763949",
+  "scope": [
+    "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml",
+    "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
+    "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml"
+  ],
+  "reference_validator_version": "0.1.7",
+  "results": [
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-strict.tsv",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-strict.log",
+      "log_sha256": "caadc48e302e4c35852382f5fa058dc9cdb180ab56c06d690ca8faa8500b56b3",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch31/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-strict.tsv\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-references.log",
+      "log_sha256": "eef5bf90f0ba60772fc63f94603b4c7a4e996ed531d7a519497b3d4df034d3d6",
+      "output_tail": "Validating kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-snippets.log",
+      "log_sha256": "d6441c5dcfaf6a072d70e8708d5fe1bbd2c2a2d31da61b3014fb014108c34cef",
+      "output_tail": "# 18 evidence snippets scanned across 1 files\n  MATCH      18\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-rank.log",
+      "log_sha256": "555ab32528628eaf5f36efad675a2f1884d3af51c55836dc3247fc8dd1d1e46f",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000184\",\n    \"name\": \"Dehalococcoides-Pelobacter Acetylene TCE Coculture\",\n    \"score\": 93.3,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 2,\n    \"interaction_evidence\": 5,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture/2026-10-06T061823Z-codex-d74031.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-strict.tsv",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-strict.log",
+      "log_sha256": "e81e7e197d0c70527b0e44ebf27a85a7cdd1a40ceb65474c413550b1cb9083ef",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch31/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-strict.tsv\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-references.log",
+      "log_sha256": "3d3f758b7bf6fc36f7dcee72568c1d5996d8a4204adda5200a533a9b9ecf6e83",
+      "output_tail": "Validating kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-snippets.log",
+      "log_sha256": "7cb30458f959a4a7649fd96c05ca0aecb145f69b34e2ebea471b4c38e6956f10",
+      "output_tail": "# 31 evidence snippets scanned across 1 files\n  MATCH      31\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-rank.log",
+      "log_sha256": "d771caacf48dc5ca55c2c0457720c06feae9d60f0df0c4de98bcafe237d014e7",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000183\",\n    \"name\": \"Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture\",\n    \"score\": 93.3,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 2,\n    \"interaction_evidence\": 7,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture/2026-10-06T061823Z-codex-91ce0c.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-strict.tsv",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-strict.log",
+      "log_sha256": "9c549bcca795b7b8059adad80ef819447e762b6141dc8f85639f62b5022eef38",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch31/src/communitymech/schema/communitymech.yaml\n\n=== validate-strict summary ===\n  files scanned:      1\n  files with ERROR:   0\n  total ERROR rows:   0\n  TSV:                /private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-strict.tsv\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-references.log",
+      "log_sha256": "42cb5844b58753d2a82d370d8a0dae638198cfb3146d0b325a1966b85097e5bc",
+      "output_tail": "Validating kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-snippets.log",
+      "log_sha256": "4450b5ff1101bc2d6072d1dbe68983556781062b26a30ff5ad5b7d81a7b14c1b",
+      "output_tail": "# 8 evidence snippets scanned across 1 files\n  MATCH      8\n  RENDERING  0\n  ASSEMBLED  0\n  WEAK       0\n  MISMATCH   0\n  NOCONTENT  0\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n\n# MISMATCH/WEAK detail\n\n# Files by RENDERING (faithful quote; differs from cache only by\n# punctuation/whitespace/Greek \u2014 this is what validate-references flags)\n\n# Top files by NOCONTENT (unverifiable; cache stub/missing)\n\n# ASSEMBLED (every part is in the source; the join is not \u2014\n# a table flattened into prose, or a quote welded from two places)\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-rank.log",
+      "log_sha256": "8836f88e20df0dea3d17dbb9e3a71845e2a222269030f047c716aa41c2744662",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000301\",\n    \"name\": \"Dehalococcoides mccartyi CWV2 Dechlorinating Consortium\",\n    \"score\": 100.0,\n    \"taxonomy\": 1,\n    \"connected_taxa\": 1,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 5,\n    \"downstream_edges\": 2,\n    \"interaction_evidence\": 6,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [],\n    \"path\": \"kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium/2026-10-06T061824Z-codex-ea8b4f.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "inventory",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "reports/causal_graph_review/build_inventory.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/inventory.log",
+      "log_sha256": "6d62c8f4a75ff99673767035a04fd1e3f801c99f133c9bb9a6eb7954c7649ff2",
+      "output_tail": "{\n  \"scope\": \"Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.\",\n  \"semantic_review_rule\": \"Structural checks and readiness scores do not establish causal support. Completed reviews must match the current record SHA-256, cover every node once with a rationale, and reproduce the current edge list.\",\n  \"records\": 460,\n  \"nodes\": 1470,\n  \"edges\": 704,\n  \"records_without_nodes\": 8,\n  \"records_without_edges\": 143,\n  \"review_status_counts\": {\n    \"needs_research\": 5,\n    \"pending\": 318,\n    \"reviewed\": 137\n  },\n  \"structural_defects\": []\n}\n"
+    },
+    {
+      "check": "network",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.cli",
+        "audit-network",
+        "--json"
+      ],
+      "exit_code": 1,
+      "expected_exit_codes": [
+        1
+      ],
+      "log": "/private/tmp/communitymech-batch31/network.log",
+      "log_sha256": "2cd39b61dfce615081637c0e72d245194c41d4a2a374d65bccad7c69fcff4e63",
+      "output_tail": "{\n          \"preferred_term\": \"Legionella MAGs\",\n          \"term\": {\n            \"id\": \"NCBITaxon:445\",\n            \"label\": \"Legionella\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"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\"\n        },\n        \"abundance_value\": \"Lower-abundance Legionella-affiliated MAGs detected during metagenomic risk assessment.\\n\",\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:41457319\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"COMPUTATIONAL\",\n            \"snippet\": \"detection of waterborne pathogens from the Legionella genus\",\n            \"explanation\": \"Supports Legionella-affiliated lower-abundance bins as monitored biosafety-relevant members of the consortium.\\n\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Legionella MAGs' has no interactions\"\n    }\n  ],\n  \"Sclerotinia_Sclerotia_12Strain_Biocontrol_SynCom\": [\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Twelve-Strain SynCom Suppression of Sclerotinia Sclerotia\",\n      \"interaction_index\": 0,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    },\n    {\n      \"type\": \"UNKNOWN_TARGET\",\n      \"interaction\": \"Trinickia MC Key Contribution to Sclerotia Mortality\",\n      \"interaction_index\": 1,\n      \"taxon\": \"Sclerotinia sclerotiorum\",\n      \"severity\": \"warning\",\n      \"message\": \"Target taxon 'Sclerotinia sclerotiorum' not found in taxonomy section (community-level scope)\"\n    }\n  ],\n  \"Space_Habitat_SevenMember_Stress_Tolerance_SynCom\": [\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Acinetobacter radioresistens 50V1\",\n      \"taxon_id\": \"NCBITaxon:40216\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Acinetobacter radioresistens 50V1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:40216\",\n            \"label\": \"Acinetobacter radioresistens\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate came from the preflight Mars Odyssey Orbiter; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"50V1\",\n          \"genome_accession\": \"GCA_002834555.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Acinetobacter radioresistens | 50V1 | Preflight Mars Odyssey Orbiter | \\u2013 | Mccoy et al., 2012 | GCA_002834555.1 | TSYB/TSYA | 37 \\u00b0C | 16\\u201318 h\",\n            \"explanation\": \"Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Acinetobacter radioresistens 50V1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Micrococcus luteus W4-Al-K1\",\n      \"taxon_id\": \"NCBITaxon:1270\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Micrococcus luteus W4-Al-K1\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1270\",\n            \"label\": \"Micrococcus luteus\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from an ISS aluminum-case touch array; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"W4-Al-K1\",\n          \"genome_accession\": \"GCA_057816565.1\"\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"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\",\n            \"explanation\": \"Identifies M. luteus W4-Al-K1 as a consortium member and gives its ISS source, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Micrococcus luteus W4-Al-K1' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Propionibacterium cyclohexanicum TA-12T\",\n      \"taxon_id\": \"NCBITaxon:64702\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Propionibacterium cyclohexanicum TA-12T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:64702\",\n            \"label\": \"Propionibacterium cyclohexanicum\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. cyclohexanicum type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"TA-12T\",\n          \"genome_accession\": \"GCA_900111365\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"16859\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"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\",\n            \"explanation\": \"Identifies P. cyclohexanicum TA-12T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Propionibacterium cyclohexanicum TA-12T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Pseudomonas antarctica CMS 35T\",\n      \"taxon_id\": \"NCBITaxon:219572\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Pseudomonas antarctica CMS 35T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:219572\",\n            \"label\": \"Pseudomonas antarctica\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the P. antarctica type strain as a biosafety-level-1 Pseudomonas surrogate.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"CMS 35T\",\n          \"genome_accession\": \"GCA_010634845\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"15318\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Pseudomonas antarctica | CMS 35 T | Antarctica | DSM 15318 T | Reddy et al., 2004 | GCA_010634845 | TSYB/TSYA | Ambient | 12\\u201316 h\",\n            \"explanation\": \"Identifies P. antarctica CMS 35T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Pseudomonas antarctica CMS 35T' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Staphylococcus capitis K1-2-2-23\",\n      \"taxon_id\": \"NCBITaxon:29388\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Staphylococcus capitis K1-2-2-23\",\n          \"term\": {\n            \"id\": \"NCBITaxon:29388\",\n            \"label\": \"Staphylococcus capitis\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The isolate was recovered from ISS V2A steel; ontology grounding is at species level.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"K1-2-2-23\",\n          \"genome_accession\": \"GCA_025272695\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"111179\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"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\",\n            \"explanation\": \"Identifies S. capitis K1-2-2-23 as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Staphylococcus capitis K1-2-2-23' has no interactions\"\n    },\n    {\n      \"type\": \"DISCONNECTED\",\n      \"taxon\": \"Streptococcus halotolerans HTS9T\",\n      \"taxon_id\": \"NCBITaxon:1814128\",\n      \"taxon_data\": {\n        \"taxon_term\": {\n          \"preferred_term\": \"Streptococcus halotolerans HTS9T\",\n          \"term\": {\n            \"id\": \"NCBITaxon:1814128\",\n            \"label\": \"Streptococcus halotolerans\"\n          },\n          \"gtdb_grounding_status\": \"UNRESOLVED\",\n          \"notes\": \"The source used the S. halotolerans type strain as a biosafety-level-1 representative.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"HTS9T\",\n          \"genome_accession\": \"GCA_001598035\",\n          \"culture_collections\": [\n            {\n              \"collection\": \"DSM\",\n              \"accession\": \"101996\"\n            }\n          ]\n        },\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42577390\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"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\",\n            \"explanation\": \"Identifies S. halotolerans HTS9T as a consortium member and gives its source, DSM number, genome accession and cultivation conditions.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Streptococcus halotolerans HTS9T' has no interactions\"\n    }\n  ]\n}\n"
+    },
+    {
+      "check": "rank-all",
+      "command": [
+        "just",
+        "rank-causal-graphs"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/rank-all.log",
+      "log_sha256": "ddc7f0b11984b9370e9ec3acf7c461f2fdbe9d158f75149deec85cc9068f8169",
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Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+    },
+    {
+      "check": "render",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/render.log",
+      "log_sha256": "994119461c668c74abea1331494e0ef404d36f344138104b0df96f11c4fc3dca",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch31/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch31/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch31/docs/index.html\n"
+    },
+    {
+      "check": "render-repeat",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/render-repeat.log",
+      "log_sha256": "994119461c668c74abea1331494e0ef404d36f344138104b0df96f11c4fc3dca",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch31/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch31/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch31/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch31/docs/index.html\n"
+    },
+    {
+      "check": "connectivity-survey",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import json,runpy; print(json.dumps(runpy.run_path(\"tests/test_community_level_connectivity_credit.py\")[\"_survey\"](),sort_keys=True))"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/connectivity-survey.log",
+      "log_sha256": "75f81e775562eccff7b05d37325e53d49d8dd9a033afb56a3af328cded2c0361",
+      "output_tail": "{\"community_level_only\": 264, \"credited_solely_by_the_rule\": 1220, \"mixed\": 124, \"records\": 460, \"taxa\": 1496, \"with_community_level\": 388}\n"
+    },
+    {
+      "check": "regressions",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch10.py",
+        "tests/test_causal_review_batch11.py",
+        "tests/test_causal_review_batch12.py",
+        "tests/test_causal_review_batch13.py",
+        "tests/test_causal_review_batch14.py",
+        "tests/test_causal_review_batch15.py",
+        "tests/test_causal_review_batch16.py",
+        "tests/test_causal_review_batch17.py",
+        "tests/test_causal_review_batch18.py",
+        "tests/test_causal_review_batch19.py",
+        "tests/test_causal_review_batch20.py",
+        "tests/test_causal_review_batch21.py",
+        "tests/test_causal_review_batch22.py",
+        "tests/test_causal_review_batch23.py",
+        "tests/test_causal_review_batch24.py",
+        "tests/test_causal_review_batch25.py",
+        "tests/test_causal_review_batch27.py",
+        "tests/test_causal_review_batch28.py",
+        "tests/test_causal_review_batch29.py",
+        "tests/test_causal_review_batch30.py",
+        "tests/test_causal_review_batch31.py",
+        "tests/test_causal_review_batch5.py",
+        "tests/test_causal_review_batch6.py",
+        "tests/test_causal_review_batch7.py",
+        "tests/test_causal_review_batch8.py",
+        "tests/test_causal_review_batch9.py",
+        "tests/test_site_audit_fixes.py",
+        "tests/test_causal_review_inventory.py",
+        "tests/test_rank_causal_graph_readiness.py",
+        "tests/test_network_auditor.py",
+        "tests/test_participating_taxa.py",
+        "tests/test_causal_descriptions_are_published.py",
+        "tests/test_published_pages_name_real_records.py",
+        "tests/test_reference_validator_actually_validates.py",
+        "tests/test_snippet_audit_artefact_classes.py",
+        "tests/test_reference_error_annotation.py",
+        "tests/test_community_level_connectivity_credit.py",
+        "tests/test_no_paywalled_text_in_repo.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/regressions.log",
+      "log_sha256": "4fe72e22ef850ff43af09eeeb2a034f46e8d41500f032bf0d4768ca56198908b",
+      "output_tail": "........................................................................ [ 20%]\n........................................................................ [ 40%]\n........................................................................ [ 61%]\n........................................................................ [ 81%]\n..................................................................       [100%]\n354 passed in 182.27s (0:03:02)\n"
+    },
+    {
+      "check": "black",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+        "--check",
+        "tests/test_causal_review_batch31.py",
+        "tests/test_participating_taxa.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/black.log",
+      "log_sha256": "b9cf511501d306d2bd8355ccb165c8ddc0a6fdd62d7c72c4a7b1795cf8934c8c",
+      "output_tail": "All done! \u2728 \ud83c\udf70 \u2728\n2 files would be left unchanged.\n"
+    },
+    {
+      "check": "ruff",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/wCcxEYRM4HeHgwYPZemHX/bin/ruff",
+        "check",
+        "tests/test_causal_review_batch31.py",
+        "tests/test_participating_taxa.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/ruff.log",
+      "log_sha256": "82b3e6a6c090a57601d22943bd23fca9218d1031dbe5a7b754092f9a156b4f18",
+      "output_tail": "All checks passed!\n"
+    },
+    {
+      "check": "diff-check",
+      "command": [
+        "git",
+        "diff",
+        "--check"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch31/diff-check.log",
+      "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+      "output_tail": ""
+    }
+  ],
+  "limitations": [
+    "Two completed graph reviews; the third has repaired existing structure but remains needs_research for possible CO structure. All eleven nodes retained; six arrows retained and one unsupported arrow removed. No new nodes/arrows or paid Edison job.",
+    "Primary-source access differs by study. The CWV2 body is an author-uploaded uncorrected proof, not the final published body. No figure images or supplement files inspected.",
+    "No new article body/PDF is committed. All caches and non-graph raw blocks preserved. Exact-pair Pelobacter rescue depends on externally read body text, not its ANAS abstract snippet. Textual MATCH is not scientific validation.",
+    "Source-only PAIRWISE entries follow the existing intrinsic-recipient convention, not self-edges or reverse exchange. Self-adversarial review is not independent approval, protected CI success or full-corpus completion.",
+    "HTML descriptions checked by exact parser and repeat renders, not browser screenshots. Post-commit docs-current is a separate publication gate.",
+    "All three reference-validator commands exit 0 but report Total checks: 0. They are no-op, not evidence validation. Independent snippet audits and source review are recorded separately."
+  ],
+  "snippet_counts_by_record": {
+    "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml": {
+      "MATCH": 18,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml": {
+      "MATCH": 31,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml": {
+      "MATCH": 8,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    }
+  },
+  "unchanged_raw_blocks": 46,
+  "unchanged_record_files": 457,
+  "unchanged_cache_files": 920,
+  "network_delta": {
+    "existing_findings_preserved": 31,
+    "new_disconnected": 0,
+    "rationale": "All prior warnings remain exactly unchanged; no structural errors or fabricated connectivity fixes."
+  },
+  "render_determinism": true,
+  "published_description_coverage": {
+    "pages": 456,
+    "nodes": 1456,
+    "arrows": 696
+  },
+  "participant_census": {
+    "connectivity_before": {
+      "community_level_only": 264,
+      "credited_solely_by_the_rule": 1220,
+      "mixed": 124,
+      "records": 460,
+      "taxa": 1496,
+      "with_community_level": 388
+    },
+    "connectivity_after": {
+      "community_level_only": 264,
+      "credited_solely_by_the_rule": 1220,
+      "mixed": 124,
+      "records": 460,
+      "taxa": 1496,
+      "with_community_level": 388
+    },
+    "exact_change": "174 -> 175 users; only the Syntrophomonas/Dhc195 coculture added",
+    "numeric_bounds_changed": false
+  },
+  "corpus": {
+    "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+    "records": 460,
+    "nodes": 1470,
+    "edges": 704,
+    "records_without_nodes": 8,
+    "records_without_edges": 143,
+    "review_status_counts": {
+      "needs_research": 5,
+      "pending": 318,
+      "reviewed": 137
+    },
+    "structural_defects": []
+  },
+  "tested_file_sha256": {
+    "reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml": "3ae6fd42367e69f8ffe653271b91ef4cabc271b302f7f729d6d1204a1d7e7b88",
+    "tests/test_causal_review_batch31.py": "eaae0577db25325acb3151834e0e15f9a7662ef5f01b0ffb6fe440a222e295da",
+    "tests/test_participating_taxa.py": "06833a684b7e82be1ed33ef8bfc1088c879f95d532ac5b624564a99a5e83397f",
+    "kb/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.yaml": "ab28a71ff971a76db7e6bc3989a24ff65fbf03b0eb1177ae70c85fab1d04c813",
+    "kb/communities/Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml": "b0c182ee42aa14442f77f15b8a8ada5172fbbd989f8175c399af7f83877b6dd2",
+    "kb/communities/Dehalococcoides_mccartyi_CWV2_Dechlorinating_Consortium.yaml": "252f1bd100591910deeb53b0de75130e7f38995f3de7a10aca6466f3f16e2c66"
+  },
+  "status": "verified_two_completed_reviews_one_needs_research_three_changed_records",
+  "reference_validator_effective_checks": 0,
+  "reference_validator_caveat": "All three reference-validator commands exit 0 but report Total checks: 0. They are no-op, not evidence validation. Independent snippet audits and source review are recorded separately."
+}
diff --git a/tests/test_causal_review_batch31.py b/tests/test_causal_review_batch31.py
new file mode 100644
index 000000000..d6e8fb77c
--- /dev/null
+++ b/tests/test_causal_review_batch31.py
@@ -0,0 +1,142 @@
+"""Keep exact-system rescue, modeled flux and condition-specific outcomes distinct."""
+
+import hashlib
+from collections import Counter
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-three-records-batch31.yaml"
+
+
+def records():
+    ledger = yaml.safe_load(LEDGER.read_text())
+    return ledger, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in ledger["records"]]
+
+
+def test_pelobacter_recipient_and_exact_pair_rescue_are_not_anas_or_reverse_exchange():
+    _, docs = records()
+    fermentation, output, relief = docs[0]["ecological_interactions"]
+    assert fermentation["interaction_type"] == "SYNTROPHY"
+    assert output["source_taxon"]["term"]["id"] == "NCBITaxon:243164"
+    assert not {"target_taxon", "interaction_type"} & output.keys()
+    assert "unchanged tceA transcript abundance" in output["description"]
+    assert output["evidence"][1]["supports"] == "PARTIAL"
+    assert relief["scope"] == "PAIRWISE" and "interaction_type" not in relief
+    assert relief["source_taxon"]["term"]["id"] == "NCBITaxon:18"
+    assert relief["target_taxon"]["term"]["id"] == "NCBITaxon:243164"
+    assert "restored TCE reductive dechlorination" in relief["description"]
+    assert relief["evidence"][0]["supports"] == "PARTIAL"
+    assert "refers to ANAS, not the defined pair" in relief["evidence"][0]["explanation"]
+    assert "Figure 2" in relief["downstream"][0]["description"]
+    assert all(n["downstream"][0]["target"] == output["name"] for n in [fermentation, relief])
+    pin = docs[0]["taxonomy"][1]["taxon_term"]["gtdb_classification"]
+    assert pin["curated"] is True and pin["gtdb_id"] == "GTDB:g__Syntrophotalea"
+    assert pin["majority_fraction"] == 0.5
+
+
+def test_syntrophomonas_recipient_phenotype_and_observed_vs_modeled_aggregation():
+    _, docs = records()
+    fermentation, output, aggregation = docs[1]["ecological_interactions"]
+    assert fermentation["interaction_type"] == "SYNTROPHY"
+    assert "externally cobalamin-supplemented" in fermentation["description"]
+    assert "donor-limited minimum-threshold assay" in fermentation["downstream"][0]["description"]
+    assert output["scope"] == "PAIRWISE"
+    assert output["source_taxon"]["term"]["id"] == "NCBITaxon:243164"
+    assert not {"target_taxon", "interaction_type"} & output.keys()
+    assert "cometabolic, not demonstrated growth-coupled" in output["description"]
+    assert aggregation["scope"] == "COMMUNITY_LEVEL"
+    assert not {"source_taxon", "target_taxon", "interaction_type"} & aggregation.keys()
+    assert {p["term"]["id"] for p in aggregation["participating_taxa"]} == {
+        "NCBITaxon:243164",
+        "NCBITaxon:863",
+    }
+    assert aggregation["evidence"][0]["evidence_source"] == "IN_VITRO"
+    model = aggregation["evidence"][1]
+    assert model["evidence_source"] == "COMPUTATIONAL" and model["supports"] == "PARTIAL"
+    assert aggregation["downstream"][0]["description"].startswith("PARTIAL -")
+    assert "not from selective disruption and rescue" in aggregation["downstream"][0]["description"]
+
+
+def test_cwv2_common_amendment_outcomes_are_not_an_outcome_to_outcome_arrow():
+    _, docs = records()
+    amendment, activity, tce, vc, _ = docs[2]["ecological_interactions"]
+    assert len(docs[2]["ecological_interactions"]) == 5
+    assert amendment["downstream"][0]["target"] == activity["name"]
+    assert activity["downstream"][0]["target"] == tce["name"]
+    assert activity["downstream"][0]["description"].startswith("PARTIAL -")
+    assert "does not selectively isolate colonization" in activity["downstream"][0]["description"]
+    assert "downstream" not in tce
+    assert "BC700" in activity["description"]
+    assert "not asserted to have the strongest adsorption" in activity["description"]
+    assert "high-inoculum" in vc["description"] and "lower-inoculum" in vc["description"]
+    assert "could instead increase vinyl chloride" in vc["description"]
+
+
+def test_cwv2_guild_profiles_do_not_establish_flux_or_field_stability():
+    _, docs = records()
+    guild = docs[2]["ecological_interactions"][-1]
+    assert "interaction_type" not in guild
+    assert "HYPOTHESIZED" in guild["description"]
+    assert "do not demonstrate hydrogen or electron flux" in guild["description"]
+    assert "long-term field stability" in guild["description"]
+    assert guild["evidence"][0]["supports"] == "PARTIAL"
+    assert "downstream" not in guild
+    assert "UNCO" in records()[0]["records"][2]["source_review"]["PMID:41442978"]["scope"]
+    assert (
+        "Final published full body not accessed"
+        in records()[0]["records"][2]["source_review"]["PMID:41442978"]["scope"]
+    )
+
+
+def test_batch31_canonical_terms_exact_anchors_and_append_only_history():
+    ledger, docs = records()
+    for row, doc in zip(ledger["records"], docs, strict=True):
+        canonical = {t["taxon_term"]["term"]["id"]: t["taxon_term"] for t in doc["taxonomy"]}
+        names = {n["name"] for n in doc["ecological_interactions"]}
+        for node in doc["ecological_interactions"]:
+            terms = node.get("participating_taxa", []) + [
+                node[k] for k in ["source_taxon", "target_taxon"] if k in node
+            ]
+            for term in terms:
+                original = canonical[term["term"]["id"]]
+                assert {k: term[k] for k in ["preferred_term", "term"]} == {
+                    k: original[k] for k in ["preferred_term", "term"]
+                }
+            assert all(
+                e["target"] in names and e["target"] != node["name"]
+                for e in node.get("downstream", [])
+            )
+        (gap,) = doc["discussions"]
+        assert gap["kind"] == "KNOWLEDGE_GAP" and gap["status"] == "OPEN"
+        assert set(gap["attaches_to"]) == {"ecological_interactions#" + n for n in names}
+        assert row["curation_events_added"] == 1 and len(row["history_files"]) == 1
+        assert doc["curation_history"][-1]["llm_assisted"] is True
+        assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+    assert "Removed the vinyl-chloride mitigation" in docs[2]["curation_history"][0]["changes"]
+
+
+def test_batch31_complete_decisions_and_pending_co_research_are_honest():
+    ledger, docs = records()
+    assert ledger["independent_approval"] is False
+    assert ledger["issues"] == [1388, 1389, 1390]
+    assert ledger["open_nongraph_followups"] == [765, 1391]
+    assert ledger["open_graph_research"] == [1392]
+    assert [r["status"] for r in ledger["records"]] == ["reviewed", "needs_research", "reviewed"]
+    assert ledger["edison"]["status"] == "dry_run_only_no_provider_job_or_charge"
+    assert sum(len(r["node_decisions"]) for r in ledger["records"]) == 11
+    assert sum(len(r["retained_edge_decisions"]) for r in ledger["records"]) == 6
+    assert sum(len(r["removed_edge_decisions"]) for r in ledger["records"]) == 1
+    for row, doc in zip(ledger["records"], docs, strict=True):
+        assert not row["renamed_nodes"] and not row["removed_node_decisions"]
+        assert Counter(d["node"] for d in row["node_decisions"]) == Counter(
+            n["name"] for n in doc["ecological_interactions"]
+        )
+        retained = {(e["source"], e["target"]) for e in row["edges_after"]}
+        removed = {(e["source"], e["target"]) for e in row["removed_edge_decisions"]}
+        assert not retained & removed
+        assert retained | removed == {(e["source"], e["target"]) for e in row["edges_before"]}
+    assert "#1392" in docs[1]["discussions"][0]["rationale"]
+    for path, digest in ledger["reference_cache_original_hashes"].items():
+        assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index f447e7f41..8d708d815 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -237,6 +237,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
     "Defined_Multispecies_Enamel_Caries_Model.yaml",
     "Defined_ThreeStrain_Organic_Nitrogen_Nitrifying_Community.yaml",
     "Dehalococcoides_Desulfovibrio_Pelosinus_Corrinoid_Triculture.yaml",
+    "Dehalococcoides_Syntrophomonas_TCE_Dechlorination_Coculture.yaml",
     "Dolichospermum_FBCC_A233_Xenic_Phycosphere_Community.yaml",
     "Drought_Rhizosphere_Iron_Actinobacteria_Community.yaml",
     "EcoFAB_Ring_Trial_SynCom17.yaml",