realmarcin · Oct 7, 2026
diff --git a/docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html b/docs/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.html
diff --git a/docs/communities/Polaromonas_Vanadium_Reduction_Community.html b/docs/communities/Polaromonas_Vanadium_Reduction_Community.html
diff --git a/docs/communities/Populus_Salt_Tolerant_SynComs.html b/docs/communities/Populus_Salt_Tolerant_SynComs.html
diff --git a/docs/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.html b/docs/communities/Poultry_Wastewater_ThreeStrain_Electroactive_Consortium.html
@@ -616,46 +616,43 @@ <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 Poultry-Wastewater Three-Strain Electroactive 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 (niche partitioning).</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="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
 
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Complementary Electroactive Consortium Performance</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>Proposed Electroactive Consortium Complementarity</h3>
                 </div>
-                <p class="prewrap interaction-description">Combining Lysinibacillus sphaericus A1, Bacillus cereus A2, and Lactococcus lactis A4 in equal volumes supplied a complementary electroactive inoculum for the poultry-wastewater microbial fuel cell.
-</p>
+                <p class="prewrap interaction-description">HYPOTHESIZED: metabolic complementarity and biofilm organization among Lysinibacillus sphaericus A1, Bacillus cereus A2 and Lactococcus lactis A4 may explain improved mixed-inoculum performance. The three-strain versus pure-culture comparison demonstrates a treatment difference, not measured resource partitioning, interspecies electron transfer or the individual necessity of a strain. Section 2.1.1 standardizes culture OD600 but leaves total mixed-versus-single inoculum volume ambiguous.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
 
+                    Lysinibacillus sphaericus A1,
 
+                    Bacillus cereus A2,
+
+                    Lactococcus lactis A4
+
+                </p>
 
 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
 
-                    <li>
-                        biological process involved in interspecies interaction between organisms
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
-                    </li>
 
-                </ul>
 
 
 
@@ -664,12 +661,12 @@ <h3>Complementary Electroactive Consortium Performance</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Consortium-Enhanced Anode Power Output
-                        <p class="prewrap causal-description">The mixed electroactive inoculum increased the microbial fuel cell&#39;s power-density output beyond the power densities produced by each strain in pure culture.</p>
+                        <p class="prewrap causal-description">HYPOTHESIZED: complementary microbial metabolism and biofilm organization may increase electron delivery and thus power output. Retain the authors proposed mechanism for the positive mixed-versus-pure comparison; no strain-resolved electron-transfer or complementarity perturbation isolates this mechanism.</p>
                     </div>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Consortium-Enhanced Chemical Oxygen Demand Removal
-                        <p class="prewrap causal-description">The mixed electroactive inoculum also improved organic-wastewater removal, producing the highest chemical oxygen demand removal among the tested inocula.</p>
+                        <p class="prewrap causal-description">HYPOTHESIZED: complementary metabolism may improve utilization of oxidizable substrates and hence COD reduction. COD is an aggregate assay in amended, sterilized wastewater, not proof of native-wastewater mineralization; Section 3.3 inconsistencies prevent certifying the exact reported ranking from concentrations.</p>
                     </div>
 
                 </div>
@@ -699,27 +696,25 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Consortium-Enhanced Anode Power Output</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
                 </div>
-                <p class="prewrap interaction-description">The three-strain consortium produced a higher microbial fuel-cell power density than L. sphaericus A1, B. cereus A2, or L. lactis A4 pure cultures over 30 days.</p>
+                <p class="prewrap interaction-description">During the 30-day dual-chamber MFC study, the consortium reached a reported maximum power density of 170 mW/m2, approximately 15% above L. sphaericus A1, 29% above B. cereus A2 and more than threefold above L. lactis A4. Preserve this positive tested-system comparison, not a claim that output remained higher at every time point. The matrix was nutrient-amended and sterilized, not raw wastewater.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
 
+                    Lysinibacillus sphaericus A1,
 
+                    Bacillus cereus A2,
+
+                    Lactococcus lactis A4
+
+                </p>
 
 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
 
-                    <li>
-                        biological process involved in interspecies interaction between organisms
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
-                    </li>
 
-                </ul>
 
 
 
@@ -748,27 +743,25 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Consortium-Enhanced Chemical Oxygen Demand Removal</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
                 </div>
-                <p class="prewrap interaction-description">The three-strain consortium removed chemical oxygen demand from amended poultry wastewater more effectively than the tested pure cultures.</p>
+                <p class="prewrap interaction-description">The abstract reports the consortium had the greatest COD removal (84.4%) in amended, sterilized model wastewater. Preserve that reported result with a source discrepancy: Section 3.3 pairs consortium 84.4% with 2150-to-436 mg/L and L. sphaericus 79.7% with 2150-to-335 mg/L, which yield approximately 79.7% and 84.4%, respectively. Do not silently swap these values or certify the exact quantitative ranking. COD cannot distinguish native-organic degradation, supplement consumption, biomass assimilation and abiotic changes.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
 
+                    Lysinibacillus sphaericus A1,
 
+                    Bacillus cereus A2,
+
+                    Lactococcus lactis A4
+
+                </p>
 
 
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
 
-                    <li>
-                        biological process involved in interspecies interaction between organisms
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
-                    </li>
 
-                </ul>
 
 
 
@@ -799,6 +792,60 @@ <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 mechanisms and reconciled measurements explain the mixed-culture advantage?
+                </h3>
+                <p class="prewrap">Both existing mechanism-to-performance directions remain HYPOTHESIZED; positive power and reported COD results remain. Full primary methods/results/discussion were read. SEM biofilm morphology is not strain-resolved transfer or causal complementarity. The OD600-normalized inoculation wording does not unambiguously establish equal total starting biomass. Section 3.3 percentages and concentrations appear crossed, and COD does not identify degradation pathways or distinguish amended from native substrates. Independent raw data or author clarification is needed before a numerical correction. Non-graph reported 84.4% remains unchanged, not certified, under #1716.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Proposed Electroactive Consortium Complementarity</code>, <code>ecological_interactions#Consortium-Enhanced Anode Power Output</code>, <code>ecological_interactions#Consortium-Enhanced Chemical Oxygen Demand Removal</code></p>
+
+
+
+                <details class="evidence-list">
+                    <summary class="muted small">2 evidence item(s)</summary>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/41594859/" rel="nofollow noreferrer">PMID:41594859</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">selecting complementary strains with diverse metabolic functions can substantially improve system performance</p>
+                        <p class="muted small prewrap">Supports the authors proposed complementarity interpretation, not a directly established niche-partitioning mechanism.</p>
+                    </div>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/41594859/" rel="nofollow noreferrer">PMID:41594859</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">The highest COD removal (84.4%) was also recorded</p>
+                        <p class="muted small prewrap">Supports the abstract-reported 84.4%, not reconciled agreement with the inconsistent Section 3.3 concentrations.</p>
+                    </div>
+
+                </details>
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1297,20 +1344,16 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
-
-            processes.push("biological process involved in interspecies interaction between organisms");
-
-
             var evidenceCount = 1;
 
             nodes.push({
                 id: intId,
-                label: "Complementary Electroactive Consortium Performance",
+                label: "Proposed Electroactive Consortium Complementarity",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1321,19 +1364,30 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lysinibacillus sphaericus A1",
+
+                "Bacillus cereus A2",
+
+                "Lactococcus lactis A4"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {
             var intId = "interaction:1";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
-
-            processes.push("biological process involved in interspecies interaction between organisms");
-
-
             var evidenceCount = 1;
 
             nodes.push({
@@ -1349,19 +1403,30 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lysinibacillus sphaericus A1",
+
+                "Bacillus cereus A2",
+
+                "Lactococcus lactis A4"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {
             var intId = "interaction:2";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
-
-            processes.push("biological process involved in interspecies interaction between organisms");
-
-
             var evidenceCount = 1;
 
             nodes.push({
@@ -1377,6 +1442,21 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lysinibacillus sphaericus A1",
+
+                "Bacillus cereus A2",
+
+                "Lactococcus lactis A4"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 

diff --git a/...euromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml b/...euromutilin_Degrading_Artificial_Consortium_5_Strain/2026-10-07T104208Z-codex-096092.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Pleuromutilin_Degrading_Artificial_Consortium_5_Strain.yaml
+  slug: Pleuromutilin_Degrading_Artificial_Consortium_5_Strain
+session:
+  id: 2026-10-07T104208Z-codex-096092
+  timestamp: '2026-10-07T10:42:08Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1711
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain positive 91.97% degradation without obligatory syntrophy.; Retain proposed
+    metabolic products/pathways with attribution and metabolomics limits.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml
diff --git a/...ory/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml b/...ory/records/Polaromonas_Vanadium_Reduction_Community/2026-10-07T104208Z-codex-da763c.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Polaromonas_Vanadium_Reduction_Community.yaml
+  slug: Polaromonas_Vanadium_Reduction_Community
+session:
+  id: 2026-10-07T104208Z-codex-da763c
+  timestamp: '2026-10-07T10:42:08Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1712
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Preserve positive enrichment reduction and qualify Polaromonas/MAG attribution.;
+    Preserve controlled enrichment precipitation without invented mineral or partner details.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261007-four-records-batch86.yaml