diff --git a/docs/communities/Lac_Pavin_Stratified_Lake_Community.html b/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
index 5ee20f071..1e63318ae 100644
--- a/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
+++ b/docs/communities/Lac_Pavin_Stratified_Lake_Community.html
@@ -601,7 +601,7 @@ <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 Lac Pavin Permanently Stratified Lake Community</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">
@@ -609,8 +609,8 @@ <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="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -618,14 +618,19 @@ <h2>Ecological Interactions</h2>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Oxygen-Driven Carbon-Fixation Niche Partitioning</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>Depth-Associated Carbon Metabolic Potential</h3>
                 </div>
-                <p class="prewrap interaction-description">Distinct C1 and CO2 fixation pathways are enriched in the oxic lake interface versus the anoxic zone and sediments, indicating oxygen-dependent niche partitioning among non-CPR bacteria and archaea.</p>
+                <p class="prewrap interaction-description">Genome-resolved metagenomics associates Calvin-cycle potential with shallower lake zones and Wood-Ljungdahl/reverse-TCA potential with anoxic water and sediments. PARTIAL - depth and oxygen co-vary with light and other geochemistry; this is genetic potential, not measured carbon-fixation flux or an isolated oxygen effect. The listed Archaea participant represents only the canonical archaeal component; most non-CPR bacterial lineages in this analysis are absent from the record roster.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    sediment methanogenic archaea
+
+                </p>
+
 
 
                 <p><strong>Metabolites:</strong>
@@ -651,21 +656,6 @@ <h3>Oxygen-Driven Carbon-Fixation Niche Partitioning</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Spatial Separation of Methane Oxidation and Production
-                        <p class="prewrap causal-description">Oxygen-driven compartmentalization separates methane oxidation in the water column from methane production by sediment methanogens.</p>
-                    </div>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> CPR and DPANN RuBisCO Distribution
-                        <p class="prewrap causal-description">The same lake-depth gradient structures RuBisCO-bearing CPR bacteria in the water column and DPANN archaea in the sediments.</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -677,7 +667,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/36694212/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36694212</a>
 
-                            - SUPPORT (IN_VIVO)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
                         <div class="snippet">"enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments"</div>
@@ -690,13 +680,18 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Spatial Separation of Methane Oxidation and Production</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>Spatial Separation Of Methane-Cycle Genetic Potential</h3>
                 </div>
-                <p class="prewrap interaction-description">Methane oxidation and its byproducts are largely spatially separated from methane production, indicating depth-resolved compartments for the two halves of the methane cycle.</p>
+                <p class="prewrap interaction-description">Methane-monooxygenase genetic potential is concentrated near the lake interface, with low-abundance occurrences in anoxic water, whereas mcr genes are mainly sediment-associated and also occur in the anoxic zone. This is largely separated potential, not strictly exclusive compartments or measured methane flux. Genome recovery is incomplete, so nondetection is not proof of absence. The listed sediment-methanogen aggregate does not resolve the missing bacterial methane oxidizers.</p>
+
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    sediment methanogenic archaea
+
+                </p>
 
 
 
@@ -734,7 +729,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/36694212/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36694212</a>
 
-                            - SUPPORT (IN_VIVO)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
                         <div class="snippet">"the oxidation of methane and its byproducts is largely spatially separated from methane production"</div>
@@ -747,14 +742,21 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>CPR and DPANN RuBisCO Distribution</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential</h3>
                 </div>
-                <p class="prewrap interaction-description">RuBisCO genes occur throughout the Lac Pavin water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in sediments, indicating depth-partitioned carbon-fixation potential in small symbiont lineages.</p>
+                <p class="prewrap interaction-description">CPR water-column genomes encode form II/III and III-c RuBisCO, and sediment DPANN genomes include form III-related enzymes. PARTIAL - these variants suggest CO2 incorporation through a free-nucleotide pathway, not complete Calvin-cycle autotrophy or measured CO2 fixation. CPR gene repertoires show weak depth differentiation overall; host-mediated selection is a hypothesis, not an established consequence of the carbon-fixation node.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    water-column Candidate Phyla Radiation (CPR) bacteria,
+
+                    sediment DPANN archaea
+
+                </p>
+
 
 
                 <p><strong>Metabolites:</strong>
@@ -791,13 +793,26 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/36694212/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36694212</a>
 
-                            - SUPPORT (IN_VIVO)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
                         <div class="snippet">"we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments"</div>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/36694212/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36694212</a>
+
+                            - PARTIAL (COMPUTATIONAL)
+                        </div>
+
+                        <div class="snippet">"Both form II/III and all form III RuBisCO likely function by incorporating carbon dioxide with a free nucleotide"</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -807,6 +822,25 @@ <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 depth-associated capacities are expressed and mediate carbon flux?
+                </h3>
+                <p class="prewrap">Drop both common-gradient arrows: co-varying genomic distributions do not establish carbon fixation as a cause of methane-cycle separation or CPR/DPANN RuBisCO distributions. Retain all three positive observations as potential. The 738 genomes cover only part of the community; nondetection and incomplete genomes cannot establish pathway absence. Oxygen, light and other geochemistry co-vary. CPR repertoires are weakly differentiated by depth, with host selection proposed. Canonical participants are incomplete: Archaea represents only the listed archaeal component, not all carbon-fixing bacteria or methane oxidizers. #1553 tracks roles and missing taxonomy/non-graph evidence. Main text/captions read, not raw genomes, separate supplements or figure pixels.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Depth-Associated Carbon Metabolic Potential</code>, <code>ecological_interactions#Spatial Separation Of Methane-Cycle Genetic Potential</code>, <code>ecological_interactions#CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1023,7 +1057,7 @@ <h2>Environmental Factors</h2>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1040,7 +1074,7 @@ <h2>Environmental Factors</h2>
 
             nodes.push({
                 id: intId,
-                label: "Oxygen-Driven Carbon-Fixation Niche Partitioning",
+                label: "Depth-Associated Carbon Metabolic Potential",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1051,11 +1085,22 @@ <h2>Environmental Factors</h2>
 
 
 
+            var participantKeys = [
+
+                "sediment methanogenic archaea"
+
+            ];
+            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 = [];
 
 
@@ -1072,7 +1117,7 @@ <h2>Environmental Factors</h2>
 
             nodes.push({
                 id: intId,
-                label: "Spatial Separation of Methane Oxidation and Production",
+                label: "Spatial Separation Of Methane-Cycle Genetic Potential",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1083,11 +1128,22 @@ <h2>Environmental Factors</h2>
 
 
 
+            var participantKeys = [
+
+                "sediment methanogenic archaea"
+
+            ];
+            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 = [];
 
 
@@ -1100,11 +1156,11 @@ <h2>Environmental Factors</h2>
             processes.push("carbon fixation");
 
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
-                label: "CPR and DPANN RuBisCO Distribution",
+                label: "CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1115,6 +1171,19 @@ <h2>Environmental Factors</h2>
 
 
 
+            var participantKeys = [
+
+                "water-column Candidate Phyla Radiation (CPR) bacteria",
+
+                "sediment DPANN archaea"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 
diff --git a/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html b/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
index e813eec2b..800e56615 100644
--- a/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
+++ b/docs/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.html
@@ -868,7 +868,7 @@ <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 Lake Washington Methane-Oxygen Methylotroph Community</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, 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 (cross-feeding).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -881,8 +881,8 @@ <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="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -893,8 +893,7 @@ <h2>Ecological Interactions</h2>
                     <h3>Methanotroph-Methylotroph Guild Coupling</h3>
                     <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">Methane-fed Lake Washington sediment communities consistently include both methane-oxidizing Methylococcaceae and non-methanotrophic methylotrophs in Methylophilaceae, supporting a coupled guild model for methane oxidation.
-</p>
+                <p class="prewrap interaction-description">Methane-fed sediment microcosms co-enrich Methylococcaceae and non-methanotrophic Methylophilaceae. PARTIAL - growth and prior stable-isotope studies support inferred methane-derived carbon coupling between guilds, but this experiment does not identify the transferred compound, directly trace methanol donation or establish reciprocal benefit. Family-level coupling is not a resolved strain pair or a universal partnership.</p>
 
 
                 <p><strong>Source Taxon:</strong> Methylococcaceae methanotrophs</p>
@@ -909,11 +908,7 @@ <h3>Methanotroph-Methylotroph Guild Coupling</h3>
 
                     methane
                     (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16183"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16183</a>),
-
-                    methanol
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17790"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17790</a>)
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16183</a>)
 
                 </p>
 
@@ -943,7 +938,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/25755930/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:25755930</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"likely involves communities composed of different functional guilds"</div>
@@ -956,27 +951,54 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/25755930/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:25755930</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"rather than a single type of microbe"</div>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/25755930/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:25755930</a>
+
+                            - PARTIAL (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"we do not have information regarding how a methanotroph can provide carbon to a community of non-methanotrophs"</div>
+
+                    </li>
+
                 </ul>
 
             </div>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Oxygen-Tension Specific Partnerships</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>Oxygen-Regime Dependent Guild Composition</h3>
                 </div>
-                <p class="prewrap interaction-description">Oxygen availability determines which methanotroph and methylotroph genera dominate methane-fed microcosms: Methylosarcina with Methylophilus at higher oxygen tension and Methylobacter with Methylotenera at lower oxygen tension.
-</p>
+                <p class="prewrap interaction-description">Under repeated methane feeding and daily gas resetting, initial oxygen regimes changed 16S relative guild composition after 10 and 16 weeks. Higher-oxygen treatments favored Methylosarcina/Methylophilus, whereas lower-oxygen treatments favored Methylobacter/Methylotenera, with intermediate mixtures and replicate exceptions. Low treatments became hypoxic before replenishment; these were not constant dissolved-oxygen levels. This establishes treatment-dependent composition, not a unique molecular partnership mechanism or absolute viable abundance. Listed participants are the reliable canonical aggregate/families/genera, not the incorrectly grounded Methylosarcina species.</p>
+
+
+
+
+                <p><strong>Participating Taxa:</strong>
 
+                    Lake Washington methane-consuming microbial community,
 
+                    Methylococcaceae methanotrophs,
 
+                    Methylophilaceae non-methanotrophic methylotrophs,
+
+                    Methylobacter,
+
+                    Methylotenera,
+
+                    Methylophilus
+
+                </p>
 
 
 
@@ -1000,14 +1022,7 @@ <h3>Oxygen-Tension Specific Partnerships</h3>
 
                     <div class="flow-item">
                         <span class="flow-arrow">→</span> Methanotroph-Methylotroph Guild Coupling
-                        <p class="prewrap causal-description">Oxygen tension selects which methanotroph and non-methanotrophic methylotroph genera persist as the methane-oxidizing guild partners.
-</p>
-                    </div>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Modeled Methylobacter-Methylomonas Exchange
-                        <p class="prewrap causal-description">Lake Washington methanotroph models tested carbon, oxygen, and nitrogen limitation, making oxygen availability a condition that modulates predicted metabolite exchange within the methane-cycling community.
-</p>
+                        <p class="prewrap causal-description">PARTIAL - changing the oxygen-feeding regime selects different relative abundances of methanotroph and methylotroph genera within the methane-fed guilds. This alters the observed guild composition, not a demonstrated specific carbon-transfer reaction or reciprocal benefit; the treatments also differ in time spent hypoxic.</p>
                     </div>
 
                 </div>
@@ -1049,18 +1064,16 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Modeled Methylobacter-Methylomonas Exchange</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
+                    <h3>Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer</h3>
                 </div>
-                <p class="prewrap interaction-description">Genome-scale metabolic modeling of Lake Washington methanotrophs predicts competitive and mutualistic interactions between Methylobacter and Methylomonas and condition-dependent extracellular metabolite exchanges.
-</p>
+                <p class="prewrap interaction-description">An OptCom genome-scale model of Methylomonas sp. LW13 and Methylobacter tundripaludum 21/22 reports conditional formaldehyde transfer from Methylomonas to Methylobacter. With imposed MB:ML growth ratios, uptake occurs in the synthetic 0.05:1 scenario but not the sediment 9.3:1 scenario. These ratios are constraints, not predicted abundances. PARTIAL - optimization, borrowed biomass/maintenance parameters and a formaldehyde-inhibition constraint shape this result; no transfer was experimentally validated here. Conflicting wording elsewhere in the source remains unresolved under #1554, so this is a qualified reported prediction, not verified flux.</p>
 
 
-                <p><strong>Source Taxon:</strong> Methylobacter</p>
+                <p><strong>Source Taxon:</strong> Methylomonas</p>
 
 
 
-                <p><strong>Target Taxon:</strong> Methylomonas</p>
+                <p><strong>Target Taxon:</strong> Methylobacter</p>
 
 
 
@@ -1106,10 +1119,10 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/32655999/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32655999</a>
 
-                            - SUPPORT (COMPUTATIONAL)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
-                        <div class="snippet">"competitive and mutualistic metabolic interactions among Methylobacter and Methylomonas"</div>
+                        <div class="snippet">"Methylobacter takes up some of the secreted formaldehyde from Methylomonas as a carbon source in addition to methane under the synthetic condition"</div>
 
                     </li>
 
@@ -1119,10 +1132,10 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/32655999/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32655999</a>
 
-                            - SUPPORT (COMPUTATIONAL)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
-                        <div class="snippet">"excretion of formaldehyde and carbon di-oxide in the community"</div>
+                        <div class="snippet">"the experimentally observed species abundance ratio was imposed on the growth rates"</div>
 
                     </li>
 
@@ -1205,6 +1218,25 @@ <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 compounds mediate guild coupling, and can the conditional two-methanotroph model result be reproduced?
+                </h3>
+                <p class="prewrap">Retain oxygen-regime selection of guild composition, but remove the cross-study arrow to the separate two-methanotroph model. The 2015 microcosms infer carbon coupling without identifying the mediator or reciprocal benefit; nitrogen-metabolism explanations are hypotheses. The 2020 model reports Methylomonas-to-Methylobacter formaldehyde transfer under imposed synthetic ratios, not the sediment ratio, and environmental CO2 export. Do not confuse the two methanotrophs with the methanotroph/methylotroph guild pair. Nutrient-rich dominance and formaldehyde-export statements conflict internally, tracked in #1554. Full main bodies were read, but no original figures, S4 workbook, SBML models or executable solutions were audited; the public supplemental endpoint failed HTTP500. #1553 tracks the Methylosarcina genus/species mismatch and other taxonomy/metadata. Omit that misgrounded species from explicit participants rather than silently validating it; the resulting connectivity warning is an unresolved roster defect, not grounds to invent an edge.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Methanotroph-Methylotroph Guild Coupling</code>, <code>ecological_interactions#Oxygen-Regime Dependent Guild Composition</code>, <code>ecological_interactions#Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1559,8 +1591,6 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             metabolites.push("methane");
 
-            metabolites.push("methanol");
-
 
             var processes = [];
 
@@ -1568,7 +1598,7 @@ <h4 style="color: var(--text);">Evidence</h4>
             processes.push("methane metabolic process");
 
 
-            var evidenceCount = 2;
+            var evidenceCount = 3;
 
             nodes.push({
                 id: intId,
@@ -1597,7 +1627,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1610,7 +1640,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             nodes.push({
                 id: intId,
-                label: "Oxygen-Tension Specific Partnerships",
+                label: "Oxygen-Regime Dependent Guild Composition",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1621,11 +1651,32 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Lake Washington methane-consuming microbial community",
+
+                "Methylococcaceae methanotrophs",
+
+                "Methylophilaceae non-methanotrophic methylotrophs",
+
+                "Methylobacter",
+
+                "Methylotenera",
+
+                "Methylophilus"
+
+            ];
+            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 = [];
 
 
@@ -1646,7 +1697,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             nodes.push({
                 id: intId,
-                label: "Modeled Methylobacter-Methylomonas Exchange",
+                label: "Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1655,14 +1706,14 @@ <h4 style="color: var(--text);">Evidence</h4>
             });
 
 
-            var srcKey = "Methylobacter";
+            var srcKey = "Methylomonas";
             if (taxonNodeIds[srcKey]) {
                 links.push({ source: taxonNodeIds[srcKey], target: intId });
             }
 
 
 
-            var tgtKey = "Methylomonas";
+            var tgtKey = "Methylobacter";
             if (taxonNodeIds[tgtKey]) {
                 links.push({ source: intId, target: taxonNodeIds[tgtKey] });
             }
diff --git a/docs/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.html b/docs/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.html
index 6fae7e0e4..21e8ebfc0 100644
--- a/docs/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.html
+++ b/docs/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.html
@@ -574,7 +574,7 @@ <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 Legume-Rhizobia Mars Simulant Symbiosis</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 (mutualism).</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">
@@ -582,8 +582,8 @@ <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="symbolSquare"
-                             data-color="#9f2ebb"></svg> Mutualism
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -592,10 +592,8 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Mars Simulant Root Nodulation</h3>
-                    <span class="interaction-type">MUTUALISM</span>
                 </div>
-                <p class="prewrap interaction-description">Sinorhizobium meliloti and Sinorhizobium medicae nodulate Medicago truncatula roots grown on MMS-1 and MMS-2 Mars soil simulants at average numbers mostly comparable to sand-grown controls.
-</p>
+                <p class="prewrap interaction-description">In separate Medicago truncatula A17 inoculations with S. meliloti 2011 or S. medicae WSM419, nodules formed on every tested MMS simulant after 14 days. Counts were mostly comparable to sand, with significant decreases for S. meliloti on MMS-1 Unsorted and S. medicae on MMS-1 Fine. These living-host greenhouse results do not establish fixed-nitrogen delivery or reciprocal benefit; the two bacterial species were alternative inoculants, not a coculture.</p>
 
 
 
@@ -625,16 +623,6 @@ <h3>Mars Simulant Root Nodulation</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Mars Simulant Nodule nifH Expression
-                        <p class="prewrap causal-description">Nodules formed on Mars soil simulants express the rhizobial nifH reporter, linking physical nodule development to nitrogen-fixation activity.</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -646,7 +634,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/34879082/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34879082</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - SUPPORT (IN_VIVO)
                         </div>
 
                         <div class="snippet">"root nodules could develop on M. truncatula roots when grown on these Mars soil simulants"</div>
@@ -659,36 +647,21 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Mars Simulant Nodule nifH Expression</h3>
-                    <span class="interaction-type">MUTUALISM</span>
+                    <h3>Mars Simulant Nodule nifH Promoter Activity</h3>
                 </div>
-                <p class="prewrap interaction-description">Sinorhizobium meliloti 1021 carrying a PnifH::uidA reporter expressed nifH inside Medicago truncatula root nodules on each tested Mars soil simulant, indicating nitrogenase-gene activity inside the nodules.</p>
+                <p class="prewrap interaction-description">S. meliloti 1021 carrying PnifH::uidA showed nodule-localized promoter activity by GUS staining at 14 days on all tested substrates. This reporter assay used S. meliloti only, not S. medicae. PARTIAL - promoter activity is evidence of nitrogenase-associated gene regulation, not direct N2-fixation flux, ammonia delivery to the host or a selective test that nodulation itself induces nifH.</p>
 
 
 
 
                 <p><strong>Participating Taxa:</strong>
 
-                    Sinorhizobium meliloti,
-
-                    Sinorhizobium medicae
+                    Sinorhizobium meliloti
 
                 </p>
 
 
 
-                <p><strong>Metabolites:</strong>
-
-                    dinitrogen
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17997"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17997</a>),
-
-                    ammonia
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16134"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16134</a>)
-
-                </p>
-
 
 
                 <p><strong>Biological Processes:</strong></p>
@@ -704,20 +677,23 @@ <h3>Mars Simulant Nodule nifH Expression</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
 
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Mars Simulant Legume-Rhizobia Support
-                        <p class="prewrap causal-description">Nitrogen-fixation gene expression in nodules shows that Mars simulant substrates can support the Medicago-rhizobia mutualism through the reporter-assayed nitrogen-fixation stage.</p>
-                    </div>
 
-                </div>
+                <h4>Evidence</h4>
+                <ul class="evidence-list">
 
+                    <li class="evidence-item">
+                        <div>
 
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/34879082/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34879082</a>
 
-                <h4>Evidence</h4>
-                <ul class="evidence-list">
+                            - PARTIAL (IN_VIVO)
+                        </div>
+
+                        <div class="snippet">"M. truncatula plants were inoculated with S. meliloti 1021 carrying the PnifH::uidA fusion"</div>
+
+                    </li>
 
                     <li class="evidence-item">
                         <div>
@@ -725,10 +701,10 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/34879082/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34879082</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VIVO)
                         </div>
 
-                        <div class="snippet">"detected nifH (a reporter gene for nitrogen fixation) expression inside these nodules"</div>
+                        <div class="snippet">"Our results show that the nifH promoter was active in the nodules"</div>
 
                     </li>
 
@@ -738,10 +714,9 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Mars Simulant Legume-Rhizobia Support</h3>
-                    <span class="interaction-type">MUTUALISM</span>
+                    <h3>Mars Simulant Dependent Plant Phenotypes</h3>
                 </div>
-                <p class="prewrap interaction-description">MMS-1 and MMS-2 Mars soil simulants support the Medicago truncatula symbiosis with Sinorhizobium meliloti and Sinorhizobium medicae; the study identified simulant chemistry, rather than grain size, as the stronger control on plant mass.</p>
+                <p class="prewrap interaction-description">At 14 days after separate rhizobial inoculations, Medicago plant mass was lower on MMS-1 variants than sand and comparable between MMS-2 Superfine and sand. Lateral-root numbers were reduced on every simulant relative to sand. HYPOTHESIZED - chemical composition may explain substrate differences, but individual chemical mediation was not selectively tested. These Earth-greenhouse, living-host endpoints do not show that nifH activity caused plant mass, prove mutual benefit or demonstrate growth under a Martian atmosphere or perchlorate exposure.</p>
 
 
 
@@ -762,15 +737,9 @@ <h3>Mars Simulant Legume-Rhizobia Support</h3>
                 <ul>
 
                     <li>
-                        nodulation
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009877"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009877</a>)
-                    </li>
-
-                    <li>
-                        nitrogen fixation
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0009399"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0009399</a>)
+                        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>
@@ -788,10 +757,10 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/34879082/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34879082</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - SUPPORT (IN_VIVO)
                         </div>
 
-                        <div class="snippet">"Mars simulant soils used in this study can support the symbiotic association between M. truncatula and its rhizobial partners"</div>
+                        <div class="snippet">"total mass of plants grown on MMS-2 Superfine soil was comparable to the total mass of plants grown on sand"</div>
 
                     </li>
 
@@ -801,10 +770,10 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/34879082/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34879082</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - SUPPORT (IN_VIVO)
                         </div>
 
-                        <div class="snippet">"the chemical composition of the simulants is more critical than their grain size for plant mass"</div>
+                        <div class="snippet">"average lateral root number was significantly reduced on plants grown on these soils if compared to plants grown on sand"</div>
 
                     </li>
 
@@ -817,6 +786,25 @@ <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>
+                    Does the observed nodule promoter activity yield fixed nitrogen and host benefit on each simulant?
+                </h3>
+                <p class="prewrap">Retain nodules, nifH promoter activity and substrate-dependent plant phenotypes; drop the anatomical-context and conclusion arrows rather than asserting causal mediation. No direct N2-fixation rate, ammonia delivery, plant nitrogen measurement or uninoculated host-benefit comparison establishes the proposed chain. The reporter used S. meliloti 1021 only; phenotype inoculations used S. meliloti 2011 or S. medicae WSM419 separately. The host is absent from the canonical roster (#1553), so listed bacteria are a partial participant set, not a complete microbial coculture. Earth greenhouse conditions and simulants without perchlorates are not Mars conditions. Chemistry is a proposed explanation, not an isolated additive perturbation. Main body and captions read, not original image pixels, separate supplements or raw measurements.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Mars Simulant Root Nodulation</code>, <code>ecological_interactions#Mars Simulant Nodule nifH Promoter Activity</code>, <code>ecological_interactions#Mars Simulant Dependent Plant Phenotypes</code></p>
+
+
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1218,7 +1206,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1259,26 +1247,20 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
-
-            metabolites.push("dinitrogen");
-
-            metabolites.push("ammonia");
-
-
             var processes = [];
 
 
             processes.push("nitrogen fixation");
 
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
-                label: "Mars Simulant Nodule nifH Expression",
+                label: "Mars Simulant Nodule nifH Promoter Activity",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1291,9 +1273,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var participantKeys = [
 
-                "Sinorhizobium meliloti",
-
-                "Sinorhizobium medicae"
+                "Sinorhizobium meliloti"
 
             ];
             participantKeys.forEach(function(key) {
@@ -1306,22 +1286,20 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "MUTUALISM";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
 
-            processes.push("nodulation");
-
-            processes.push("nitrogen fixation");
+            processes.push("biological process involved in interspecies interaction between organisms");
 
 
             var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
-                label: "Mars Simulant Legume-Rhizobia Support",
+                label: "Mars Simulant Dependent Plant Phenotypes",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
diff --git a/history/records/Lac_Pavin_Stratified_Lake_Community/2026-10-06T213201Z-codex-0a8ad0.yaml b/history/records/Lac_Pavin_Stratified_Lake_Community/2026-10-06T213201Z-codex-0a8ad0.yaml
new file mode 100644
index 000000000..6a592f25f
--- /dev/null
+++ b/history/records/Lac_Pavin_Stratified_Lake_Community/2026-10-06T213201Z-codex-0a8ad0.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
+  slug: Lac_Pavin_Stratified_Lake_Community
+session:
+  id: 2026-10-06T213201Z-codex-0a8ad0
+  timestamp: '2026-10-06T21:32:01Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1550
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Bound Lac Pavin depth-associated genetic potential and remove common-gradient arrows.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
diff --git a/history/records/Lake_Washington_Methane_Oxygen_Methylotroph_Community/2026-10-06T213201Z-codex-640dcb.yaml b/history/records/Lake_Washington_Methane_Oxygen_Methylotroph_Community/2026-10-06T213201Z-codex-640dcb.yaml
new file mode 100644
index 000000000..a1216001f
--- /dev/null
+++ b/history/records/Lake_Washington_Methane_Oxygen_Methylotroph_Community/2026-10-06T213201Z-codex-640dcb.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
+  slug: Lake_Washington_Methane_Oxygen_Methylotroph_Community
+session:
+  id: 2026-10-06T213201Z-codex-640dcb
+  timestamp: '2026-10-06T21:32:01Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1551
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Separate oxygen guild selection from the conditional Methylomonas-to-Methylobacter
+    model.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
diff --git a/history/records/Legume_Rhizobia_Mars_Simulant_Symbiosis/2026-10-06T213202Z-codex-75eca2.yaml b/history/records/Legume_Rhizobia_Mars_Simulant_Symbiosis/2026-10-06T213202Z-codex-75eca2.yaml
new file mode 100644
index 000000000..9281308b2
--- /dev/null
+++ b/history/records/Legume_Rhizobia_Mars_Simulant_Symbiosis/2026-10-06T213202Z-codex-75eca2.yaml
@@ -0,0 +1,24 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
+  slug: Legume_Rhizobia_Mars_Simulant_Symbiosis
+session:
+  id: 2026-10-06T213202Z-codex-75eca2
+  timestamp: '2026-10-06T21:32:02Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1552
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Separate living-host nodulation, nifH promoter activity and substrate phenotypes.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
diff --git a/kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml b/kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
index 45c09284d..d96fca1cd 100644
--- a/kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
+++ b/kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
@@ -87,86 +87,109 @@ taxonomy:
       sediment methanogens that vary on the centimeter scale
     explanation: Supports the diverse sediment methanogen community.
 ecological_interactions:
-- name: Oxygen-Driven Carbon-Fixation Niche Partitioning
-  description: Distinct C1 and CO2 fixation pathways are enriched in the oxic
-    lake interface versus the anoxic zone and sediments, indicating
-    oxygen-dependent niche partitioning among non-CPR bacteria and archaea.
-  interaction_type: NICHE_PARTITIONING
+- name: Depth-Associated Carbon Metabolic Potential
+  description: Genome-resolved metagenomics associates Calvin-cycle potential with shallower lake zones and Wood-Ljungdahl/reverse-TCA
+    potential with anoxic water and sediments. PARTIAL - depth and oxygen co-vary with light and other geochemistry;
+    this is genetic potential, not measured carbon-fixation flux or an isolated oxygen effect. The listed Archaea
+    participant represents only the canonical archaeal component; most non-CPR bacterial lineages in this analysis
+    are absent from the record roster.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: carbon dioxide
     term:
       id: CHEBI:16526
       label: carbon dioxide
+    notes: Genome-inferred metabolic context; no measured rate or inter-organism transfer.
   biological_processes:
   - preferred_term: carbon fixation
     term:
       id: GO:0015977
       label: carbon fixation
-  downstream:
-  - target: Spatial Separation of Methane Oxidation and Production
-    description: Oxygen-driven compartmentalization separates methane oxidation
-      in the water column from methane production by sediment methanogens.
-  - target: CPR and DPANN RuBisCO Distribution
-    description: The same lake-depth gradient structures RuBisCO-bearing CPR
-      bacteria in the water column and DPANN archaea in the sediments.
+    notes: Functional-potential annotation, not a direct activity assay.
   evidence:
   - reference: PMID:36694212
-    supports: SUPPORT
-    evidence_source: IN_VIVO
-    snippet: enrichment of distinct C1 and CO2 fixation pathways in the oxic
-      lake interface and anoxic zone/sediments
-    explanation: Supports the oxygen-driven niche partitioning of carbon fixation.
-- name: Spatial Separation of Methane Oxidation and Production
-  description: Methane oxidation and its byproducts are largely spatially
-    separated from methane production, indicating depth-resolved compartments
-    for the two halves of the methane cycle.
-  interaction_type: NICHE_PARTITIONING
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments
+    explanation: Supports depth-associated genome-derived potential; no expression, rate or selective causal perturbation
+      is measured.
+  participating_taxa:
+  - preferred_term: sediment methanogenic archaea
+    term:
+      id: NCBITaxon:2157
+      label: Archaea
+- name: Spatial Separation Of Methane-Cycle Genetic Potential
+  description: Methane-monooxygenase genetic potential is concentrated near the lake interface, with low-abundance
+    occurrences in anoxic water, whereas mcr genes are mainly sediment-associated and also occur in the anoxic zone.
+    This is largely separated potential, not strictly exclusive compartments or measured methane flux. Genome recovery
+    is incomplete, so nondetection is not proof of absence. The listed sediment-methanogen aggregate does not resolve
+    the missing bacterial methane oxidizers.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: methane
     term:
       id: CHEBI:16183
       label: methane
+    notes: Genome-inferred metabolic context; no measured rate or inter-organism transfer.
   biological_processes:
   - preferred_term: methanogenesis
     term:
       id: GO:0015948
       label: methanogenesis
+    notes: Functional-potential annotation, not a direct activity assay.
   evidence:
   - reference: PMID:36694212
-    supports: SUPPORT
-    evidence_source: IN_VIVO
-    snippet: the oxidation of methane and its byproducts is largely spatially
-      separated from methane production
-    explanation: Supports the spatial separation of methane oxidation and
-      production.
-- name: CPR and DPANN RuBisCO Distribution
-  description: RuBisCO genes occur throughout the Lac Pavin water column and
-    sediments, including form II/III and form III-related enzymes encoded by
-    CPR bacteria in the water column and DPANN archaea in sediments, indicating
-    depth-partitioned carbon-fixation potential in small symbiont lineages.
-  interaction_type: NICHE_PARTITIONING
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: the oxidation of methane and its byproducts is largely spatially separated from methane production
+    explanation: Supports depth-associated genome-derived potential; no expression, rate or selective causal perturbation
+      is measured.
+  participating_taxa:
+  - preferred_term: sediment methanogenic archaea
+    term:
+      id: NCBITaxon:2157
+      label: Archaea
+- name: CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
+  description: CPR water-column genomes encode form II/III and III-c RuBisCO, and sediment DPANN genomes include
+    form III-related enzymes. PARTIAL - these variants suggest CO2 incorporation through a free-nucleotide pathway,
+    not complete Calvin-cycle autotrophy or measured CO2 fixation. CPR gene repertoires show weak depth differentiation
+    overall; host-mediated selection is a hypothesis, not an established consequence of the carbon-fixation node.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: carbon dioxide
     term:
       id: CHEBI:16526
       label: carbon dioxide
+    notes: Genome-inferred metabolic context; no measured rate or inter-organism transfer.
   biological_processes:
   - preferred_term: carbon fixation
     term:
       id: GO:0015977
       label: carbon fixation
+    notes: Functional-potential annotation, not a direct activity assay.
   evidence:
   - reference: PMID:36694212
-    supports: SUPPORT
-    evidence_source: IN_VIVO
-    snippet: we detected evidence for RuBisCO throughout the water column and sediments, including
-      form II/III and form III-related enzymes encoded by CPR bacteria in the water column
-      and DPANN archaea in the sediments
-    explanation: Supports carbon-fixation potential across CPR bacteria in the
-      water column and DPANN archaea in Lac Pavin sediments.
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and
+      form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments
+    explanation: Supports depth-associated genome-derived potential; no expression, rate or selective causal perturbation
+      is measured.
+  - reference: PMID:36694212
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: Both form II/III and all form III RuBisCO likely function by incorporating carbon dioxide with a free
+      nucleotide
+    explanation: Identifies the proposed nucleotide-associated function, not a complete autotrophic pathway.
+  participating_taxa:
+  - preferred_term: water-column Candidate Phyla Radiation (CPR) bacteria
+    term:
+      id: NCBITaxon:1783273
+      label: Patescibacteria group
+  - preferred_term: sediment DPANN archaea
+    term:
+      id: NCBITaxon:1783276
+      label: Nanobdellati
 environmental_factors:
 - name: Oxygen gradient
   value: oxic interface to anoxic sediments
@@ -249,3 +272,27 @@ rare_earth_elements_present: []
 metal_relevance: NOT_APPLICABLE
 metal_notes: No metal or rare earth element processing role is curated for this
   stratified-lake community.
+discussions:
+- discussion_id: pavin_genomic_potential_and_depth_covariation
+  prompt: Which depth-associated capacities are expressed and mediate carbon flux?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Depth-Associated Carbon Metabolic Potential
+  - ecological_interactions#Spatial Separation Of Methane-Cycle Genetic Potential
+  - ecological_interactions#CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
+  rationale: 'Drop both common-gradient arrows: co-varying genomic distributions do not establish carbon fixation
+    as a cause of methane-cycle separation or CPR/DPANN RuBisCO distributions. Retain all three positive observations
+    as potential. The 738 genomes cover only part of the community; nondetection and incomplete genomes cannot establish
+    pathway absence. Oxygen, light and other geochemistry co-vary. CPR repertoires are weakly differentiated by
+    depth, with host selection proposed. Canonical participants are incomplete: Archaea represents only the listed
+    archaeal component, not all carbon-fixing bacteria or methane oxidizers. #1553 tracks roles and missing taxonomy/non-graph
+    evidence. Main text/captions read, not raw genomes, separate supplements or figure pixels.'
+  posed_by: codex
+  posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T21:31:59Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Bound Lac Pavin depth-associated genetic potential and remove common-gradient arrows. Issue #1550; reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml b/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
index 01f611bae..db6f63574 100644
--- a/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
+++ b/kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
@@ -279,10 +279,10 @@ taxonomy:
     explanation: Supports Methylophilus as a higher-oxygen methylotroph partner.
 ecological_interactions:
 - name: Methanotroph-Methylotroph Guild Coupling
-  description: >
-    Methane-fed Lake Washington sediment communities consistently include both
-    methane-oxidizing Methylococcaceae and non-methanotrophic methylotrophs in
-    Methylophilaceae, supporting a coupled guild model for methane oxidation.
+  description: Methane-fed sediment microcosms co-enrich Methylococcaceae and non-methanotrophic Methylophilaceae.
+    PARTIAL - growth and prior stable-isotope studies support inferred methane-derived carbon coupling between guilds,
+    but this experiment does not identify the transferred compound, directly trace methanol donation or establish
+    reciprocal benefit. Family-level coupling is not a resolved strain pair or a universal partnership.
   interaction_type: CROSS_FEEDING
   scope: PAIRWISE
   source_taxon:
@@ -300,11 +300,8 @@ ecological_interactions:
     term:
       id: CHEBI:16183
       label: methane
-  - preferred_term: methanol
-    term:
-      id: CHEBI:17790
-      label: methanol
-    notes: Likely one-carbon intermediate supporting methylotroph partners.
+    notes: Externally supplied methane supports the enrichment; methane is not established as the directly transferred
+      donor-to-recipient compound.
   biological_processes:
   - preferred_term: methane metabolic process
     term:
@@ -312,21 +309,30 @@ ecological_interactions:
       label: methane metabolic process
   evidence:
   - reference: PMID:25755930
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: likely involves communities composed of different functional guilds
-    explanation: Supports the guild-coupling interpretation for methane oxidation.
+    explanation: Supports the guild-level interpretation, not a resolved carbon mediator or reciprocal benefit in
+      this microcosm.
   - reference: PMID:25755930
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
     snippet: rather than a single type of microbe
-    explanation: Supports a community-level methane oxidation model instead of a single taxon model.
-- name: Oxygen-Tension Specific Partnerships
-  description: >
-    Oxygen availability determines which methanotroph and methylotroph genera
-    dominate methane-fed microcosms: Methylosarcina with Methylophilus at higher
-    oxygen tension and Methylobacter with Methylotenera at lower oxygen tension.
-  interaction_type: NICHE_PARTITIONING
+    explanation: Supports the guild-level interpretation, not a resolved carbon mediator or reciprocal benefit in
+      this microcosm.
+  - reference: PMID:25755930
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: we do not have information regarding how a methanotroph can provide carbon to a community of non-methanotrophs
+    explanation: Explicit limitation on the transfer mechanism; prior isotope studies are contextual evidence.
+- name: Oxygen-Regime Dependent Guild Composition
+  description: Under repeated methane feeding and daily gas resetting, initial oxygen regimes changed 16S relative
+    guild composition after 10 and 16 weeks. Higher-oxygen treatments favored Methylosarcina/Methylophilus, whereas
+    lower-oxygen treatments favored Methylobacter/Methylotenera, with intermediate mixtures and replicate exceptions.
+    Low treatments became hypoxic before replenishment; these were not constant dissolved-oxygen levels. This establishes
+    treatment-dependent composition, not a unique molecular partnership mechanism or absolute viable abundance.
+    Listed participants are the reliable canonical aggregate/families/genera, not the incorrectly grounded Methylosarcina
+    species.
   scope: COMMUNITY_LEVEL
   biological_processes:
   - preferred_term: methane metabolic process
@@ -335,55 +341,82 @@ ecological_interactions:
       label: methane metabolic process
   downstream:
   - target: Methanotroph-Methylotroph Guild Coupling
-    description: >
-      Oxygen tension selects which methanotroph and non-methanotrophic
-      methylotroph genera persist as the methane-oxidizing guild partners.
-  - target: Modeled Methylobacter-Methylomonas Exchange
-    description: >
-      Lake Washington methanotroph models tested carbon, oxygen, and nitrogen
-      limitation, making oxygen availability a condition that modulates
-      predicted metabolite exchange within the methane-cycling community.
+    description: PARTIAL - changing the oxygen-feeding regime selects different relative abundances of methanotroph
+      and methylotroph genera within the methane-fed guilds. This alters the observed guild composition, not a demonstrated
+      specific carbon-transfer reaction or reciprocal benefit; the treatments also differ in time spent hypoxic.
   evidence:
   - reference: PMID:25755930
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: different species persisted under different oxygen tensions
-    explanation: Supports oxygen-tension-dependent membership.
+    explanation: Supports controlled oxygen-regime effects on relative guild composition, with intermediate/replicate
+      variation rather than exclusive partner pairs.
   - reference: PMID:25755930
     supports: SUPPORT
     evidence_source: IN_VITRO
     snippet: oxygen availability is at least one major factor determining specific partnerships in methane oxidation
-    explanation: Supports oxygen availability as a driver of partnership composition.
-- name: Modeled Methylobacter-Methylomonas Exchange
-  description: >
-    Genome-scale metabolic modeling of Lake Washington methanotrophs predicts
-    competitive and mutualistic interactions between Methylobacter and
-    Methylomonas and condition-dependent extracellular metabolite exchanges.
-  interaction_type: NICHE_PARTITIONING
-  scope: PAIRWISE
-  source_taxon:
-    preferred_term: Methylobacter
+    explanation: Supports controlled oxygen-regime effects on relative guild composition, with intermediate/replicate
+      variation rather than exclusive partner pairs.
+  participating_taxa:
+  - preferred_term: Lake Washington methane-consuming microbial community
+    term:
+      id: NCBITaxon:131567
+      label: cellular organisms
+  - preferred_term: Methylococcaceae methanotrophs
+    term:
+      id: NCBITaxon:403
+      label: Methylococcaceae
+  - preferred_term: Methylophilaceae non-methanotrophic methylotrophs
+    term:
+      id: NCBITaxon:32011
+      label: Methylophilaceae
+  - preferred_term: Methylobacter
     term:
       id: NCBITaxon:429
       label: Methylobacter
-  target_taxon:
+  - preferred_term: Methylotenera
+    term:
+      id: NCBITaxon:359407
+      label: Methylotenera
+  - preferred_term: Methylophilus
+    term:
+      id: NCBITaxon:16
+      label: Methylophilus
+- name: Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
+  description: 'An OptCom genome-scale model of Methylomonas sp. LW13 and Methylobacter tundripaludum 21/22 reports
+    conditional formaldehyde transfer from Methylomonas to Methylobacter. With imposed MB:ML growth ratios, uptake
+    occurs in the synthetic 0.05:1 scenario but not the sediment 9.3:1 scenario. These ratios are constraints, not
+    predicted abundances. PARTIAL - optimization, borrowed biomass/maintenance parameters and a formaldehyde-inhibition
+    constraint shape this result; no transfer was experimentally validated here. Conflicting wording elsewhere in
+    the source remains unresolved under #1554, so this is a qualified reported prediction, not verified flux.'
+  scope: PAIRWISE
+  source_taxon:
     preferred_term: Methylomonas
     term:
       id: NCBITaxon:416
       label: Methylomonas
+  target_taxon:
+    preferred_term: Methylobacter
+    term:
+      id: NCBITaxon:429
+      label: Methylobacter
   metabolites:
   - preferred_term: methane
     term:
       id: CHEBI:16183
       label: methane
+    notes: Shared external substrate in the model, not donor-to-recipient transfer.
   - preferred_term: carbon dioxide
     term:
       id: CHEBI:16526
       label: carbon dioxide
+    notes: Modeled export to the environment by both taxa, not partner-directed exchange.
   - preferred_term: formaldehyde
     term:
       id: CHEBI:16842
       label: formaldehyde
+    notes: Conditional modeled Methylomonas-to-Methylobacter transfer; source wording discrepancies and lack of
+      experimental validation remain explicit.
   biological_processes:
   - preferred_term: methane metabolic process
     term:
@@ -391,15 +424,18 @@ ecological_interactions:
       label: methane metabolic process
   evidence:
   - reference: PMID:32655999
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: COMPUTATIONAL
-    snippet: competitive and mutualistic metabolic interactions among Methylobacter and Methylomonas
-    explanation: Supports modeled interaction types between the two methanotroph genera.
+    snippet: Methylobacter takes up some of the secreted formaldehyde from Methylomonas as a carbon source in addition
+      to methane under the synthetic condition
+    explanation: Results explicitly reports direction and synthetic-condition uptake; the main-text inconsistencies
+      remain unresolved.
   - reference: PMID:32655999
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: COMPUTATIONAL
-    snippet: excretion of formaldehyde and carbon di-oxide in the community
-    explanation: Supports predicted extracellular metabolite exchange (formaldehyde, CO2) in the community model.
+    snippet: the experimentally observed species abundance ratio was imposed on the growth rates
+    explanation: The sediment/synthetic abundance ratios constrain the optimization; they are not recovered model
+      predictions.
 environmental_factors:
 - name: Methane amendment
   value: methane supplied at the same concentration in each microcosm
@@ -623,3 +659,31 @@ metal_relevance: NOT_APPLICABLE
 metal_notes: >
   No metal or rare earth element processing role is curated for this
   methane-consuming freshwater sediment community.
+discussions:
+- discussion_id: washington_experiment_model_and_mediator_limits
+  prompt: Which compounds mediate guild coupling, and can the conditional two-methanotroph model result be reproduced?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Methanotroph-Methylotroph Guild Coupling
+  - ecological_interactions#Oxygen-Regime Dependent Guild Composition
+  - ecological_interactions#Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
+  rationale: 'Retain oxygen-regime selection of guild composition, but remove the cross-study arrow to the separate
+    two-methanotroph model. The 2015 microcosms infer carbon coupling without identifying the mediator or reciprocal
+    benefit; nitrogen-metabolism explanations are hypotheses. The 2020 model reports Methylomonas-to-Methylobacter
+    formaldehyde transfer under imposed synthetic ratios, not the sediment ratio, and environmental CO2 export.
+    Do not confuse the two methanotrophs with the methanotroph/methylotroph guild pair. Nutrient-rich dominance
+    and formaldehyde-export statements conflict internally, tracked in #1554. Full main bodies were read, but no
+    original figures, S4 workbook, SBML models or executable solutions were audited; the public supplemental endpoint
+    failed HTTP500. #1553 tracks the Methylosarcina genus/species mismatch and other taxonomy/metadata. Omit that
+    misgrounded species from explicit participants rather than silently validating it; the resulting connectivity
+    warning is an unresolved roster defect, not grounds to invent an edge.'
+  posed_by: codex
+  posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T21:32:00Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Separate oxygen guild selection from the conditional Methylomonas-to-Methylobacter model. Issue #1551;
+    reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml'
+  llm_assisted: true
diff --git a/kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml b/kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
index e3f45fa95..dd2412ad5 100644
--- a/kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
+++ b/kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
@@ -117,11 +117,11 @@ taxonomy:
     explanation: Names Sinorhizobium medicae as a rhizobial symbiont in the study.
 ecological_interactions:
 - name: Mars Simulant Root Nodulation
-  description: >
-    Sinorhizobium meliloti and Sinorhizobium medicae nodulate Medicago
-    truncatula roots grown on MMS-1 and MMS-2 Mars soil simulants at average
-    numbers mostly comparable to sand-grown controls.
-  interaction_type: MUTUALISM
+  description: In separate Medicago truncatula A17 inoculations with S. meliloti 2011 or S. medicae WSM419, nodules
+    formed on every tested MMS simulant after 14 days. Counts were mostly comparable to sand, with significant decreases
+    for S. meliloti on MMS-1 Unsorted and S. medicae on MMS-1 Fine. These living-host greenhouse results do not
+    establish fixed-nitrogen delivery or reciprocal benefit; the two bacterial species were alternative inoculants,
+    not a coculture.
   scope: COMMUNITY_LEVEL
   participating_taxa:
   - preferred_term: Sinorhizobium meliloti
@@ -137,63 +137,47 @@ ecological_interactions:
     term:
       id: GO:0009877
       label: nodulation
-  downstream:
-  - target: Mars Simulant Nodule nifH Expression
-    description: Nodules formed on Mars soil simulants express the rhizobial
-      nifH reporter, linking physical nodule development to nitrogen-fixation
-      activity.
   evidence:
   - reference: PMID:34879082
     supports: SUPPORT
-    evidence_source: IN_VITRO
+    evidence_source: IN_VIVO
     snippet: root nodules could develop on M. truncatula roots when grown on these Mars soil simulants
-    explanation: Supports functional nodulation of the host legume on Mars soil simulants.
-- name: Mars Simulant Nodule nifH Expression
-  description: Sinorhizobium meliloti 1021 carrying a PnifH::uidA reporter
-    expressed nifH inside Medicago truncatula root nodules on each tested Mars
-    soil simulant, indicating nitrogenase-gene activity inside the nodules.
-  interaction_type: MUTUALISM
+    explanation: Supports living-host nodulation on simulants; Results includes two reduced-count exceptions and
+      no direct nitrogen-fixation flux assay.
+- name: Mars Simulant Nodule nifH Promoter Activity
+  description: S. meliloti 1021 carrying PnifH::uidA showed nodule-localized promoter activity by GUS staining at
+    14 days on all tested substrates. This reporter assay used S. meliloti only, not S. medicae. PARTIAL - promoter
+    activity is evidence of nitrogenase-associated gene regulation, not direct N2-fixation flux, ammonia delivery
+    to the host or a selective test that nodulation itself induces nifH.
   scope: COMMUNITY_LEVEL
   participating_taxa:
   - preferred_term: Sinorhizobium meliloti
     term:
       id: NCBITaxon:382
       label: Sinorhizobium meliloti
-  - preferred_term: Sinorhizobium medicae
-    term:
-      id: NCBITaxon:110321
-      label: Sinorhizobium medicae
-  metabolites:
-  - preferred_term: dinitrogen
-    term:
-      id: CHEBI:17997
-      label: dinitrogen
-  - preferred_term: ammonia
-    term:
-      id: CHEBI:16134
-      label: ammonia
   biological_processes:
   - preferred_term: nitrogen fixation
     term:
       id: GO:0009399
       label: nitrogen fixation
-  downstream:
-  - target: Mars Simulant Legume-Rhizobia Support
-    description: Nitrogen-fixation gene expression in nodules shows that Mars
-      simulant substrates can support the Medicago-rhizobia mutualism through
-      the reporter-assayed nitrogen-fixation stage.
+    notes: Nitrogen-fixation pathway context for a promoter reporter, not directly measured fixation.
   evidence:
   - reference: PMID:34879082
-    supports: SUPPORT
-    evidence_source: IN_VITRO
-    snippet: detected nifH (a reporter gene for nitrogen fixation) expression inside these nodules
-    explanation: Supports active nitrogen fixation (nifH expression) inside the nodules.
-- name: Mars Simulant Legume-Rhizobia Support
-  description: MMS-1 and MMS-2 Mars soil simulants support the Medicago
-    truncatula symbiosis with Sinorhizobium meliloti and Sinorhizobium medicae;
-    the study identified simulant chemistry, rather than grain size, as the
-    stronger control on plant mass.
-  interaction_type: MUTUALISM
+    supports: PARTIAL
+    evidence_source: IN_VIVO
+    snippet: M. truncatula plants were inoculated with S. meliloti 1021 carrying the PnifH::uidA fusion
+    explanation: Identifies the reporter-specific bacterial participant and living-host context.
+  - reference: PMID:34879082
+    supports: PARTIAL
+    evidence_source: IN_VIVO
+    snippet: Our results show that the nifH promoter was active in the nodules
+    explanation: Supports promoter activity only; nitrogen fixation and ammonia transfer were not directly assayed.
+- name: Mars Simulant Dependent Plant Phenotypes
+  description: At 14 days after separate rhizobial inoculations, Medicago plant mass was lower on MMS-1 variants
+    than sand and comparable between MMS-2 Superfine and sand. Lateral-root numbers were reduced on every simulant
+    relative to sand. HYPOTHESIZED - chemical composition may explain substrate differences, but individual chemical
+    mediation was not selectively tested. These Earth-greenhouse, living-host endpoints do not show that nifH activity
+    caused plant mass, prove mutual benefit or demonstrate growth under a Martian atmosphere or perchlorate exposure.
   scope: COMMUNITY_LEVEL
   participating_taxa:
   - preferred_term: Sinorhizobium meliloti
@@ -205,29 +189,23 @@ ecological_interactions:
       id: NCBITaxon:110321
       label: Sinorhizobium medicae
   biological_processes:
-  - preferred_term: nodulation
-    term:
-      id: GO:0009877
-      label: nodulation
-  - preferred_term: nitrogen fixation
+  - preferred_term: biological process involved in interspecies interaction between organisms
     term:
-      id: GO:0009399
-      label: nitrogen fixation
+      id: GO:0044419
+      label: biological process involved in interspecies interaction between organisms
   evidence:
   - reference: PMID:34879082
     supports: SUPPORT
-    evidence_source: IN_VITRO
-    snippet: Mars simulant soils used in this study can support the symbiotic association
-      between M. truncatula and its rhizobial partners
-    explanation: Supports the paper's conclusion that the tested Mars simulants
-      can support the legume-rhizobia association.
+    evidence_source: IN_VIVO
+    snippet: total mass of plants grown on MMS-2 Superfine soil was comparable to the total mass of plants grown
+      on sand
+    explanation: Positive substrate comparison in living hosts, not nitrogen-fixation mediation.
   - reference: PMID:34879082
     supports: SUPPORT
-    evidence_source: IN_VITRO
-    snippet: the chemical composition of the simulants is more critical than their grain size
-      for plant mass
-    explanation: Links the supported symbiosis to the observed plant-mass
-      difference between MMS-2 and MMS-1 simulants.
+    evidence_source: IN_VIVO
+    snippet: average lateral root number was significantly reduced on plants grown on these soils if compared to
+      plants grown on sand
+    explanation: 'Results qualification of the abstract: all simulants reduced lateral roots relative to sand.'
 environmental_factors:
 - name: Mojave Mars Simulant grades (MMS-1) and MMS-2 substrate
   value: MMS-1 (Coarse/Fine/Unsorted/Superfine) and MMS-2
@@ -379,3 +357,28 @@ cultivation_setup:
     snippet: The different plant phenotypes (total plant mass, lateral root number, average nodule number)
       were recorded 14 days post-inoculation.
     explanation: Gives the post-inoculation duration.
+discussions:
+- discussion_id: mars_reporter_flux_and_host_benefit
+  prompt: Does the observed nodule promoter activity yield fixed nitrogen and host benefit on each simulant?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Mars Simulant Root Nodulation
+  - ecological_interactions#Mars Simulant Nodule nifH Promoter Activity
+  - ecological_interactions#Mars Simulant Dependent Plant Phenotypes
+  rationale: Retain nodules, nifH promoter activity and substrate-dependent plant phenotypes; drop the anatomical-context
+    and conclusion arrows rather than asserting causal mediation. No direct N2-fixation rate, ammonia delivery,
+    plant nitrogen measurement or uninoculated host-benefit comparison establishes the proposed chain. The reporter
+    used S. meliloti 1021 only; phenotype inoculations used S. meliloti 2011 or S. medicae WSM419 separately. The
+    host is absent from the canonical roster (#1553), so listed bacteria are a partial participant set, not a complete
+    microbial coculture. Earth greenhouse conditions and simulants without perchlorates are not Mars conditions.
+    Chemistry is a proposed explanation, not an isolated additive perturbation. Main body and captions read, not
+    original image pixels, separate supplements or raw measurements.
+  posed_by: codex
+  posed_date: '2026-10-06'
+curation_history:
+- timestamp: '2026-10-06T21:32:00Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: 'Separate living-host nodulation, nifH promoter activity and substrate phenotypes. Issue #1552; reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml'
+  llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index d8672024d..39636c5d3 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -5,6 +5,29 @@ source-based self-adversarial review. These records are not independent approval
 or proof that every graph is complete. The current inventory and summary distinguish
 `reviewed`, `pending` and `needs_research`.
 
+## Batch62: Lake Potential, Modeled Transfer And Host Reporters
+
+[Decisions](decisions/20261006-lakes-mars-batch62.yaml),
+[validation](validation-20261006-batch62.json) and
+[self-adversarial review](adversarial-review-20261006-batch62.yaml) account for
+nine retained nodes and six original arrows. Five common-driver, cross-study or
+anatomical/conclusion arrows are removed; oxygen-regime selection of Lake
+Washington guild composition remains explicitly bounded.
+
+Lac Pavin records genomic potential, not measured flux. Lake Washington's
+conditional model transfer runs from Methylomonas to Methylobacter; the imposed
+ratios are not predictions. Mars-simulant nodulation, S. meliloti-only nifH
+promoter activity and plant phenotypes remain distinct living-host results.
+
+All four fresh primary main bodies and embedded captions/table text were read,
+not original figures, separate supplements, raw data or executable models.
+The public supplemental download failed HTTP500; conflicting model wording stays
+open under #1554. Non-graph taxonomy and metadata #1553 remain unresolved,
+including the explicitly omitted misgrounded Methylosarcina species. All 920
+caches are unchanged and all 16 retained graph excerpts match fresh primary text.
+Repairs #1550-#1552 await protected-main merge. No new graph structure or paid
+Edison run is claimed; this is self-review, not independent approval.
+
 ## Batch61: LBNL Plant, Gut And Soil Models
 
 [Decisions](decisions/20261006-lbnl-batch61.yaml),
diff --git a/reports/causal_graph_review/adversarial-review-20261006-batch62.yaml b/reports/causal_graph_review/adversarial-review-20261006-batch62.yaml
new file mode 100644
index 000000000..32576beae
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261006-batch62.yaml
@@ -0,0 +1,221 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c56006a21ada62691625b6513f72f781cd5f8a18
+scope:
+- kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
+- kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
+- kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
+validation_report: reports/causal_graph_review/validation-20261006-batch62.json
+findings:
+- issue: 1550
+  severity: P2
+  status: addressed_in_this_change
+  finding: Lac Pavin genomic-potential overclaims and common-driver arrows.
+  disposition: Close only after protected-main merge.
+- issue: 1551
+  severity: P2
+  status: addressed_in_this_change
+  finding: Washington modeled donor direction and cross-study causal bridge.
+  disposition: Close only after protected-main merge.
+- issue: 1552
+  severity: P2
+  status: addressed_in_this_change
+  finding: Mars reporter participant/evidence context and unsupported flux/mediation claims.
+  disposition: Close only after protected-main merge.
+- issue: 1553
+  severity: P2
+  status: unresolved_non_graph
+  finding: Taxonomy and non-graph mechanism/environment metadata, including one exposed misgrounded-species
+    connectivity warning.
+  disposition: Keep OPEN after graph repair merge.
+- issue: 1554
+  severity: P2
+  status: unresolved_research
+  finding: Contradictory model-paper wording needs supplementary flux/model or author verification.
+  disposition: Keep OPEN after graph repair merge.
+adversarial_checks:
+- Read whole three records and all four fresh primary main bodies, Methods, Results, Discussion and embedded
+  captions/table text. Account for all9 original nodes and6 arrows. Original figure pixels, separate supplements,
+  raw data and executable models not audited; no invented supplementary-cell or reproduced-flux claims.
+- 'Lac Pavin: preserve depth-associated genomic potential, not measured flux or expression. Drop both
+  common-gradient arrows; oxygen co-varies with other geochemistry and is not isolated experimentally.
+  Retain low-abundance anoxic methane oxidizers and anoxic mcr occurrence, without absolute spatial exclusion
+  or absence inferred from incomplete genome recovery.'
+- 'Lac Pavin: distinguish CPR/DPANN II/III and III RuBisCO nucleotide-associated incorporation from complete
+  Calvin-cycle autotrophy. Weak CPR gene-repertoire differentiation and host-selection hypothesis remain
+  explicit. Canonical Archaea/CPR/DPANN participants are a partial roster, not a substitute for missing
+  non-CPR bacterial lineages.'
+- 'Washington: positive guild carbon coupling is retained as inferred family-level CROSS_FEEDING with
+  PARTIAL support. Remove untraced methanol assignment; supplied methane is external context, not direct
+  donor transfer. Prior isotope findings are not newly measured in the 2015 experiment, and reciprocal
+  benefit/mechanism is unresolved.'
+- 'Washington: retain oxygen-feeding-regime selection of relative guild composition, including hypoxic
+  periods, intermediate mixtures and replicate exceptions. Drop the bridge to a separate two-methanotroph
+  model; those partners are not the two different functional guilds. Relative 16S does not prove absolute
+  viable abundance.'
+- 'Washington model: correct reported formaldehyde direction to Methylomonas -> Methylobacter. Preserve
+  conditional synthetic uptake and lack of uptake under sediment constraints. MB:ML ratios0.05:1 and9.3:1
+  are imposed, not recovered predictions. CO2 is environmental export; borrowed parameters, optimization
+  and inhibition constraints bound interpretation.'
+- 'Washington source contradictions are not silently resolved: nutrient-rich dominance and formaldehyde-export
+  wording conflict. Keep reported conditional transfer with PARTIAL support and source uncertainty;1554
+  requests S4/SBML/solution or author clarification. Public supplemental HTTP500 and blocked web access
+  do not justify bypass or a claim that supplements were inspected.'
+- 'Mars: living-host IN_VIVO evidence, alternative S. meliloti2011/S. medicaeWSM419 inoculations and S.
+  meliloti1021-only reporter are distinct. Preserve nodule count exceptions, promoter activity and plant
+  mass/lateral-root observations. Remove N2/ammonia mediator assignment and both anatomical/conclusion
+  arrows; neither establishes flux, delivery, mutual benefit or causal induction.'
+- 'Mars: Results lateral-root reductions qualify the abstract. Earth greenhouse and simulants without
+  perchlorates are not Mars atmosphere experiments. Chemical mediation is hypothetical; host identity
+  remains missing from the canonical roster and1553 tracks non-graph repairs.'
+- Full biological diffs, participant registry and focused tests reviewed.457 other records and raw non-graph
+  blocks,920 caches unchanged. Canonical roster/scope census unchanged; one newly exposed Methylosarcina
+  connectivity warning is expected from omitting the misgrounded species, tracked1553. All36 prior warnings
+  remain, no structural defects and no auditor-rule changes.
+- Actual final-state schema, strict, terms, references, snippets, history, corpus audit, deterministic
+  render and regression outputs captured. Exact descriptions parsed across456 pages, not browser screenshots.
+  Post-commit docs-current is a separate publication gate.
+- Deduplication:848 all-state issue titles/bodies and35 scoped ignored/hidden local matches.497 and related301
+  issue bodies read, not every comment/PR/local file.1550-1552 addressed but OPEN until protected-main
+  merge;1553/1554 remain unresolved afterward. Exact-head self-review is COMMENT, never independent approval.
+  No new causal structure or paid Edison job.
+verification:
+  combined_regressions: 570 passed in 294.68s (0:04:54)
+  new_regression_tests: 9
+  schema_strict_terms_history: Passed with actual outputs/digests
+  references: CLI Total checks counts reported issues, not executed checks. MATCH does not establish scientific
+    entailment or full historical provenance. All920 caches unchanged;16 retained graph excerpts independently
+    match four fresh primary bodies. Non-graph1553, source discrepancy1554 and existing476/1091/1095 remain
+    unresolved.
+  snippet_counts_by_record:
+    kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml:
+      MATCH: 12
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml:
+      MATCH: 39
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml:
+      MATCH: 22
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+  primary_graph_snippet_proof:
+    primary_matched_graph_snippets: 16
+    primary_main_bodies: 4
+    paid_submissions: 0
+    new_nodes_or_arrows: 0
+    supplement_model_reproduction: false
+  network:
+    existing_findings_preserved: 36
+    added_findings:
+      Lake_Washington_Methane_Oxygen_Methylotroph_Community:
+      - type: DISCONNECTED
+        taxon: Methylosarcina
+        taxon_id: NCBITaxon:105972
+        taxon_data:
+          taxon_term:
+            preferred_term: Methylosarcina
+            term:
+              id: NCBITaxon:105972
+              label: Methylosarcina fibrata
+            gtdb_grounding_status: GROUNDED
+            gtdb_classification:
+              gtdb_id: GTDB:s__Methylosarcina_fibrata
+              gtdb_taxon: Methylosarcina fibrata
+              gtdb_lineage: d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina;s__Methylosarcina
+                fibrata
+              ncbi_source_id: NCBITaxon:105972
+              majority_fraction: 1.0
+              total_genomes: 1
+              is_reclassified: false
+              mapping_source: kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)
+            notes: Higher-oxygen methanotrophic genus in Lake Washington methane-fed microcosms.
+          functional_role:
+          - PRIMARY_DEGRADER
+          evidence:
+          - reference: PMID:25755930
+            supports: SUPPORT
+            evidence_source: IN_VITRO
+            snippet: species of the genera Methylosarcina and Methylophilus
+            explanation: Supports Methylosarcina as a higher-oxygen methanotrophic player.
+        message: Taxon 'Methylosarcina' has no interactions
+    removed_findings: {}
+    interpretation: One explicit connectivity warning for the misgrounded Methylosarcina species omitted
+      from participants. Tracked unresolved under1553; do not hide it with an invented interaction. No
+      auditor-rule change.
+  black_ruff_diff: passed
+  tested_file_sha256:
+    reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml: 105f4884b019cdcffca553d02ac889af1e788e0423bcffb2872051828dc82bfb
+    tests/test_causal_review_batch62.py: 934d6b969143b1b8d2095d86087f28f63122d4939905d33160b61979d1df85f4
+    tests/test_participating_taxa.py: 3f397a2f0e9c221dcd6a8b93929e5ac392c73d495549a0c8cc8ff310d5b6c9e2
+    kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml: 6b0d06a73fb3eaee96fe5cb7c9a8edac412e72a92de38813cbc89d640aed98b2
+    kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml: 8398eb23db4f653e903319d33c8c308f4f212b35b922c324cb5dae1f022b6144
+    kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml: b7a2b149c446b51c8db592cc9cca8c52c14f69f4f367940267c3bf69e08927b5
+    reports/causal_graph_review/README.md: 31fa6facb0c417e448bf30cb8d6f81f668ec6f7266538b923bc898cfda3fb667
+  unchanged_caches: 920
+  edison:
+    required_for_this_repair: false
+    provider_submissions: 0
+    credits_spent: 0
+    reason: Existing-node/arrow repairs only; no new causal structure.
+  post_commit_docs_current: Separate publication gate, not asserted before commit.
+participant_census:
+  measurements:
+    baseline:
+      records: 460
+      with_community_level: 391
+      mixed: 124
+      community_level_only: 267
+      taxa: 1507
+      credited_solely_by_the_rule: 1238
+    current:
+      records: 460
+      with_community_level: 391
+      mixed: 124
+      community_level_only: 267
+      taxa: 1507
+      credited_solely_by_the_rule: 1238
+  interpretation: Canonical roster/scope census unchanged. Explicit participants now exclude the misgrounded
+    Methylosarcina species, producing one tracked warning. This coarse census does not measure within-community
+    participant coverage or resolve missing taxa.
+corpus:
+  records: 460
+  nodes: 1454
+  edges: 645
+  review_status_counts:
+    needs_research: 21
+    pending: 239
+    reviewed: 200
+limitations:
+- All nine original nodes retained and six arrows reviewed; five unsupported common-driver, cross-study
+  or anatomical/conclusion arrows removed. Oxygen-regime selection of guild composition retained. No new
+  graph structure or paid Edison submission.
+- All four fresh open-access primary main bodies and embedded captions/table text read. Original figure
+  pixels, separate supplements, raw data and executable models not audited. Public Europe PMC supplemental
+  request failed HTTP500; no blocked access bypassed.
+- Lac Pavin metagenomic potential is not expression or flux; depth/geochemical covariation and weak CPR
+  repertoire differentiation remain explicit.
+- Lake Washington inferred guild carbon coupling and conditional two-methanotroph OptCom transfer are
+  distinct. Source wording contradictions remain unresolved under1554; no verified numerical flux/dominance
+  claim.
+- Mars Earth-greenhouse nodulation, S. meliloti-only promoter reporter and plant endpoints do not establish
+  N2-fixation flux, ammonia delivery, mutual benefit or Martian-atmosphere performance.
+- Canonical taxonomy and raw non-graph blocks are preserved, not recertified. Partial participant coverage
+  and the omitted misgrounded Methylosarcina entry remain explicit;1553 stays open.
+- All920 reference caches unchanged; retained graph excerpts match fresh primary text without certifying
+  all historical cache/non-graph provenance.
+- 848 all-state issue titles/bodies and35 scoped ignored/hidden local matches searched; matching497 and
+  related301 bodies read, not every comment/PR/local file. Self-adversarial review is not independent
+  approval.1550-1552 stay OPEN until protected-main merge;1553/1554 stay OPEN until resolved.
diff --git a/reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml b/reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
new file mode 100644
index 000000000..70618af25
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
@@ -0,0 +1,255 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: c56006a21ada62691625b6513f72f781cd5f8a18
+baseline_commit: c56006a21ada62691625b6513f72f781cd5f8a18
+base_tree: 5486948a93fce857123843f9b769924c6dad06b6
+pre_source_baseline_sha256: 7c3d8629d45259d45083a3f9af248336dbba038fd87731ef304089bae311cd99
+issues:
+- 1550
+- 1551
+- 1552
+unresolved_non_graph_issues:
+- 1553
+unresolved_research_issues:
+- 1554
+issue_deduplication:
+  all_state_issue_titles_and_bodies: 848
+  ignored_hidden_local_search: true
+  matching_local_files: 35
+  matching_issues:
+  - 497
+  related_issue_read: 301
+reference_cache_original_hashes:
+  references_cache/PMID_34879082.txt: b79dada3be43d46d0fc2316afd3cf7b9094adf49abb7249608d228679ab14388
+  references_cache/PMID_25755930.md: acf184095d1ed26e541794fd2f3ae593c9154e6b09b27463d3bc101693d8565d
+  references_cache/PMID_36694212.txt: c63cb1a398e61890fb1e7d90904d83140c09c253dc50ea1f02bb338f3c71020c
+  references_cache/PMID_36694212.md: 5f155286ea5bdea6834f3565c5640a5e1d6c6bb5641b20053a58f2e8f09711b4
+  references_cache/PMID_32655999.txt: d8dd6f8473511c34a53eeba347b1010bdd4a0be127a4d14c408efb6ca34cd252
+  references_cache/PMID_32655999.md: a02d836f20338a56780230046d87f3183de501bef0028885a90fb4c4527a9341
+  references_cache/PMID_25755930.txt: d90da07c8f3b8346f7632e004acff6998e44c166cdf5058bf2872946041fb1f7
+primary_artifacts:
+  /private/tmp/communitymech-batch62/pavin-primary.xml: 9b1084ef7a135f81d4d61e67c45e21dc539aa2b0c750bf7047d099d2e84d6f6a
+  /private/tmp/communitymech-batch62/pavin-primary.txt: 8d7016185a8c6d9081b442496f0db8036a8ea6954630df96cd154d521a71a098
+  /private/tmp/communitymech-batch62/washington-oxygen-primary.xml: 14ff89a3e79e08a81f1b63af1927aa830e14bc9651a531ce4675b98fdb812ace
+  /private/tmp/communitymech-batch62/washington-oxygen-primary.txt: 06005e6bcfa41dcb27d5af370a7508964e525ef3c8ef948dad3b317e7d9990e2
+  /private/tmp/communitymech-batch62/washington-model-primary.xml: afefa0854d91ded8c5114f8b38022be7720717dc31371515ee3742686e6e2542
+  /private/tmp/communitymech-batch62/washington-model-primary.txt: 242eeaaf2d6eedc69e46bee89d88f614ce114ab97fc65df06def4569d8bb476a
+  /private/tmp/communitymech-batch62/mars-primary.xml: 2ccdc268b0ecb532c4bb42ba51debbe3d7e5b368cd958c69a34664aa11754cf3
+  /private/tmp/communitymech-batch62/mars-primary.txt: c2ba2b091823cfffe9059cf6b4687284caa44773c109b29324bfa6b4858f19fd
+primary_urls:
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9875498/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4349146/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7333651/fullTextXML
+- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8654199/fullTextXML
+primary_graph_snippet_count: 16
+edison:
+  required_for_this_repair: false
+  provider_submissions: 0
+  credits_spent: 0
+  reason: Existing-node/arrow repairs only; no new causal structure.
+limitations:
+- All nine original nodes retained and six arrows reviewed; five unsupported common-driver, cross-study or anatomical/conclusion
+  arrows removed. Oxygen-regime selection of guild composition retained. No new graph structure or paid Edison submission.
+- All four fresh open-access primary main bodies and embedded captions/table text read. Original figure pixels,
+  separate supplements, raw data and executable models not audited. Public Europe PMC supplemental request failed
+  HTTP500; no blocked access bypassed.
+- Lac Pavin metagenomic potential is not expression or flux; depth/geochemical covariation and weak CPR repertoire
+  differentiation remain explicit.
+- Lake Washington inferred guild carbon coupling and conditional two-methanotroph OptCom transfer are distinct.
+  Source wording contradictions remain unresolved under1554; no verified numerical flux/dominance claim.
+- Mars Earth-greenhouse nodulation, S. meliloti-only promoter reporter and plant endpoints do not establish N2-fixation
+  flux, ammonia delivery, mutual benefit or Martian-atmosphere performance.
+- Canonical taxonomy and raw non-graph blocks are preserved, not recertified. Partial participant coverage and the
+  omitted misgrounded Methylosarcina entry remain explicit;1553 stays open.
+- All920 reference caches unchanged; retained graph excerpts match fresh primary text without certifying all historical
+  cache/non-graph provenance.
+- 848 all-state issue titles/bodies and35 scoped ignored/hidden local matches searched; matching497 and related301
+  bodies read, not every comment/PR/local file. Self-adversarial review is not independent approval.1550-1552 stay
+  OPEN until protected-main merge;1553/1554 stay OPEN until resolved.
+records:
+- path: kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml
+  id: CommunityMech:000226
+  original_sha256: 16a06577e166398170588e9c08f71ea1f753c65b31036c72158403255fb7afc2
+  record_sha256: 6b0d06a73fb3eaee96fe5cb7c9a8edac412e72a92de38813cbc89d640aed98b2
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
+  scope: Whole record and every original node/arrow.
+  summary: Bound Lac Pavin depth-associated genetic potential and remove common-gradient arrows.
+  renamed_nodes:
+    Oxygen-Driven Carbon-Fixation Niche Partitioning: Depth-Associated Carbon Metabolic Potential
+    Spatial Separation of Methane Oxidation and Production: Spatial Separation Of Methane-Cycle Genetic Potential
+    CPR and DPANN RuBisCO Distribution: CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
+  node_decisions:
+  - node: Depth-Associated Carbon Metabolic Potential
+    rationale: Retain depth-associated carbon-metabolism potential without isolated oxygen causality.
+  - node: Spatial Separation Of Methane-Cycle Genetic Potential
+    rationale: Retain spatially enriched methane-cycle genes, not measured or strictly separated flux.
+  - node: CPR And DPANN RuBisCO-Associated CO2 Incorporation Potential
+    rationale: Retain RuBisCO-associated nucleotide/CO2 potential without asserting Calvin-cycle autotrophy.
+  removed_node_decisions: []
+  edges_before:
+  - source: Oxygen-Driven Carbon-Fixation Niche Partitioning
+    target: Spatial Separation of Methane Oxidation and Production
+    description: Oxygen-driven compartmentalization separates methane oxidation in the water column from methane
+      production by sediment methanogens.
+  - source: Oxygen-Driven Carbon-Fixation Niche Partitioning
+    target: CPR and DPANN RuBisCO Distribution
+    description: The same lake-depth gradient structures RuBisCO-bearing CPR bacteria in the water column and DPANN
+      archaea in the sediments.
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions:
+  - source: Oxygen-Driven Carbon-Fixation Niche Partitioning
+    target: Spatial Separation of Methane Oxidation and Production
+    rationale: Shared depth/geochemistry is a common association, not carbon fixation causing this target.
+  - source: Oxygen-Driven Carbon-Fixation Niche Partitioning
+    target: CPR and DPANN RuBisCO Distribution
+    rationale: Shared depth/geochemistry is a common association, not carbon fixation causing this target.
+  references:
+  - PMID:36694212
+  issues:
+  - 1550
+  - 1553
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Lac_Pavin_Stratified_Lake_Community/2026-10-06T213201Z-codex-0a8ad0.yaml
+  source_review:
+    scope: Complete XML primary body, abstract, embedded table text and captions; not original figure pixels, separate
+      supplements, raw data or executable models.
+    urls:
+    - https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9875498/fullTextXML
+    all_retained_graph_snippets_primary_matched: true
+    cache_provenance_certified: false
+- path: kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml
+  id: CommunityMech:000261
+  original_sha256: 0ea08711fd6f9e156eb62b779d29cd853338f2f15eb02acb63f19a051a2b1b8d
+  record_sha256: 8398eb23db4f653e903319d33c8c308f4f212b35b922c324cb5dae1f022b6144
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
+  scope: Whole record and every original node/arrow.
+  summary: Separate oxygen guild selection from the conditional Methylomonas-to-Methylobacter model.
+  renamed_nodes:
+    Oxygen-Tension Specific Partnerships: Oxygen-Regime Dependent Guild Composition
+    Modeled Methylobacter-Methylomonas Exchange: Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
+  node_decisions:
+  - node: Methanotroph-Methylotroph Guild Coupling
+    rationale: Retain inferred family-level carbon coupling without identifying methanol or reciprocal benefit.
+  - node: Oxygen-Regime Dependent Guild Composition
+    rationale: Retain experimentally selected guild composition, not constant oxygen or exclusive partner pairs.
+  - node: Modeled Methylomonas-To-Methylobacter Formaldehyde Transfer
+    rationale: Correct the reported conditional model-transfer direction and distinguish imposed ratios from predictions.
+  removed_node_decisions: []
+  edges_before:
+  - source: Oxygen-Tension Specific Partnerships
+    target: Methanotroph-Methylotroph Guild Coupling
+    description: 'Oxygen tension selects which methanotroph and non-methanotrophic methylotroph genera persist as
+      the methane-oxidizing guild partners.
+
+      '
+  - source: Oxygen-Tension Specific Partnerships
+    target: Modeled Methylobacter-Methylomonas Exchange
+    description: 'Lake Washington methanotroph models tested carbon, oxygen, and nitrogen limitation, making oxygen
+      availability a condition that modulates predicted metabolite exchange within the methane-cycling community.
+
+      '
+  edges_after:
+  - source: Oxygen-Regime Dependent Guild Composition
+    target: Methanotroph-Methylotroph Guild Coupling
+    description: PARTIAL - changing the oxygen-feeding regime selects different relative abundances of methanotroph
+      and methylotroph genera within the methane-fed guilds. This alters the observed guild composition, not a demonstrated
+      specific carbon-transfer reaction or reciprocal benefit; the treatments also differ in time spent hypoxic.
+  retained_edge_decisions:
+  - source: Oxygen-Regime Dependent Guild Composition
+    target: Methanotroph-Methylotroph Guild Coupling
+    rationale: Controlled oxygen-feeding regimes select relative guild composition; mediator and reciprocal benefit
+      remain untested.
+  removed_edge_decisions:
+  - source: Oxygen-Tension Specific Partnerships
+    target: Modeled Methylobacter-Methylomonas Exchange
+    rationale: Separate experiments and different functional guilds do not form a demonstrated causal chain.
+  references:
+  - PMID:25755930
+  - PMID:32655999
+  issues:
+  - 1551
+  - 1553
+  - 1554
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Lake_Washington_Methane_Oxygen_Methylotroph_Community/2026-10-06T213201Z-codex-640dcb.yaml
+  source_review:
+    scope: Complete XML primary body, abstract, embedded table text and captions; not original figure pixels, separate
+      supplements, raw data or executable models.
+    urls:
+    - https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4349146/fullTextXML
+    - https://www.ebi.ac.uk/europepmc/webservices/rest/PMC7333651/fullTextXML
+    all_retained_graph_snippets_primary_matched: true
+    cache_provenance_certified: false
+- path: kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml
+  id: CommunityMech:000311
+  original_sha256: 278040a0740189cf4333706d146eb92674d1176e8eb891f3247a9debd63b0470
+  record_sha256: b7a2b149c446b51c8db592cc9cca8c52c14f69f4f367940267c3bf69e08927b5
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml
+  scope: Whole record and every original node/arrow.
+  summary: Separate living-host nodulation, nifH promoter activity and substrate phenotypes.
+  renamed_nodes:
+    Mars Simulant Nodule nifH Expression: Mars Simulant Nodule nifH Promoter Activity
+    Mars Simulant Legume-Rhizobia Support: Mars Simulant Dependent Plant Phenotypes
+  node_decisions:
+  - node: Mars Simulant Root Nodulation
+    rationale: Retain living-host nodulation with bacterial alternatives and the two count exceptions.
+  - node: Mars Simulant Nodule nifH Promoter Activity
+    rationale: Restrict the reporter to S. meliloti and promoter activity rather than nitrogen-fixation flux.
+  - node: Mars Simulant Dependent Plant Phenotypes
+    rationale: Retain measured mass/lateral-root responses without asserted chemical or nifH mediation.
+  removed_node_decisions: []
+  edges_before:
+  - source: Mars Simulant Root Nodulation
+    target: Mars Simulant Nodule nifH Expression
+    description: Nodules formed on Mars soil simulants express the rhizobial nifH reporter, linking physical nodule
+      development to nitrogen-fixation activity.
+  - source: Mars Simulant Nodule nifH Expression
+    target: Mars Simulant Legume-Rhizobia Support
+    description: Nitrogen-fixation gene expression in nodules shows that Mars simulant substrates can support the
+      Medicago-rhizobia mutualism through the reporter-assayed nitrogen-fixation stage.
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions:
+  - source: Mars Simulant Root Nodulation
+    target: Mars Simulant Nodule nifH Expression
+    rationale: Nodule compartment/reporter localization and the paper conclusion do not demonstrate causal mediation.
+  - source: Mars Simulant Nodule nifH Expression
+    target: Mars Simulant Legume-Rhizobia Support
+    rationale: Nodule compartment/reporter localization and the paper conclusion do not demonstrate causal mediation.
+  references:
+  - PMID:34879082
+  issues:
+  - 1552
+  - 1553
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Legume_Rhizobia_Mars_Simulant_Symbiosis/2026-10-06T213202Z-codex-75eca2.yaml
+  source_review:
+    scope: Complete XML primary body, abstract, embedded table text and captions; not original figure pixels, separate
+      supplements, raw data or executable models.
+    urls:
+    - https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8654199/fullTextXML
+    all_retained_graph_snippets_primary_matched: true
+    cache_provenance_certified: false
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index df00b04ab..60ea0c575 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -217,9 +217,9 @@ kb/communities/Kombucha_KMC_IMBG1_Fermentation_Community.yaml	CommunityMech:0001
 kb/communities/LBNL_Brachypodium_Drought_SynCom15.yaml	CommunityMech:000088	a7e41d95bc05106486f450153065da247369b854b757d68d451bea5e64e0b8e4	5	0	75.0	reports/causal_graph_review/decisions/20261006-lbnl-batch61.yaml	reviewed
 kb/communities/LBNL_Human_Gut_Interaction_SynCom.yaml	CommunityMech:000122	aa02533254dbc2a5f78544e1d3155b49f65ba8cffaa2f88b99d625ebf91cd816	3	1	90.0	reports/causal_graph_review/decisions/20261006-lbnl-batch61.yaml	reviewed
 kb/communities/LBNL_Switchgrass_Soil_SynCom16.yaml	CommunityMech:000087	9e12c5c9efe9440e6ae98386a71eaba63198a4eb71fca5a7bd25dcb1cc188562	3	0	75.0	reports/causal_graph_review/decisions/20261006-lbnl-batch61.yaml	reviewed
-kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml	CommunityMech:000226	16a06577e166398170588e9c08f71ea1f753c65b31036c72158403255fb7afc2	3	2	100.0		pending
-kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml	CommunityMech:000261	0ea08711fd6f9e156eb62b779d29cd853338f2f15eb02acb63f19a051a2b1b8d	3	2	100.0		pending
-kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml	CommunityMech:000311	278040a0740189cf4333706d146eb92674d1176e8eb891f3247a9debd63b0470	3	2	100.0		pending
+kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml	CommunityMech:000226	6b0d06a73fb3eaee96fe5cb7c9a8edac412e72a92de38813cbc89d640aed98b2	3	0	65.0	reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml	reviewed
+kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml	CommunityMech:000261	8398eb23db4f653e903319d33c8c308f4f212b35b922c324cb5dae1f022b6144	3	1	82.7	reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml	reviewed
+kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml	CommunityMech:000311	b7a2b149c446b51c8db592cc9cca8c52c14f69f4f367940267c3bf69e08927b5	3	0	65.0	reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml	reviewed
 kb/communities/Leptolyngbya_Pseudomonas_Mangrove_Coculture.yaml	CommunityMech:000452	7fc5189e7aa91a1a29fb3ea160153fbddfa33aa94e17763e67e1ffdab415284d	2	0	57.5		pending
 kb/communities/Lotus_LjSC3.yaml	CommunityMech:000040	81768be4db4e8af59540012d84a49fe1f27fd379beaaf6340c903b5a0c881227	3	2	100.0		pending
 kb/communities/Lunar_Martian_Simulant_PGPB_Lettuce_SynCom.yaml	CommunityMech:000304	7fed94bd84ab7db9e213c5f8f66c28823330da904a3f20ec5188000d8eea7185	3	2	100.0		pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 87209fe4b..ebce42831 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": 1454,
-  "edges": 650,
+  "edges": 645,
   "records_without_nodes": 8,
-  "records_without_edges": 156,
+  "records_without_edges": 158,
   "review_status_counts": {
     "needs_research": 21,
-    "pending": 242,
-    "reviewed": 197
+    "pending": 239,
+    "reviewed": 200
   },
   "structural_defects": [],
   "network_audit": [
@@ -820,6 +820,47 @@
       "message": "Taxon 'Pseudomonas fluorescens' has no interactions",
       "severity": "warning"
     },
+    {
+      "record": "Lake_Washington_Methane_Oxygen_Methylotroph_Community",
+      "type": "DISCONNECTED",
+      "taxon": "Methylosarcina",
+      "taxon_id": "NCBITaxon:105972",
+      "taxon_data": {
+        "taxon_term": {
+          "preferred_term": "Methylosarcina",
+          "term": {
+            "id": "NCBITaxon:105972",
+            "label": "Methylosarcina fibrata"
+          },
+          "gtdb_grounding_status": "GROUNDED",
+          "gtdb_classification": {
+            "gtdb_id": "GTDB:s__Methylosarcina_fibrata",
+            "gtdb_taxon": "Methylosarcina fibrata",
+            "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina;s__Methylosarcina fibrata",
+            "ncbi_source_id": "NCBITaxon:105972",
+            "majority_fraction": 1.0,
+            "total_genomes": 1,
+            "is_reclassified": false,
+            "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+          },
+          "notes": "Higher-oxygen methanotrophic genus in Lake Washington methane-fed microcosms."
+        },
+        "functional_role": [
+          "PRIMARY_DEGRADER"
+        ],
+        "evidence": [
+          {
+            "reference": "PMID:25755930",
+            "supports": "SUPPORT",
+            "evidence_source": "IN_VITRO",
+            "snippet": "species of the genera Methylosarcina and Methylophilus",
+            "explanation": "Supports Methylosarcina as a higher-oxygen methanotrophic player."
+          }
+        ]
+      },
+      "message": "Taxon 'Methylosarcina' has no interactions",
+      "severity": "warning"
+    },
     {
       "record": "Mangrove_Benzene_MFC_Bioanode_Consortium",
       "type": "DISCONNECTED",
diff --git a/reports/causal_graph_review/validation-20261006-batch62.json b/reports/causal_graph_review/validation-20261006-batch62.json
new file mode 100644
index 000000000..db0f666f2
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261006-batch62.json
@@ -0,0 +1,855 @@
+{
+  "base_commit": "c56006a21ada62691625b6513f72f781cd5f8a18",
+  "scope": [
+    "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml",
+    "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
+    "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml"
+  ],
+  "reference_validator_version": "0.1.7",
+  "results": [
+    {
+      "check": "Lac_Pavin_Stratified_Lake_Community-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Lac_Pavin_Stratified_Lake_Community-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-strict.tsv",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-strict.log",
+      "log_sha256": "5cb0938ea8f839022beeed667d2b501fbbbeb0056bc97c86d44f876b9f4fa250",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch62/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-batch62/Lac_Pavin_Stratified_Lake_Community-strict.tsv\n"
+    },
+    {
+      "check": "Lac_Pavin_Stratified_Lake_Community-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Lac_Pavin_Stratified_Lake_Community-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-references.log",
+      "log_sha256": "580f84eb5649c5c167d58fe8d64bc1393396ae72f058e4b8e8096423be5648eb",
+      "output_tail": "Validating kb/communities/Lac_Pavin_Stratified_Lake_Community.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/Lac_Pavin_Stratified_Lake_Community.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": "Lac_Pavin_Stratified_Lake_Community-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-snippets.log",
+      "log_sha256": "389f1d2b093a1648cf407d53853e429a283f80eed2628a1a14cf1f38649ca780",
+      "output_tail": "# 12 evidence snippets scanned across 1 files\n  MATCH      12\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": "Lac_Pavin_Stratified_Lake_Community-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-rank.log",
+      "log_sha256": "7a0d0de0ac0b54d95ecb374db6153369733648e15f54489cafb088814e1bf93f",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000226\",\n    \"name\": \"Lac Pavin Permanently Stratified Lake Community\",\n    \"score\": 65.0,\n    \"taxonomy\": 3,\n    \"connected_taxa\": 3,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 4,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Lac_Pavin_Stratified_Lake_Community-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Lac_Pavin_Stratified_Lake_Community/2026-10-06T213201Z-codex-0a8ad0.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lac_Pavin_Stratified_Lake_Community-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-strict.tsv",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-strict.log",
+      "log_sha256": "6c7661633fb24571d076b30eea4cde4018cd365b57d7634f3c7a0fcc983d0e5d",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch62/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-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-strict.tsv\n"
+    },
+    {
+      "check": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-references.log",
+      "log_sha256": "51abd5a435b75285d0f41d359abb181326401dab2e8a86023ffbc154fa17a4c5",
+      "output_tail": "Validating kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.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/Lake_Washington_Methane_Oxygen_Methylotroph_Community.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": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-snippets.log",
+      "log_sha256": "099668d6a47e477533c63ee93f8ac643e975f7ba771cac4e617c7d6488845349",
+      "output_tail": "# 39 evidence snippets scanned across 1 files\n  MATCH      39\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": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-rank.log",
+      "log_sha256": "61e6af98e2a389aff2670c9481a3883aff2e1134df71dc67f47a3d0e5ba858c1",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000261\",\n    \"name\": \"Lake Washington Methane-Oxygen Methylotroph Community\",\n    \"score\": 82.7,\n    \"taxonomy\": 8,\n    \"connected_taxa\": 7,\n    \"disconnected_taxa\": 1,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 1,\n    \"interaction_evidence\": 7,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_downstream\",\n      \"interaction_type\",\n      \"disconnected_taxa\"\n    ],\n    \"path\": \"kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Lake_Washington_Methane_Oxygen_Methylotroph_Community-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Lake_Washington_Methane_Oxygen_Methylotroph_Community/2026-10-06T213201Z-codex-640dcb.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Lake_Washington_Methane_Oxygen_Methylotroph_Community-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Legume_Rhizobia_Mars_Simulant_Symbiosis-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Legume_Rhizobia_Mars_Simulant_Symbiosis-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-strict.tsv",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-strict.log",
+      "log_sha256": "f597b2b685ecba6470bbaec1f8de0db01c17b434d2a23ef7d1050fd72efc48a4",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch62/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-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-strict.tsv\n"
+    },
+    {
+      "check": "Legume_Rhizobia_Mars_Simulant_Symbiosis-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Legume_Rhizobia_Mars_Simulant_Symbiosis-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-references.log",
+      "log_sha256": "aaf0633ba03e9b69ef35ba6aec96bdb9615106d88f40b591b47ba12f07e1aef6",
+      "output_tail": "Validating kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.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/Legume_Rhizobia_Mars_Simulant_Symbiosis.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": "Legume_Rhizobia_Mars_Simulant_Symbiosis-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-snippets.log",
+      "log_sha256": "96a23c88588d68e990af5d62f9c27df12879566b4125e7703a275c3bfa7adcd7",
+      "output_tail": "# 22 evidence snippets scanned across 1 files\n  MATCH      22\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": "Legume_Rhizobia_Mars_Simulant_Symbiosis-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-rank.log",
+      "log_sha256": "1faaf89bd424d46e04f93d1e3c1589fca1e15beef6f67630c9c47905ae24ce02",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000311\",\n    \"name\": \"Legume-Rhizobia Mars Simulant Symbiosis\",\n    \"score\": 65.0,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 5,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Legume_Rhizobia_Mars_Simulant_Symbiosis-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Legume_Rhizobia_Mars_Simulant_Symbiosis/2026-10-06T213202Z-codex-75eca2.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/Legume_Rhizobia_Mars_Simulant_Symbiosis-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-batch62/inventory.log",
+      "log_sha256": "63599fbafaea770eb702848d2edd92ea4a06fa48663347391343254129577f8f",
+      "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\": 1454,\n  \"edges\": 645,\n  \"records_without_nodes\": 8,\n  \"records_without_edges\": 158,\n  \"review_status_counts\": {\n    \"needs_research\": 21,\n    \"pending\": 239,\n    \"reviewed\": 200\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-batch62/network.log",
+      "log_sha256": "96b4ce3ebd766ca4c94c7bf99af48351f69170f4f40e2bab5d53e8674fff4f14",
+      "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-batch62/rank-all.log",
+      "log_sha256": "126e75c473da0dfafefc461a94358dcd3e413ace0233cc4ec790b31accc8140c",
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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 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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-batch62/render.log",
+      "log_sha256": "0f4d4a14e824c8bc1cfbc16f59d29aa0c402b362bc3987ff54ba60cd215eb89a",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 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/private/tmp/communitymech-causal-batch62/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 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Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch62/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch62/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch62/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-batch62/render-repeat.log",
+      "log_sha256": "0f4d4a14e824c8bc1cfbc16f59d29aa0c402b362bc3987ff54ba60cd215eb89a",
+      "output_tail": "sm.html\n  \u2713 Synechococcus_Bacillus_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch62/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch62/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch62/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch62/docs/index.html\n"
+    },
+    {
+      "check": "connectivity-survey",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import json,pathlib,runpy\nfn=runpy.run_path('tests/test_community_level_connectivity_credit.py')['_survey']\nresult={}\nfor name,root in [('baseline',pathlib.Path('/private/tmp/communitymech-causal-batch61')),('current',pathlib.Path.cwd())]:\n paths=sorted(p for r in ['kb/communities','data/isolates'] for p in (root/r).rglob('*.yaml'))\n assert len(paths)==460\n fn.__globals__['record_files']=lambda:paths\n result[name]=fn()\nprint(json.dumps(result))\n"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/connectivity-survey.log",
+      "log_sha256": "2dcbda64d4b5530059ac8ad2c76a801bffcf051d557341927f6c204fb4d3f7e5",
+      "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 391, \"mixed\": 124, \"community_level_only\": 267, \"taxa\": 1507, \"credited_solely_by_the_rule\": 1238}, \"current\": {\"records\": 460, \"with_community_level\": 391, \"mixed\": 124, \"community_level_only\": 267, \"taxa\": 1507, \"credited_solely_by_the_rule\": 1238}}\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_batch32.py",
+        "tests/test_causal_review_batch33.py",
+        "tests/test_causal_review_batch34.py",
+        "tests/test_causal_review_batch35.py",
+        "tests/test_causal_review_batch36.py",
+        "tests/test_causal_review_batch37.py",
+        "tests/test_causal_review_batch38.py",
+        "tests/test_causal_review_batch39.py",
+        "tests/test_causal_review_batch40.py",
+        "tests/test_causal_review_batch41.py",
+        "tests/test_causal_review_batch42.py",
+        "tests/test_causal_review_batch43.py",
+        "tests/test_causal_review_batch44.py",
+        "tests/test_causal_review_batch45.py",
+        "tests/test_causal_review_batch46.py",
+        "tests/test_causal_review_batch47.py",
+        "tests/test_causal_review_batch48.py",
+        "tests/test_causal_review_batch49.py",
+        "tests/test_causal_review_batch5.py",
+        "tests/test_causal_review_batch50.py",
+        "tests/test_causal_review_batch51.py",
+        "tests/test_causal_review_batch52.py",
+        "tests/test_causal_review_batch53.py",
+        "tests/test_causal_review_batch54.py",
+        "tests/test_causal_review_batch55.py",
+        "tests/test_causal_review_batch56.py",
+        "tests/test_causal_review_batch57.py",
+        "tests/test_causal_review_batch58.py",
+        "tests/test_causal_review_batch59.py",
+        "tests/test_causal_review_batch6.py",
+        "tests/test_causal_review_batch60.py",
+        "tests/test_causal_review_batch61.py",
+        "tests/test_causal_review_batch62.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-batch62/regressions.log",
+      "log_sha256": "90477bfff6a90543a5d4256640a3c2148818fd50b511b5070cfd6e0ae248d6f2",
+      "output_tail": "........................................................................ [ 12%]\n........................................................................ [ 25%]\n........................................................................ [ 37%]\n........................................................................ [ 50%]\n........................................................................ [ 63%]\n........................................................................ [ 75%]\n........................................................................ [ 88%]\n..................................................................       [100%]\n570 passed in 294.68s (0:04:54)\n"
+    },
+    {
+      "check": "black",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/3Q_kifQtLB624D5bBWGIf/bin/black",
+        "--check",
+        "tests/test_causal_review_batch62.py",
+        "tests/test_participating_taxa.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/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_batch62.py",
+        "tests/test_participating_taxa.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/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-batch62/diff-check.log",
+      "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+      "output_tail": ""
+    },
+    {
+      "check": "primary-graph-proof",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-c",
+        "import hashlib,json,pathlib,yaml\nP=pathlib.Path\nledger=yaml.safe_load(P('reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml').read_text())\nmanifest=json.loads(P('/private/tmp/communitymech-batch62/primary-manifest.json').read_text())\nprimary={v['pmid']:''.join(P(v['extracted_body']).read_text().split()) for v in manifest.values()}\nfor path,digest in ledger['primary_artifacts'].items():\n assert hashlib.sha256(P(path).read_bytes()).hexdigest()==digest\ncount=0\nfor row in ledger['records']:\n doc=yaml.safe_load(P(row['path']).read_text())\n for node in doc['ecological_interactions']:\n  for ev in node['evidence']:\n   assert ''.join(ev['snippet'].split()) in primary[ev['reference'].split(':')[1]]\n   count+=1\nassert count==ledger['primary_graph_snippet_count']==16\nassert ledger['edison']['provider_submissions']==ledger['edison']['credits_spent']==0\nprint(json.dumps({'primary_matched_graph_snippets':count,'primary_main_bodies':4,'paid_submissions':0,'new_nodes_or_arrows':0,'supplement_model_reproduction':False}))\n"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch62/primary-graph-proof.log",
+      "log_sha256": "6364fc8681e57b34fdf7fe310651778d69ded9d8b8c4bbf5977b30441d632739",
+      "output_tail": "{\"primary_matched_graph_snippets\": 16, \"primary_main_bodies\": 4, \"paid_submissions\": 0, \"new_nodes_or_arrows\": 0, \"supplement_model_reproduction\": false}\n"
+    }
+  ],
+  "limitations": [
+    "All nine original nodes retained and six arrows reviewed; five unsupported common-driver, cross-study or anatomical/conclusion arrows removed. Oxygen-regime selection of guild composition retained. No new graph structure or paid Edison submission.",
+    "All four fresh open-access primary main bodies and embedded captions/table text read. Original figure pixels, separate supplements, raw data and executable models not audited. Public Europe PMC supplemental request failed HTTP500; no blocked access bypassed.",
+    "Lac Pavin metagenomic potential is not expression or flux; depth/geochemical covariation and weak CPR repertoire differentiation remain explicit.",
+    "Lake Washington inferred guild carbon coupling and conditional two-methanotroph OptCom transfer are distinct. Source wording contradictions remain unresolved under1554; no verified numerical flux/dominance claim.",
+    "Mars Earth-greenhouse nodulation, S. meliloti-only promoter reporter and plant endpoints do not establish N2-fixation flux, ammonia delivery, mutual benefit or Martian-atmosphere performance.",
+    "Canonical taxonomy and raw non-graph blocks are preserved, not recertified. Partial participant coverage and the omitted misgrounded Methylosarcina entry remain explicit;1553 stays open.",
+    "All920 reference caches unchanged; retained graph excerpts match fresh primary text without certifying all historical cache/non-graph provenance.",
+    "848 all-state issue titles/bodies and35 scoped ignored/hidden local matches searched; matching497 and related301 bodies read, not every comment/PR/local file. Self-adversarial review is not independent approval.1550-1552 stay OPEN until protected-main merge;1553/1554 stay OPEN until resolved.",
+    "Exact HTML-description parser and repeat-render checks, not browser screenshots. Post-commit docs-current is separate."
+  ],
+  "snippet_counts_by_record": {
+    "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml": {
+      "MATCH": 12,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml": {
+      "MATCH": 39,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml": {
+      "MATCH": 22,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    }
+  },
+  "unchanged_raw_blocks": 45,
+  "unchanged_record_files": 457,
+  "unchanged_cache_files": 920,
+  "edison": {
+    "required_for_this_repair": false,
+    "provider_submissions": 0,
+    "credits_spent": 0,
+    "reason": "Existing-node/arrow repairs only; no new causal structure."
+  },
+  "primary_artifacts": {
+    "/private/tmp/communitymech-batch62/pavin-primary.xml": "9b1084ef7a135f81d4d61e67c45e21dc539aa2b0c750bf7047d099d2e84d6f6a",
+    "/private/tmp/communitymech-batch62/pavin-primary.txt": "8d7016185a8c6d9081b442496f0db8036a8ea6954630df96cd154d521a71a098",
+    "/private/tmp/communitymech-batch62/washington-oxygen-primary.xml": "14ff89a3e79e08a81f1b63af1927aa830e14bc9651a531ce4675b98fdb812ace",
+    "/private/tmp/communitymech-batch62/washington-oxygen-primary.txt": "06005e6bcfa41dcb27d5af370a7508964e525ef3c8ef948dad3b317e7d9990e2",
+    "/private/tmp/communitymech-batch62/washington-model-primary.xml": "afefa0854d91ded8c5114f8b38022be7720717dc31371515ee3742686e6e2542",
+    "/private/tmp/communitymech-batch62/washington-model-primary.txt": "242eeaaf2d6eedc69e46bee89d88f614ce114ab97fc65df06def4569d8bb476a",
+    "/private/tmp/communitymech-batch62/mars-primary.xml": "2ccdc268b0ecb532c4bb42ba51debbe3d7e5b368cd958c69a34664aa11754cf3",
+    "/private/tmp/communitymech-batch62/mars-primary.txt": "c2ba2b091823cfffe9059cf6b4687284caa44773c109b29324bfa6b4858f19fd"
+  },
+  "network_delta": {
+    "existing_findings_preserved": 36,
+    "added_findings": {
+      "Lake_Washington_Methane_Oxygen_Methylotroph_Community": [
+        {
+          "type": "DISCONNECTED",
+          "taxon": "Methylosarcina",
+          "taxon_id": "NCBITaxon:105972",
+          "taxon_data": {
+            "taxon_term": {
+              "preferred_term": "Methylosarcina",
+              "term": {
+                "id": "NCBITaxon:105972",
+                "label": "Methylosarcina fibrata"
+              },
+              "gtdb_grounding_status": "GROUNDED",
+              "gtdb_classification": {
+                "gtdb_id": "GTDB:s__Methylosarcina_fibrata",
+                "gtdb_taxon": "Methylosarcina fibrata",
+                "gtdb_lineage": "d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylosarcina;s__Methylosarcina fibrata",
+                "ncbi_source_id": "NCBITaxon:105972",
+                "majority_fraction": 1.0,
+                "total_genomes": 1,
+                "is_reclassified": false,
+                "mapping_source": "kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)"
+              },
+              "notes": "Higher-oxygen methanotrophic genus in Lake Washington methane-fed microcosms."
+            },
+            "functional_role": [
+              "PRIMARY_DEGRADER"
+            ],
+            "evidence": [
+              {
+                "reference": "PMID:25755930",
+                "supports": "SUPPORT",
+                "evidence_source": "IN_VITRO",
+                "snippet": "species of the genera Methylosarcina and Methylophilus",
+                "explanation": "Supports Methylosarcina as a higher-oxygen methanotrophic player."
+              }
+            ]
+          },
+          "message": "Taxon 'Methylosarcina' has no interactions"
+        }
+      ]
+    },
+    "removed_findings": {},
+    "interpretation": "One explicit connectivity warning for the misgrounded Methylosarcina species omitted from participants. Tracked unresolved under1553; do not hide it with an invented interaction. No auditor-rule change."
+  },
+  "render_determinism": true,
+  "published_description_coverage": {
+    "pages": 456,
+    "nodes": 1440,
+    "arrows": 637
+  },
+  "participant_census": {
+    "measurements": {
+      "baseline": {
+        "records": 460,
+        "with_community_level": 391,
+        "mixed": 124,
+        "community_level_only": 267,
+        "taxa": 1507,
+        "credited_solely_by_the_rule": 1238
+      },
+      "current": {
+        "records": 460,
+        "with_community_level": 391,
+        "mixed": 124,
+        "community_level_only": 267,
+        "taxa": 1507,
+        "credited_solely_by_the_rule": 1238
+      }
+    },
+    "interpretation": "Canonical roster/scope census unchanged. Explicit participants now exclude the misgrounded Methylosarcina species, producing one tracked warning. This coarse census does not measure within-community participant coverage or resolve missing taxa."
+  },
+  "network_warning_count": 37,
+  "corpus": {
+    "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+    "records": 460,
+    "nodes": 1454,
+    "edges": 645,
+    "records_without_nodes": 8,
+    "records_without_edges": 158,
+    "review_status_counts": {
+      "needs_research": 21,
+      "pending": 239,
+      "reviewed": 200
+    },
+    "structural_defects": []
+  },
+  "tested_file_sha256": {
+    "reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml": "105f4884b019cdcffca553d02ac889af1e788e0423bcffb2872051828dc82bfb",
+    "tests/test_causal_review_batch62.py": "934d6b969143b1b8d2095d86087f28f63122d4939905d33160b61979d1df85f4",
+    "tests/test_participating_taxa.py": "3f397a2f0e9c221dcd6a8b93929e5ac392c73d495549a0c8cc8ff310d5b6c9e2",
+    "kb/communities/Lac_Pavin_Stratified_Lake_Community.yaml": "6b0d06a73fb3eaee96fe5cb7c9a8edac412e72a92de38813cbc89d640aed98b2",
+    "kb/communities/Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml": "8398eb23db4f653e903319d33c8c308f4f212b35b922c324cb5dae1f022b6144",
+    "kb/communities/Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml": "b7a2b149c446b51c8db592cc9cca8c52c14f69f4f367940267c3bf69e08927b5",
+    "reports/causal_graph_review/README.md": "31fa6facb0c417e448bf30cb8d6f81f668ec6f7266538b923bc898cfda3fb667"
+  },
+  "status": "verified_lakes_mars_graph_review",
+  "pre_research_baseline": {
+    "base_commit": "c56006a21ada62691625b6513f72f781cd5f8a18",
+    "base_tree": "5486948a93fce857123843f9b769924c6dad06b6",
+    "research_worktree": "/private/tmp/communitymech-causal-batch61",
+    "checks": [
+      {
+        "name": "rank",
+        "command": [
+          "just",
+          "rank-causal-graphs"
+        ],
+        "exit_code": 0,
+        "expected_exit_code": 0,
+        "log": "/private/tmp/communitymech-batch62/baseline-rank.log",
+        "sha256": "2a06dea519ee81b927da13d07efdf87eedda73a453f63be6228db440e79f3e8d",
+        "output_tail": "/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"
+      },
+      {
+        "name": "just-network",
+        "command": [
+          "just",
+          "audit-network-json"
+        ],
+        "exit_code": 2,
+        "expected_exit_code": 2,
+        "log": "/private/tmp/communitymech-batch62/baseline-just-network.log",
+        "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff",
+        "output_tail": "uv run communitymech audit-network --json\nerror: Failed to spawn: `communitymech`\n  Caused by: No such file or directory (os error 2)\nerror: recipe `audit-network-json` failed on line 574 with exit code 2\n"
+      },
+      {
+        "name": "network",
+        "command": [
+          "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+          "-m",
+          "communitymech.cli",
+          "audit-network",
+          "--json"
+        ],
+        "exit_code": 1,
+        "expected_exit_code": 1,
+        "log": "/private/tmp/communitymech-batch62/baseline-network.log",
+        "sha256": "0955d3471f474fec8dcceb846ff932573d11c9833de73b2b2822241553762186",
+        "output_tail": "            \"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"
+      },
+      {
+        "name": "downstream",
+        "command": [
+          "rg",
+          "--no-ignore",
+          "--hidden",
+          "-n",
+          "downstream:",
+          "kb/communities",
+          "data/isolates",
+          "--glob",
+          "*.yaml"
+        ],
+        "exit_code": 0,
+        "expected_exit_code": 0,
+        "log": "/private/tmp/communitymech-batch62/baseline-downstream.log",
+        "sha256": "089b811ad7d0da3e32929d8e49df2cc5654a5648b78cdadd5352d7d9c6addd3b",
+        "output_tail": "kb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:80:  downstream:\nkb/communities/Cable_Bacteria_Photosynthetic_Biofilm_Sediment.yaml:117:  downstream:\nkb/communities/Dangl_SynComm_35.yaml:244:  downstream:\nkb/communities/Dangl_SynComm_35.yaml:322:  downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:160:  downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:195:  downstream:\nkb/communities/Sichuan_Shai_Vinegar_Yeast_Flavor_SynCom.yaml:233:  downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:311:  downstream:\nkb/communities/Chlamydomonas_Bacterial_H2_Consortium.yaml:365:  downstream:\nkb/communities/SO3_BS3_Lithium_Battery_Bioleaching_Consortium.yaml:141:  downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:76:  downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:95:  downstream:\nkb/communities/Phylogenetically_Diverse_Denitrifying_SynCom.yaml:122:  downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:120:  downstream:\nkb/communities/Synechococcus_Bacillus_SPC.yaml:152:  downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:104:  downstream:\nkb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml:127:  downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:157:  downstream:\nkb/communities/Methylotuvimicrobium_Synechococcus_Gas_Feedstock_Coculture.yaml:203:  downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:247:  downstream:\nkb/communities/Clostridium_Carboxidivorans_Kluyveri_CO_Chain_Elongation_Coculture.yaml:344:  downstream:\nkb/communities/Emiliania_Phaeobacter_Dynamic_Interaction.yaml:143:  downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:123:  downstream:\nkb/communities/Pepper_Phytophthora_SynCom5.yaml:146:  downstream:\nkb/communities/PMI_Variovorax_Thermotolerance_Collection.yaml:330:  downstream:\n"
+      }
+    ],
+    "baseline_sha256": "7c3d8629d45259d45083a3f9af248336dbba038fd87731ef304089bae311cd99"
+  },
+  "reference_validator_caveat": "CLI Total checks counts reported issues, not executed checks. MATCH does not establish scientific entailment or full historical provenance. All920 caches unchanged;16 retained graph excerpts independently match four fresh primary bodies. Non-graph1553, source discrepancy1554 and existing476/1091/1095 remain unresolved."
+}
diff --git a/tests/test_causal_review_batch62.py b/tests/test_causal_review_batch62.py
new file mode 100644
index 000000000..4442f12f8
--- /dev/null
+++ b/tests/test_causal_review_batch62.py
@@ -0,0 +1,151 @@
+"""Separate genomic potential, modeled transfer and measured host endpoints."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261006-lakes-mars-batch62.yaml"
+P = "Lac_Pavin_Stratified_Lake_Community"
+W = "Lake_Washington_Methane_Oxygen_Methylotroph_Community"
+M = "Legume_Rhizobia_Mars_Simulant_Symbiosis"
+
+
+def records():
+    ledger = yaml.safe_load(LEDGER.read_text())
+    rows = {Path(r["path"]).stem: r for r in ledger["records"]}
+    docs = {name: yaml.safe_load((ROOT / r["path"]).read_text()) for name, r in rows.items()}
+    return ledger, rows, docs
+
+
+def test_pavin_depth_potential_is_not_flux_or_common_driver_causality():
+    _, rows, docs = records()
+    carbon, methane, rubisco = docs[P]["ecological_interactions"]
+    assert "genetic potential, not measured carbon-fixation flux" in carbon["description"]
+    assert "not strictly exclusive compartments" in methane["description"]
+    assert "nondetection is not proof of absence" in methane["description"]
+    assert "free-nucleotide pathway" in rubisco["description"]
+    assert "weak depth differentiation" in rubisco["description"]
+    assert len(rows[P]["removed_edge_decisions"]) == 2
+    for node in [carbon, methane, rubisco]:
+        assert "downstream" not in node and "interaction_type" not in node
+        assert all(e["evidence_source"] == "COMPUTATIONAL" for e in node["evidence"])
+        assert all(e["supports"] == "PARTIAL" for e in node["evidence"])
+
+
+def test_pavin_participants_remain_partial_canonical_components():
+    _, _, docs = records()
+    carbon, methane, rubisco = docs[P]["ecological_interactions"]
+    assert [t["term"]["id"] for t in carbon["participating_taxa"]] == ["NCBITaxon:2157"]
+    assert methane["participating_taxa"] == carbon["participating_taxa"]
+    assert [t["term"]["id"] for t in rubisco["participating_taxa"]] == [
+        "NCBITaxon:1783273",
+        "NCBITaxon:1783276",
+    ]
+    assert "absent from the record roster" in carbon["description"]
+    assert "missing bacterial methane oxidizers" in methane["description"]
+
+
+def test_washington_guild_coupling_does_not_identify_methanol():
+    _, _, docs = records()
+    guild = docs[W]["ecological_interactions"][0]
+    assert guild["interaction_type"] == "CROSS_FEEDING"
+    assert [m["term"]["id"] for m in guild["metabolites"]] == ["CHEBI:16183"]
+    assert "not established as the directly transferred" in guild["metabolites"][0]["notes"]
+    assert "prior stable-isotope studies" in guild["description"]
+    assert "does not identify the transferred compound" in guild["description"]
+    assert all(e["supports"] == "PARTIAL" for e in guild["evidence"])
+
+
+def test_washington_oxygen_selection_survives_without_cross_study_bridge():
+    _, rows, docs = records()
+    guild, oxygen, model = docs[W]["ecological_interactions"]
+    assert len(oxygen["downstream"]) == 1
+    assert oxygen["downstream"][0]["target"] == guild["name"]
+    assert oxygen["downstream"][0]["description"].startswith("PARTIAL -")
+    assert "not constant dissolved-oxygen" in oxygen["description"]
+    assert "intermediate mixtures and replicate exceptions" in oxygen["description"]
+    assert all(t["term"]["id"] != "NCBITaxon:105972" for t in oxygen["participating_taxa"])
+    assert "downstream" not in model
+    assert len(rows[W]["retained_edge_decisions"]) == 1
+    assert len(rows[W]["removed_edge_decisions"]) == 1
+
+
+def test_washington_conditional_model_transfer_has_correct_direction_and_limits():
+    ledger, _, docs = records()
+    model = docs[W]["ecological_interactions"][2]
+    assert model["source_taxon"]["term"]["id"] == "NCBITaxon:416"
+    assert model["target_taxon"]["term"]["id"] == "NCBITaxon:429"
+    assert "interaction_type" not in model
+    assert "synthetic 0.05:1 scenario but not the sediment 9.3:1" in model["description"]
+    assert "constraints, not predicted abundances" in model["description"]
+    assert "no transfer was experimentally validated here" in model["description"]
+    assert "#1554" in model["description"]
+    assert all(e["evidence_source"] == "COMPUTATIONAL" for e in model["evidence"])
+    assert all(e["supports"] == "PARTIAL" for e in model["evidence"])
+    assert "not partner-directed exchange" in model["metabolites"][1]["notes"]
+    assert ledger["unresolved_research_issues"] == [1554]
+
+
+def test_mars_living_host_reporter_is_not_nitrogen_fixation_flux():
+    _, rows, docs = records()
+    nodules, reporter, phenotype = docs[M]["ecological_interactions"]
+    assert "alternative inoculants, not a coculture" in nodules["description"]
+    assert "MMS-1 Unsorted" in nodules["description"] and "MMS-1 Fine" in nodules["description"]
+    assert [t["term"]["id"] for t in reporter["participating_taxa"]] == ["NCBITaxon:382"]
+    assert "metabolites" not in reporter
+    assert "not direct N2-fixation flux" in reporter["description"]
+    for node in [nodules, reporter, phenotype]:
+        assert "interaction_type" not in node and "downstream" not in node
+        assert all(e["evidence_source"] == "IN_VIVO" for e in node["evidence"])
+    assert len(rows[M]["removed_edge_decisions"]) == 2
+
+
+def test_mars_plant_endpoints_do_not_assert_chemical_or_reporter_mediation():
+    _, _, docs = records()
+    phenotype = docs[M]["ecological_interactions"][2]
+    assert "Lateral-root numbers were reduced on every simulant" in phenotype["description"]
+    assert "HYPOTHESIZED" in phenotype["description"]
+    assert "individual chemical mediation was not selectively tested" in phenotype["description"]
+    assert "Martian atmosphere or perchlorate exposure" in phenotype["description"]
+    assert phenotype["biological_processes"][0]["term"]["id"] == "GO:0044419"
+
+
+def test_batch62_caches_and_canonical_participants_are_not_silently_rewritten():
+    ledger, _, docs = records()
+    for path, digest in ledger["reference_cache_original_hashes"].items():
+        assert hashlib.sha256((ROOT / path).read_bytes()).hexdigest() == digest
+    for doc in docs.values():
+        canonical = {
+            t["taxon_term"]["preferred_term"]: t["taxon_term"]["term"] for t in doc["taxonomy"]
+        }
+        for node in doc["ecological_interactions"]:
+            taxa = node.get("participating_taxa", []) + [
+                node[k] for k in ["source_taxon", "target_taxon"] if k in node
+            ]
+            for taxon in taxa:
+                assert canonical[taxon["preferred_term"]] == taxon["term"]
+        assert "#1553" in doc["discussions"][-1]["rationale"]
+    assert ledger["unresolved_non_graph_issues"] == [1553]
+    assert ledger["edison"]["provider_submissions"] == 0
+    assert ledger["primary_graph_snippet_count"] == 16
+
+
+def test_batch62_all_nodes_arrows_anchors_and_histories_are_recorded():
+    ledger, rows, docs = records()
+    assert ledger["independent_approval"] is False
+    assert ledger["issues"] == [1550, 1551, 1552]
+    assert sum(len(r["node_decisions"]) for r in rows.values()) == 9
+    assert sum(len(r["edges_before"]) for r in rows.values()) == 6
+    assert sum(len(r["edges_after"]) for r in rows.values()) == 1
+    assert sum(len(r["removed_edge_decisions"]) for r in rows.values()) == 5
+    for name, row in rows.items():
+        doc = docs[name]
+        assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+        assert doc["curation_history"][-1]["llm_assisted"] is True
+        assert len(row["history_files"]) == 1 and row["status"] == "reviewed"
+        names = {n["name"] for n in doc["ecological_interactions"]}
+        assert {d["node"] for d in row["node_decisions"]} == names
+        assert {a.split("#", 1)[1] for a in doc["discussions"][-1]["attaches_to"]} == names
+        assert doc["discussions"][-1]["status"] == "OPEN"
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index 037a624d7..aad046222 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -310,6 +310,8 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
     "LBNL_Brachypodium_Drought_SynCom15.yaml",
     "LBNL_Human_Gut_Interaction_SynCom.yaml",
     "LBNL_Switchgrass_Soil_SynCom16.yaml",
+    "Lac_Pavin_Stratified_Lake_Community.yaml",
+    "Lake_Washington_Methane_Oxygen_Methylotroph_Community.yaml",
     "Legume_Rhizobia_Mars_Simulant_Symbiosis.yaml",
     "Lunar_Simulant_Phosphate_Solubilizing_Bacteria_Nicotiana.yaml",
     "MSC1_Dominant_Core.yaml",