diff --git a/docs/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.html b/docs/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.html
index d6332d033..b975255dd 100644
--- a/docs/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.html
+++ b/docs/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.html
@@ -726,7 +726,7 @@ <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 Space Habitat Seven-Member Stress-Tolerance SynCom</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 (competition).</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">
@@ -734,8 +734,8 @@ <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="symbolTimes"
-                             data-color="#a91919"></svg> Competition
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -744,9 +744,8 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation</h3>
-                    <span class="interaction-type">COMPETITION</span>
                 </div>
-                <p class="prewrap interaction-description">After 24 h co-cultivation, culturable B. subtilis CFU were significantly lower in the whole seven-member consortium than in B. subtilis single culture under the tested recovery conditions. The source discusses possible antimicrobial competition but does not resolve which partner, metabolite or mechanism drove this effect.</p>
+                <p class="prewrap interaction-description">After co-cultivation, culturable B. subtilis CFU were significantly lower in the whole seven-member laboratory consortium than in single culture under the tested recovery conditions. This is decreased cultivability, not definitive loss of viability or demonstrated reciprocal negative effects on a pair of partners. The source discusses possible competition, but does not identify a causal partner or confirmed metabolite activity.</p>
 
 
 
@@ -781,6 +780,19 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42577390/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42577390</a>
+
+                            - SUPPORT (IN_VITRO)
+                        </div>
+
+                        <div class="snippet">"reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability"</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -826,7 +838,7 @@ <h2>Associated Datasets</h2>
         </section>
 
         <section id="discussions">
-            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
 
             <div class="discussion">
                 <h3>
@@ -841,6 +853,56 @@ <h3>
 
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Does the reported colony-recovery decrease establish reciprocal competition or loss of viability?
+                </h3>
+                <p class="prewrap">The measured decrease is retained. COMPETITION requires both partners to be negatively affected; this result does not establish that relationship. Candidate genomic functions are not confirmed activity. This metadata review adds no stress-survival procedures or new partner mechanisms.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation</code></p>
+
+
+
+                <details class="evidence-list">
+                    <summary class="muted small">2 evidence item(s)</summary>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/42577390/" rel="nofollow noreferrer">PMID:42577390</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability</p>
+                        <p class="muted small prewrap">The source explicitly limits interpretation of reduced colony recovery.</p>
+                    </div>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/42577390/" rel="nofollow noreferrer">PMID:42577390</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">these findings reflect genomic potential rather than confirmed metabolite activity.</p>
+                        <p class="muted small prewrap">Bounds the source interpretation; no metabolite-mediated causal edge is established.</p>
+                    </div>
+
+                </details>
+
+
             </div>
 
         </section>
@@ -1184,12 +1246,12 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "COMPETITION";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
 
-            var evidenceCount = 1;
+            var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
diff --git a/docs/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.html b/docs/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.html
index 04067e949..69e0f20e4 100644
--- a/docs/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.html
+++ b/docs/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.html
@@ -592,7 +592,7 @@ <h2>Ecological Interactions</h2>
                 <div class="interaction-header">
                     <h3>SynCom phenanthrene removal in lettuce pots</h3>
                 </div>
-                <p class="prewrap interaction-description">As a two-member synthetic community, Sphingobium sp. RS2 and Nitrososphaera viennensis EN76 were associated with 90.02% PHE removal from soil and an 81.07% reduction of PHE transfer to lettuce. Pairwise exchange metabolites were not resolved in the accessible abstract.</p>
+                <p class="prewrap interaction-description">In lettuce-soil pots, SynCom addition was associated with 90.02% PHE removal from soil and an 81.07% reduction of PHE transfer to lettuce. These are pot-level outcomes, not isolated contributions of each inoculant or a traced interspecies exchange in the accessible abstract.</p>
 
 
 
@@ -633,7 +633,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - SUPPORT (IN_VIVO)
                         </div>
 
                         <div class="snippet">"The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the soil and 81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom."</div>
@@ -646,35 +646,16 @@ <h4>Evidence</h4>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>SynCom soil carbon restoration</h3>
+                    <h3>SynCom soil carbon endpoints and modeled guild associations</h3>
                 </div>
-                <p class="prewrap interaction-description">SynCom addition increased soil organic carbon, microbial carbon, and total carbon, and random-forest/PLS-PM modeling linked those effects to a sustained increase in the absolute abundance of soil carbon-fixing and PHE-degrading microorganisms.</p>
+                <p class="prewrap interaction-description">SynCom addition significantly increased soil organic carbon, microbial carbon and total carbon content in the pot experiment. PARTIAL: random-forest/PLS-PM analysis links these outcomes to increased absolute abundances of carbon-fixing and PHE-degrading soil microorganisms. Carbon stocks and modeled associations do not themselves quantify carbon-fixation flux, establish exchanged carbon, or isolate each inoculant contribution.</p>
 
 
 
 
 
 
-                <p><strong>Metabolites:</strong>
-
-                    carbon dioxide
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>)
-
-                </p>
-
-
-
-                <p><strong>Biological Processes:</strong></p>
-                <ul>
-
-                    <li>
-                        carbon fixation
-                        (<a href="http://amigo.geneontology.org/amigo/term/GO:0015977"
-                            class="term-link" target="_blank" rel="noopener noreferrer">GO:0015977</a>)
-                    </li>
 
-                </ul>
 
 
 
@@ -689,7 +670,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - SUPPORT (IN_VIVO)
                         </div>
 
                         <div class="snippet">"Soil organic carbon, microbial carbon, and total carbon content were also significantly increased."</div>
@@ -702,7 +683,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>
 
-                            - SUPPORT (COMPUTATIONAL)
+                            - PARTIAL (COMPUTATIONAL)
                         </div>
 
                         <div class="snippet">"demonstrated that these effects were primarily driven by a continuous increase in the absolute abundance of soil carbon-fixing microorganisms and PHE-degrading microorganisms after SynCom addition."</div>
@@ -719,7 +700,7 @@ <h4>Evidence</h4>
         <!-- Associated Datasets -->
 
         <section id="discussions">
-            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
 
             <div class="discussion">
                 <h3>
@@ -756,6 +737,41 @@ <h3>
 
             </div>
 
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    What source evidence separates the observed soil carbon increase from carbon-fixation flux and causal contributions of the two inoculants?
+                </h3>
+                <p class="prewrap">The accessible abstract supports positive pot endpoints and the authors modeled guild-abundance interpretation. It does not resolve member-specific exchange or direct flux; full methods and model specification were not read. Prior environmental grounding and computational provenance fixes are preserved.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#SynCom phenanthrene removal in lettuce pots</code>, <code>ecological_interactions#SynCom soil carbon endpoints and modeled guild associations</code></p>
+
+
+
+                <details class="evidence-list">
+                    <summary class="muted small">1 evidence item(s)</summary>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VIVO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/41967346/" rel="nofollow noreferrer">PMID:41967346</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">Soil organic carbon, microbial carbon, and total carbon content were also significantly increased.</p>
+                        <p class="muted small prewrap">Supports increased soil organic, microbial, and total carbon after SynCom addition.</p>
+                    </div>
+
+                </details>
+
+
+            </div>
+
         </section>
 
         <!-- Environmental Factors -->
@@ -1166,21 +1182,13 @@ <h4 style="color: var(--text);">Evidence</h4>
             var intType = "UNKNOWN";
             var metabolites = [];
 
-
-            metabolites.push("carbon dioxide");
-
-
             var processes = [];
 
-
-            processes.push("carbon fixation");
-
-
             var evidenceCount = 2;
 
             nodes.push({
                 id: intId,
-                label: "SynCom soil carbon restoration",
+                label: "SynCom soil carbon endpoints and modeled guild associations",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
diff --git a/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html b/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
index 4dc3d1159..496596156 100644
--- a/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
+++ b/docs/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.html
@@ -585,7 +585,7 @@ <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 Sphingobium-Rhodococcus Lignin-Dimer Valorization Coculture</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, 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">
@@ -593,13 +593,8 @@ <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="symbolDiamond"
-                             data-color="#57c7ab"></svg> Cross-feeding
-                    </div>
-                    <div class="legend-item">
-                        <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -607,11 +602,9 @@ <h2>Ecological Interactions</h2>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
+                    <h3>Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling</h3>
                 </div>
-                <p class="prewrap interaction-description">Sphingobium sp. cleaves lignin-derived dimers, supplying aromatic intermediates that R. opacus can funnel into target products.
-</p>
+                <p class="prewrap interaction-description">HYPOTHESIZED: the designed coculture systems combine the lignin-dimer-cleavage bacterium Sphingobium sp. with the monomer-conversion bacterium R. opacus. PARTIAL: this supports a cleavage-to-conversion design, but the accessible abstract does not trace a specific exchanged intermediate between partners or identify each strain/formulation variant. Listed metabolites are feedstock context, not a measured exchange pool.</p>
 
 
                 <p><strong>Source Taxon:</strong> Sphingobium sp.</p>
@@ -642,9 +635,8 @@ <h3>Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling</h3>
                     <strong>Downstream Effects:</strong>
 
                     <div class="flow-item">
-                        <span class="flow-arrow">→</span> Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
-                        <p class="prewrap causal-description">Sphingobium cleavage of lignin-derived dimers supplies the monomers that R. opacus funnels into cis,cis-muconate and gallate in the designed coculture.
-</p>
+                        <span class="flow-arrow">→</span> Reported Lignin-Dimer Conversion Outcomes
+                        <p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: dimer cleavage is the designed upstream step supplying substrates for monomer conversion in the source coculture systems. The abstract implies this coupling but does not trace the transferred intermediate, isolate its causal contribution, or demonstrate simultaneous muconate/gallate production by one formulation.</p>
                     </div>
 
                 </div>
@@ -660,37 +652,22 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/36030484/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36030484</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"combining lignin-derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium Rhodococcus opacus"</div>
 
                     </li>
 
-                    <li class="evidence-item">
-                        <div>
-
-                            <a href="https://pubmed.ncbi.nlm.nih.gov/36030484/"
-                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:36030484</a>
-
-                            - SUPPORT (IN_VITRO)
-                        </div>
-
-                        <div class="snippet">"lignin-derived aromatic monomers have been funneled to target compounds"</div>
-
-                    </li>
-
                 </ul>
 
             </div>
 
             <div class="interaction-card">
                 <div class="interaction-header">
-                    <h3>Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate</h3>
-                    <span class="interaction-type">CROSS_FEEDING</span>
+                    <h3>Reported Lignin-Dimer Conversion Outcomes</h3>
                 </div>
-                <p class="prewrap interaction-description">The coculture converts multiple lignin-derived dimers with different linkage classes into cis,cis-muconate and gallate.
-</p>
+                <p class="prewrap interaction-description">The developed coculture systems converted multiple lignin-derived dimer classes to cis,cis-muconate. The abstract separately reports potential for gallate conversion; this is not a coequal quantified product result or demonstrated simultaneous production of both products by one formulation. Exact strain/formulation variants are not resolved by the accessible abstract.</p>
 
 
 
@@ -703,9 +680,9 @@ <h3>Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate</h3>
                     (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=32379"
                         class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:32379</a>),
 
-                    gallic acid
-                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=30778"
-                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:30778</a>)
+                    gallate
+                    (<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16918"
+                        class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16918</a>)
 
                 </p>
 
@@ -727,7 +704,7 @@ <h4>Evidence</h4>
                             - SUPPORT (IN_VITRO)
                         </div>
 
-                        <div class="snippet">"funnel multiple lignin-derived dimers to cis, cis-muconate and gallate"</div>
+                        <div class="snippet">"were converted to cis, cis-muconate"</div>
 
                     </li>
 
@@ -740,7 +717,7 @@ <h4>Evidence</h4>
                             - SUPPORT (IN_VITRO)
                         </div>
 
-                        <div class="snippet">"were converted to cis, cis-muconate"</div>
+                        <div class="snippet">"the developed coculture systems also showed potential in conversion of lignin-derived dimers to gallate."</div>
 
                     </li>
 
@@ -751,10 +728,8 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Lignin-Dimer Linkage-Class Substrate Range</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
                 </div>
-                <p class="prewrap interaction-description">The coculture system was tested across several low-molecular-weight lignin-derived dimer linkage types, broadening biological funneling beyond aromatic monomers.
-</p>
+                <p class="prewrap interaction-description">The abstract reports conversion of beta-O-4, 4-O-5, beta-5, beta-beta, beta-1 and 5-5 lignin-derived dimers to cis,cis-muconate using the developed coculture systems. This is substrate-range evidence, not distinct partner niches or reduced competition. It does not constitute a separate causal driver of the product node.</p>
 
 
 
@@ -773,17 +748,6 @@ <h3>Lignin-Dimer Linkage-Class Substrate Range</h3>
 
 
 
-                <div class="interaction-flow">
-                    <strong>Downstream Effects:</strong>
-
-                    <div class="flow-item">
-                        <span class="flow-arrow">→</span> Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
-                        <p class="prewrap causal-description">Activity across beta-O-4, 4-O-5, and beta-5 dimer linkage classes broadens the substrate pool that the Sphingobium-Rhodococcus coculture can funnel into cis,cis-muconate and gallate.
-</p>
-                    </div>
-
-                </div>
-
 
 
                 <h4>Evidence</h4>
@@ -873,6 +837,45 @@ <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 exact coculture variants and transferred intermediates underlie the reported muconate outcomes and qualified gallate potential?
+                </h3>
+                <p class="prewrap">The abstract describes systems plural and combines cleavage and monomer-conversion roles. Keep the existing direction as HYPOTHESIZED/PARTIAL and preserve substrate coverage, without converting background monomer studies into this-system evidence or asserting simultaneous products. The primary publisher URL redirected to an abstract/access page; no full body or supplement was read.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling</code>, <code>ecological_interactions#Reported Lignin-Dimer Conversion Outcomes</code>, <code>ecological_interactions#Lignin-Dimer Linkage-Class Substrate Range</code></p>
+
+
+
+                <details class="evidence-list">
+                    <summary class="muted small">1 evidence item(s)</summary>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">PARTIAL</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/36030484/" rel="nofollow noreferrer">PMID:36030484</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">combining lignin-derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium Rhodococcus opacus</p>
+                        <p class="muted small prewrap">Supports the designed cleavage/conversion coupling, not direct tracing of exchanged intermediates; the removed second quotation described previous studies.</p>
+                    </div>
+
+                </details>
+
+
+            </div>
+
+        </section>
 
         <!-- Environmental Factors -->
 
@@ -1153,7 +1156,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1164,11 +1167,11 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-            var evidenceCount = 2;
+            var evidenceCount = 1;
 
             nodes.push({
                 id: intId,
-                label: "Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling",
+                label: "Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1193,13 +1196,13 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:1";
-            var intType = "CROSS_FEEDING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
             metabolites.push("cis,cis-muconate");
 
-            metabolites.push("gallic acid");
+            metabolites.push("gallate");
 
 
             var processes = [];
@@ -1208,7 +1211,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             nodes.push({
                 id: intId,
-                label: "Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate",
+                label: "Reported Lignin-Dimer Conversion Outcomes",
                 type: "interaction",
                 interactionType: intType,
                 metabolites: metabolites,
@@ -1223,7 +1226,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:2";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
diff --git a/docs/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.html b/docs/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.html
index f3bfdc11f..05a7094c7 100644
--- a/docs/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.html
+++ b/docs/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.html
@@ -580,7 +580,7 @@ <h2>Ecological Interactions</h2>
                 <div class="interaction-header">
                     <h3>Staged cattle-manure wastewater valorization</h3>
                 </div>
-                <p class="prewrap interaction-description">The staged two-member SYC consortium converted cattle manure wastewater into stable bioactive fermentation broth and maintained stronger viable bacterial density than the S2-8-1 monoculture or simultaneous co-culture.</p>
+                <p class="prewrap interaction-description">Among the tested S2-8-1 monoculture, simultaneous co-culture and staged SYC systems, SYC maintained the highest viable bacterial density. The source describes the resulting cattle-manure wastewater broth as stable and bioactive; this is bounded to the reported experiment, not demonstrated reciprocal benefit or universal functional stability.</p>
 
 
 
@@ -630,7 +630,7 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>SYC rhizosphere nitrification and maize promotion</h3>
                 </div>
-                <p class="prewrap interaction-description">Fermentation broth from SYC increased rhizosphere nitrification, nitrate availability, photosynthetic performance, cytokinin accumulation, and maize whole-plant dry matter in a soil-maize pot experiment.</p>
+                <p class="prewrap interaction-description">In a soil-maize pot experiment, SYC enhanced rhizosphere nitrification, nitrate availability, photosynthetic performance and cytokinin accumulation. Whole-plant dry matter increased by 41.4% versus the water control, not the monoculture or simultaneous-culture comparator used for broth density. The accessible abstract does not isolate cytokinin accumulation or the transcript response as the cause of plant growth.</p>
 
 
 
@@ -680,6 +680,19 @@ <h4>Evidence</h4>
 
                     </li>
 
+                    <li class="evidence-item">
+                        <div>
+
+                            <a href="https://pubmed.ncbi.nlm.nih.gov/42341825/"
+                               class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42341825</a>
+
+                            - SUPPORT (IN_VIVO)
+                        </div>
+
+                        <div class="snippet">"The consortium also improved photosynthetic performance and cytokinin accumulation."</div>
+
+                    </li>
+
                 </ul>
 
             </div>
@@ -688,10 +701,16 @@ <h4>Evidence</h4>
                 <div class="interaction-header">
                     <h3>S2-8-1 nitrogen and cytokinin-related gene upregulation</h3>
                 </div>
-                <p class="prewrap interaction-description">Comparative metatranscriptomics under SYC conditions found significant upregulation of S2-8-1 heterotrophic ammonia oxidation-related genes and cytokinin-related genes.</p>
+                <p class="prewrap interaction-description">Comparative metatranscriptomics under SYC conditions found significant upregulation of S2-8-1 heterotrophic ammonia oxidation-related and cytokinin-related genes. This is a member-specific transcript observation, not demonstrated protein activity, metabolic flux, or a proven mediator of the broth-density or maize-growth outcomes.</p>
+
+
 
 
+                <p><strong>Participating Taxa:</strong>
 
+                    Ensifer sp. S2-8-1
+
+                </p>
 
 
 
@@ -727,7 +746,7 @@ <h4>Evidence</h4>
         <!-- Associated Datasets -->
 
         <section id="discussions">
-            <h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
+            <h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
 
             <div class="discussion">
                 <h3>
@@ -742,6 +761,41 @@ <h3>
 
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Does the S2-8-1 transcript response causally mediate the separately reported broth and maize endpoints?
+                </h3>
+                <p class="prewrap">The accessible abstract reports comparative transcript abundance and suggests coordinated pathway activation. It does not isolate the transcript changes as causal mediators. Keep the observed endpoints separate, the transcript node scoped only to Ensifer, and no downstream arrows. Exact full-text methods were not read.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Staged cattle-manure wastewater valorization</code>, <code>ecological_interactions#SYC rhizosphere nitrification and maize promotion</code>, <code>ecological_interactions#S2-8-1 nitrogen and cytokinin-related gene upregulation</code></p>
+
+
+
+                <details class="evidence-list">
+                    <summary class="muted small">1 evidence item(s)</summary>
+
+                    <div class="evidence">
+                        <div class="evidence-head">
+                            <span class="badge small">IN_VITRO</span>
+                            <span class="badge small">SUPPORT</span>
+
+
+
+                                <a href="https://pubmed.ncbi.nlm.nih.gov/42341825/" rel="nofollow noreferrer">PMID:42341825</a>
+
+
+                        </div>
+                        <p class="snippet small prewrap">Comparative metatranscriptomic analysis revealed significant upregulation of heterotrophic ammonia oxidation-related genes (CYP450) and cytokinin-related genes (miaA and LOG) in S2-8-1 under SYC conditions</p>
+                        <p class="muted small prewrap">Supports reported transcript upregulation specifically in S2-8-1, not direct pathway activity or causal mediation of other endpoints.</p>
+                    </div>
+
+                </details>
+
+
             </div>
 
         </section>
@@ -1021,7 +1075,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
             var processes = [];
 
-            var evidenceCount = 2;
+            var evidenceCount = 3;
 
             nodes.push({
                 id: intId,
@@ -1060,6 +1114,17 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Ensifer sp. S2-8-1"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 
diff --git a/history/records/Space_Habitat_SevenMember_Stress_Tolerance_SynCom/2026-10-08T012746Z-codex-2f9387.yaml b/history/records/Space_Habitat_SevenMember_Stress_Tolerance_SynCom/2026-10-08T012746Z-codex-2f9387.yaml
new file mode 100644
index 000000000..cf764f1ae
--- /dev/null
+++ b/history/records/Space_Habitat_SevenMember_Stress_Tolerance_SynCom/2026-10-08T012746Z-codex-2f9387.yaml
@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
+  slug: Space_Habitat_SevenMember_Stress_Tolerance_SynCom
+session:
+  id: 2026-10-08T012746Z-codex-2f9387
+  timestamp: '2026-10-08T01:27:46Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1823
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain reduced B. subtilis colony recovery and its canonical participant; remove
+    categorical competition and distinguish cultivability from definitive viability loss.
+  details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
diff --git a/history/records/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom/2026-10-08T012747Z-codex-83fd7a.yaml b/history/records/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom/2026-10-08T012747Z-codex-83fd7a.yaml
new file mode 100644
index 000000000..910f6f47e
--- /dev/null
+++ b/history/records/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom/2026-10-08T012747Z-codex-83fd7a.yaml
@@ -0,0 +1,26 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
+  slug: Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom
+session:
+  id: 2026-10-08T012747Z-codex-83fd7a
+  timestamp: '2026-10-08T01:27:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1824
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain positive lettuce-pot PHE outcomes with IN_VIVO provenance and no inferred
+    exchange.; Retain carbon-content measurements and qualify modeled drivers; remove carbon-dioxide/fixation
+    annotations not established by stock endpoints.
+  details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
diff --git a/history/records/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture/2026-10-08T012747Z-codex-3f6f74.yaml b/history/records/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture/2026-10-08T012747Z-codex-3f6f74.yaml
new file mode 100644
index 000000000..365727ed1
--- /dev/null
+++ b/history/records/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture/2026-10-08T012747Z-codex-3f6f74.yaml
@@ -0,0 +1,29 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
+  slug: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+session:
+  id: 2026-10-08T012747Z-codex-3f6f74
+  timestamp: '2026-10-08T01:27:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1825
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain designed pairwise cleavage/conversion coupling and its existing direction
+    as HYPOTHESIZED/PARTIAL; remove the background-study quotation and categorical cross-feeding.;
+    Preserve muconate conversion separately from gallate potential across source systems;
+    correct the graph gallate identity using the existing local descriptor.; Retain reported
+    dimer substrate coverage; remove niche-partitioning classification and the product restatement
+    arrow.
+  details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
diff --git a/history/records/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom/2026-10-08T012747Z-codex-9305dd.yaml b/history/records/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom/2026-10-08T012747Z-codex-9305dd.yaml
new file mode 100644
index 000000000..31fb5ad93
--- /dev/null
+++ b/history/records/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom/2026-10-08T012747Z-codex-9305dd.yaml
@@ -0,0 +1,27 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
+  slug: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+session:
+  id: 2026-10-08T012747Z-codex-9305dd
+  timestamp: '2026-10-08T01:27:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1826
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Retain tested broth-density comparison without universal stability or reciprocal-benefit
+    claims.; Preserve positive maize-pot endpoints and the water-control dry-matter comparator
+    without inferred mediator arrows.; Restrict the transcript observation to canonical Ensifer
+    S2-8-1 and distinguish it from protein activity, flux or causal mediation.
+  details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
diff --git a/kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml b/kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
index 487761a72..7ce42d46c 100644
--- a/kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
+++ b/kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
@@ -213,13 +213,10 @@ taxonomy:
     explanation: Identifies A. radioresistens 50V1 as a consortium member and gives its spacecraft-associated source, genome accession and cultivation conditions.
 ecological_interactions:
 - name: Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
-  description: >-
-    After 24 h co-cultivation, culturable B. subtilis CFU were significantly
-    lower in the whole seven-member consortium than in B. subtilis single culture
-    under the tested recovery conditions. The source discusses possible
-    antimicrobial competition but does not resolve which partner, metabolite or
-    mechanism drove this effect.
-  interaction_type: COMPETITION
+  description: After co-cultivation, culturable B. subtilis CFU were significantly lower in the whole seven-member
+    laboratory consortium than in single culture under the tested recovery conditions. This is decreased cultivability,
+    not definitive loss of viability or demonstrated reciprocal negative effects on a pair of partners. The source
+    discusses possible competition, but does not identify a causal partner or confirmed metabolite activity.
   scope: COMMUNITY_LEVEL
   participating_taxa:
   - preferred_term: Bacillus subtilis W2-B1-K4
@@ -230,13 +227,17 @@ ecological_interactions:
   - reference: PMID:42577390
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: >-
-      Quantification of viable cells of B. subtilis revealed an increase of
-      CFU/mL when co-cultivated with A. radioresistens and M. luteus ,
-      respectively, and decrease of CFU/mL when co-cultivated with S. capitis
-      and P. antarctica , and a statistically significant decrease of CFU/mL when
-      co-cultivated with the whole consortium ( p = 0.008)
-    explanation: Supports the whole-consortium decrease in culturable B. subtilis recovery.
+    snippet: Quantification of viable cells of B. subtilis revealed an increase of CFU/mL when co-cultivated with
+      A. radioresistens and M. luteus , respectively, and decrease of CFU/mL when co-cultivated with S. capitis
+      and P. antarctica , and a statistically significant decrease of CFU/mL when co-cultivated with the whole consortium
+      ( p = 0.008)
+    explanation: Supports the whole-consortium decrease in recoverable B. subtilis CFU, not reciprocal negative
+      fitness effects or a resolved mechanism.
+  - reference: PMID:42577390
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability
+    explanation: The source explicitly limits interpretation of reduced colony recovery.
 environmental_factors:
 - name: Desiccation stress
   value: 1, 7, 14, 21 and 28 days
@@ -347,23 +348,46 @@ external_resources:
     explanation: Lists the exact primary publication for this synthetic space-habitat consortium.
 discussions:
 - discussion_id: stress_protection_mechanisms_unresolved
-  prompt: >-
-    Which consortium members or metabolites drive the stressor-specific changes
-    in B. subtilis and S. capitis survival inside the full consortium?
+  prompt: Which consortium members or metabolites drive the stressor-specific changes in B. subtilis and S. capitis
+    survival inside the full consortium?
   kind: KNOWLEDGE_GAP
   status: OPEN
   attaches_to:
   - ecological_interactions#Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
-  rationale: >-
-    The study showed stressor-specific differences between single-species and
-    consortium survival, and it discusses candidate explanations including
-    nutrient release, protective dead-cell material, catalase usage, antimicrobial
-    peptides and biosynthetic gene clusters. The experiments did not identify a
-    causal partner or measured metabolite, so no pairwise protective edge is
-    asserted here.
+  rationale: The study showed stressor-specific differences between single-species and consortium survival, and
+    it discusses candidate explanations including nutrient release, protective dead-cell material, catalase usage,
+    antimicrobial peptides and biosynthetic gene clusters. The experiments did not identify a causal partner or
+    measured metabolite, so no pairwise protective edge is asserted here.
   posed_by: codex
   posed_date: '2026-09-11'
+- discussion_id: space_cultivability_not_reciprocal_competition
+  prompt: Does the reported colony-recovery decrease establish reciprocal competition or loss of viability?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
+  rationale: The measured decrease is retained. COMPETITION requires both partners to be negatively affected; this
+    result does not establish that relationship. Candidate genomic functions are not confirmed activity. This metadata
+    review adds no stress-survival procedures or new partner mechanisms.
+  evidence:
+  - reference: PMID:42577390
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability
+    explanation: The source explicitly limits interpretation of reduced colony recovery.
+  - reference: PMID:42577390
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: these findings reflect genomic potential rather than confirmed metabolite activity.
+    explanation: Bounds the source interpretation; no metabolite-mediated causal edge is established.
 metals_present: []
 rare_earth_elements_present: []
 metal_relevance: NOT_APPLICABLE
 metal_notes: No metal or rare earth element processing role is curated for this synthetic space-habitat stress-tolerance consortium.
+curation_history:
+- timestamp: '2026-10-08T01:27:44Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: Retain reduced B. subtilis colony recovery and its canonical participant; remove categorical competition
+    and distinguish cultivability from definitive viability loss. Issue#1823; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  llm_assisted: true
diff --git a/kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml b/kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
index 4193cdb89..a39599be4 100644
--- a/kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
+++ b/kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
@@ -116,9 +116,9 @@ taxonomy:
     explanation: Identifies Nitrososphaera viennensis EN76 as the carbon-sequestering archaeal SynCom member.
 ecological_interactions:
 - name: SynCom phenanthrene removal in lettuce pots
-  description: As a two-member synthetic community, Sphingobium sp. RS2 and Nitrososphaera viennensis EN76 were associated
-    with 90.02% PHE removal from soil and an 81.07% reduction of PHE transfer to lettuce. Pairwise exchange metabolites were
-    not resolved in the accessible abstract.
+  description: In lettuce-soil pots, SynCom addition was associated with 90.02% PHE removal from soil and an 81.07%
+    reduction of PHE transfer to lettuce. These are pot-level outcomes, not isolated contributions of each inoculant
+    or a traced interspecies exchange in the accessible abstract.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: phenanthrene
@@ -133,38 +133,29 @@ ecological_interactions:
   evidence:
   - reference: PMID:41967346
     supports: SUPPORT
-    evidence_source: IN_VITRO
-    snippet: The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the soil and
-      81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom.
+    evidence_source: IN_VIVO
+    snippet: The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the
+      soil and 81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom.
     explanation: Supports consortium-linked phenanthrene removal from soil and reduced transfer to lettuce.
-- name: SynCom soil carbon restoration
-  description: SynCom addition increased soil organic carbon, microbial carbon, and total carbon, and random-forest/PLS-PM
-    modeling linked those effects to a sustained increase in the absolute abundance of soil carbon-fixing and PHE-degrading
-    microorganisms.
+- name: SynCom soil carbon endpoints and modeled guild associations
+  description: 'SynCom addition significantly increased soil organic carbon, microbial carbon and total carbon content
+    in the pot experiment. PARTIAL: random-forest/PLS-PM analysis links these outcomes to increased absolute abundances
+    of carbon-fixing and PHE-degrading soil microorganisms. Carbon stocks and modeled associations do not themselves
+    quantify carbon-fixation flux, establish exchanged carbon, or isolate each inoculant contribution.'
   scope: COMMUNITY_LEVEL
-  metabolites:
-  - preferred_term: carbon dioxide
-    term:
-      id: CHEBI:16526
-      label: carbon dioxide
-  biological_processes:
-  - preferred_term: carbon fixation
-    term:
-      id: GO:0015977
-      label: carbon fixation
   evidence:
   - reference: PMID:41967346
     supports: SUPPORT
-    evidence_source: IN_VITRO
+    evidence_source: IN_VIVO
     snippet: Soil organic carbon, microbial carbon, and total carbon content were also significantly increased.
     explanation: Supports increased soil organic, microbial, and total carbon after SynCom addition.
   - reference: PMID:41967346
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: COMPUTATIONAL
-    snippet: demonstrated that these effects were primarily driven by a continuous increase in the absolute abundance of soil
-      carbon-fixing microorganisms and PHE-degrading microorganisms after SynCom addition.
-    explanation: Supports the modeled association between SynCom addition and increased absolute abundances of carbon-fixing
-      and PHE-degrading microorganisms.
+    snippet: demonstrated that these effects were primarily driven by a continuous increase in the absolute abundance
+      of soil carbon-fixing microorganisms and PHE-degrading microorganisms after SynCom addition.
+    explanation: Supports the authors statistical driver interpretation, not direct carbon-fixation flux or experimentally
+      isolated mediation.
     computational_provenance:
       prediction_type: STATISTICAL_INFERENCE
       tools:
@@ -172,8 +163,9 @@ ecological_interactions:
         role: ranked inferred drivers of SynCom-associated phenanthrene and carbon outcomes
       - tool_name: partial least-squares path modeling
         role: modeled paths linking SynCom addition, microbial absolute abundances, and carbon/PHE outcomes
-      parameters: Combined random forest and PLS-PM over the pot experiment to infer that carbon-fixing and PHE-degrading
-        microorganism abundances primarily drove the reported SynCom effects.
+      parameters: Abstract-reported random forest and PLS-PM over pot-experiment outcomes and soil microbial guild
+        abundances; software versions and full model specification were not verified. This is statistical inference,
+        not a direct flux measurement.
 environmental_factors:
 - name: Phenanthrene contamination
   value: phenanthrene-contaminated soil
@@ -263,22 +255,41 @@ metal_notes: The accessible abstract reports organic-pollutant bioremediation of
   or rare-earth processing.
 discussions:
 - discussion_id: phenanthrene_carbon_syncom_cultivation_details
-  prompt: What phenanthrene soil dose, SynCom inoculation amounts, strain ratio, pot conditions, and carbon-assay timing were
-    used for the Sphingobium-Nitrososphaera SynCom?
+  prompt: What phenanthrene soil dose, SynCom inoculation amounts, strain ratio, pot conditions, and carbon-assay
+    timing were used for the Sphingobium-Nitrososphaera SynCom?
   kind: KNOWLEDGE_GAP
   status: OPEN
   attaches_to:
   - engineering_design
   - growth_media#Phenanthrene-contaminated lettuce pot soil
-  rationale: The PubMed abstract names the exact members and reports PHE, lettuce-transfer, and carbon endpoints, but Elsevier
-    full text was not open-access through Europe PMC during curation, leaving exact cultivation parameters unresolved.
+  rationale: The PubMed abstract names the exact members and reports PHE, lettuce-transfer, and carbon endpoints,
+    but Elsevier full text was not open-access through Europe PMC during curation, leaving exact cultivation parameters
+    unresolved.
   evidence:
   - reference: PMID:41967346
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the soil and
-      81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom.
-    explanation: Shows that the abstract reports pot-level outcomes without exposing the pot setup or inoculation details.
+    snippet: The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the
+      soil and 81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom.
+    explanation: Shows that the abstract reports pot-level outcomes without exposing the pot setup or inoculation
+      details.
+- discussion_id: phenanthrene_carbon_stocks_and_inferred_drivers
+  prompt: What source evidence separates the observed soil carbon increase from carbon-fixation flux and causal
+    contributions of the two inoculants?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#SynCom phenanthrene removal in lettuce pots
+  - ecological_interactions#SynCom soil carbon endpoints and modeled guild associations
+  rationale: The accessible abstract supports positive pot endpoints and the authors modeled guild-abundance interpretation.
+    It does not resolve member-specific exchange or direct flux; full methods and model specification were not read.
+    Prior environmental grounding and computational provenance fixes are preserved.
+  evidence:
+  - reference: PMID:41967346
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: Soil organic carbon, microbial carbon, and total carbon content were also significantly increased.
+    explanation: Supports increased soil organic, microbial, and total carbon after SynCom addition.
 curation_history:
 - timestamp: '2026-09-13T13:42:30Z'
   curator: claude
@@ -288,6 +299,13 @@ curation_history:
 - timestamp: '2026-09-13T14:31:47Z'
   curator: codex
   action: ADDRESS_ADVERSARIAL_REVIEW
-  changes: Narrowed abstract-supported community-level effects to untyped interactions and marked RF/PLS-PM driver evidence
-    as COMPUTATIONAL with provenance for issues 847 and 848.
+  changes: Narrowed abstract-supported community-level effects to untyped interactions and marked RF/PLS-PM driver
+    evidence as COMPUTATIONAL with provenance for issues 847 and 848.
+  llm_assisted: true
+- timestamp: '2026-10-08T01:27:45Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: Retain positive lettuce-pot PHE outcomes with IN_VIVO provenance and no inferred exchange.; Retain carbon-content
+    measurements and qualify modeled drivers; remove carbon-dioxide/fixation annotations not established by stock
+    endpoints. Issue#1824; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
   llm_assisted: true
diff --git a/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml b/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
index 7af20281d..f09bd8b05 100644
--- a/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
+++ b/kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
@@ -109,11 +109,11 @@ taxonomy:
     snippet: funnel multiple lignin-derived dimers to cis, cis-muconate and gallate
     explanation: Supports the R. opacus role in product funneling within the coculture system.
 ecological_interactions:
-- name: Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling
-  description: >
-    Sphingobium sp. cleaves lignin-derived dimers, supplying aromatic
-    intermediates that R. opacus can funnel into target products.
-  interaction_type: CROSS_FEEDING
+- name: Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling
+  description: 'HYPOTHESIZED: the designed coculture systems combine the lignin-dimer-cleavage bacterium Sphingobium
+    sp. with the monomer-conversion bacterium R. opacus. PARTIAL: this supports a cleavage-to-conversion design,
+    but the accessible abstract does not trace a specific exchanged intermediate between partners or identify each
+    strain/formulation variant. Listed metabolites are feedstock context, not a measured exchange pool.'
   scope: PAIRWISE
   source_taxon:
     preferred_term: Sphingobium sp.
@@ -136,67 +136,58 @@ ecological_interactions:
       label: guaiacylglycerol-beta-guaiacyl ether
     notes: Representative beta-O-4 lignin-derived dimer substrate tested in the study.
   downstream:
-  - target: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
-    description: >
-      Sphingobium cleavage of lignin-derived dimers supplies the monomers that
-      R. opacus funnels into cis,cis-muconate and gallate in the designed
-      coculture.
+  - target: Reported Lignin-Dimer Conversion Outcomes
+    description: 'HYPOTHESIZED/PARTIAL: dimer cleavage is the designed upstream step supplying substrates for monomer
+      conversion in the source coculture systems. The abstract implies this coupling but does not trace the transferred
+      intermediate, isolate its causal contribution, or demonstrate simultaneous muconate/gallate production by
+      one formulation.'
   evidence:
   - reference: PMID:36030484
-    supports: SUPPORT
-    evidence_source: IN_VITRO
-    snippet: combining lignin-derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium Rhodococcus opacus
-    explanation: Supports cross-feeding between the dimer-cleaving and monomer-converting partners.
-  - reference: PMID:36030484
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
-    snippet: lignin-derived aromatic monomers have been funneled to target compounds
-    explanation: Supports aromatic monomer funneling as the downstream conversion task.
-- name: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
-  description: >
-    The coculture converts multiple lignin-derived dimers with different linkage
-    classes into cis,cis-muconate and gallate.
-  interaction_type: CROSS_FEEDING
+    snippet: combining lignin-derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium
+      Rhodococcus opacus
+    explanation: Supports the designed cleavage/conversion coupling, not direct tracing of exchanged intermediates;
+      the removed second quotation described previous studies.
+- name: Reported Lignin-Dimer Conversion Outcomes
+  description: The developed coculture systems converted multiple lignin-derived dimer classes to cis,cis-muconate.
+    The abstract separately reports potential for gallate conversion; this is not a coequal quantified product result
+    or demonstrated simultaneous production of both products by one formulation. Exact strain/formulation variants
+    are not resolved by the accessible abstract.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: cis,cis-muconate
     term:
       id: CHEBI:32379
       label: cis,cis-muconate
-  - preferred_term: gallic acid
+  - preferred_term: gallate
     term:
-      id: CHEBI:30778
-      label: gallic acid
-    notes: The publication reports gallate as a target product.
+      id: CHEBI:16918
+      label: gallate
+    notes: Qualified conversion potential in the abstract, not a quantified simultaneous product endpoint.
   evidence:
   - reference: PMID:36030484
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: funnel multiple lignin-derived dimers to cis, cis-muconate and gallate
-    explanation: Supports the target product profile for the coculture.
+    snippet: were converted to cis, cis-muconate
+    explanation: The preceding abstract list identifies the converted lignin-dimer classes; this is the measured
+      product claim.
   - reference: PMID:36030484
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: were converted to cis, cis-muconate
-    explanation: Supports conversion of several lignin-derived dimer classes to cis,cis-muconate.
+    snippet: the developed coculture systems also showed potential in conversion of lignin-derived dimers to gallate.
+    explanation: Preserves the source qualification of gallate as conversion potential, not a coequal quantified
+      endpoint.
 - name: Lignin-Dimer Linkage-Class Substrate Range
-  description: >
-    The coculture system was tested across several low-molecular-weight
-    lignin-derived dimer linkage types, broadening biological funneling beyond
-    aromatic monomers.
-  interaction_type: NICHE_PARTITIONING
+  description: The abstract reports conversion of beta-O-4, 4-O-5, beta-5, beta-beta, beta-1 and 5-5 lignin-derived
+    dimers to cis,cis-muconate using the developed coculture systems. This is substrate-range evidence, not distinct
+    partner niches or reduced competition. It does not constitute a separate causal driver of the product node.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: lignin
     term:
       id: CHEBI:6457
       label: lignin
-  downstream:
-  - target: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
-    description: >
-      Activity across beta-O-4, 4-O-5, and beta-5 dimer linkage classes
-      broadens the substrate pool that the Sphingobium-Rhodococcus coculture can
-      funnel into cis,cis-muconate and gallate.
   evidence:
   - reference: PMID:36030484
     supports: SUPPORT
@@ -348,3 +339,35 @@ metal_relevance: NOT_APPLICABLE
 metal_notes: >
   No metal or rare earth element processing role is curated for this
   lignin-dimer valorization coculture.
+discussions:
+- discussion_id: lignin_coupling_and_formulation_limits
+  prompt: Which exact coculture variants and transferred intermediates underlie the reported muconate outcomes and
+    qualified gallate potential?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling
+  - ecological_interactions#Reported Lignin-Dimer Conversion Outcomes
+  - ecological_interactions#Lignin-Dimer Linkage-Class Substrate Range
+  rationale: The abstract describes systems plural and combines cleavage and monomer-conversion roles. Keep the
+    existing direction as HYPOTHESIZED/PARTIAL and preserve substrate coverage, without converting background monomer
+    studies into this-system evidence or asserting simultaneous products. The primary publisher URL redirected to
+    an abstract/access page; no full body or supplement was read.
+  evidence:
+  - reference: PMID:36030484
+    supports: PARTIAL
+    evidence_source: IN_VITRO
+    snippet: combining lignin-derived dimers cleavage bacterium Sphingobium sp. and monomers conversion bacterium
+      Rhodococcus opacus
+    explanation: Supports the designed cleavage/conversion coupling, not direct tracing of exchanged intermediates;
+      the removed second quotation described previous studies.
+curation_history:
+- timestamp: '2026-10-08T01:27:46Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: Retain designed pairwise cleavage/conversion coupling and its existing direction as HYPOTHESIZED/PARTIAL;
+    remove the background-study quotation and categorical cross-feeding.; Preserve muconate conversion separately
+    from gallate potential across source systems; correct the graph gallate identity using the existing local descriptor.;
+    Retain reported dimer substrate coverage; remove niche-partitioning classification and the product restatement
+    arrow. Issue#1825; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  llm_assisted: true
diff --git a/kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml b/kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
index 8d4f925b7..d9e5b4bfd 100644
--- a/kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
+++ b/kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
@@ -101,8 +101,10 @@ taxonomy:
     explanation: Identifies B. subtilis as the auxiliary strain in the SYC consortium.
 ecological_interactions:
 - name: Staged cattle-manure wastewater valorization
-  description: The staged two-member SYC consortium converted cattle manure wastewater into stable bioactive fermentation
-    broth and maintained stronger viable bacterial density than the S2-8-1 monoculture or simultaneous co-culture.
+  description: Among the tested S2-8-1 monoculture, simultaneous co-culture and staged SYC systems, SYC maintained
+    the highest viable bacterial density. The source describes the resulting cattle-manure wastewater broth as stable
+    and bioactive; this is bounded to the reported experiment, not demonstrated reciprocal benefit or universal
+    functional stability.
   scope: COMMUNITY_LEVEL
   evidence:
   - reference: PMID:42341825
@@ -113,12 +115,14 @@ ecological_interactions:
   - reference: PMID:42341825
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: The staged "pre-modification followed by synergy" consortium effectively converts cattle manure wastewater into
-      a stable and bioactive fermentation broth
+    snippet: The staged "pre-modification followed by synergy" consortium effectively converts cattle manure wastewater
+      into a stable and bioactive fermentation broth
     explanation: Supports conversion of cattle manure wastewater by the staged consortium.
 - name: SYC rhizosphere nitrification and maize promotion
-  description: Fermentation broth from SYC increased rhizosphere nitrification, nitrate availability, photosynthetic performance,
-    cytokinin accumulation, and maize whole-plant dry matter in a soil-maize pot experiment.
+  description: In a soil-maize pot experiment, SYC enhanced rhizosphere nitrification, nitrate availability, photosynthetic
+    performance and cytokinin accumulation. Whole-plant dry matter increased by 41.4% versus the water control,
+    not the monoculture or simultaneous-culture comparator used for broth density. The accessible abstract does
+    not isolate cytokinin accumulation or the transcript response as the cause of plant growth.
   scope: COMMUNITY_LEVEL
   metabolites:
   - preferred_term: nitrate
@@ -129,24 +133,37 @@ ecological_interactions:
   - reference: PMID:42341825
     supports: SUPPORT
     evidence_source: IN_VIVO
-    snippet: SYC significantly enhanced rhizosphere nitrification, increased NO3--N availability, and promoted maize growth
+    snippet: SYC significantly enhanced rhizosphere nitrification, increased NO3--N availability, and promoted maize
+      growth
     explanation: Supports the pot-experiment nitrogen and maize-growth effects of SYC.
   - reference: PMID:42341825
     supports: SUPPORT
     evidence_source: IN_VIVO
     snippet: resulting in a 41.4% increase in whole-plant dry matter compared with the water control
     explanation: Quantifies the maize dry-matter increase after SYC treatment.
+  - reference: PMID:42341825
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: The consortium also improved photosynthetic performance and cytokinin accumulation.
+    explanation: Supports these reported pot-treatment endpoints without proving their mediation of growth.
 - name: S2-8-1 nitrogen and cytokinin-related gene upregulation
   description: Comparative metatranscriptomics under SYC conditions found significant upregulation of S2-8-1 heterotrophic
-    ammonia oxidation-related genes and cytokinin-related genes.
+    ammonia oxidation-related and cytokinin-related genes. This is a member-specific transcript observation, not
+    demonstrated protein activity, metabolic flux, or a proven mediator of the broth-density or maize-growth outcomes.
   scope: COMMUNITY_LEVEL
   evidence:
   - reference: PMID:42341825
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: Comparative metatranscriptomic analysis revealed significant upregulation of heterotrophic ammonia oxidation-related
-      genes (CYP450) and cytokinin-related genes (miaA and LOG) in S2-8-1 under SYC conditions
-    explanation: Supports S2-8-1 transcriptional activation in the staged consortium.
+    snippet: Comparative metatranscriptomic analysis revealed significant upregulation of heterotrophic ammonia
+      oxidation-related genes (CYP450) and cytokinin-related genes (miaA and LOG) in S2-8-1 under SYC conditions
+    explanation: Supports reported transcript upregulation specifically in S2-8-1, not direct pathway activity or
+      causal mediation of other endpoints.
+  participating_taxa:
+  - preferred_term: Ensifer sp. S2-8-1
+    term:
+      id: NCBITaxon:106591
+      label: Ensifer
 related_ingredients:
 - preferred_term: nitrate
   chebi_term:
@@ -208,17 +225,36 @@ external_resources:
     explanation: Lists the primary publication for the SYC consortium.
 discussions:
 - discussion_id: syc_staging_and_manure_wastewater_recipe
-  prompt: Which precise cattle-manure wastewater composition, pre-modification sequence, staging interval, inoculation ratio,
-    temperature, and aeration conditions were used for the Ensifer sp. S2-8-1/Bacillus subtilis SYC consortium?
+  prompt: Which precise cattle-manure wastewater composition, pre-modification sequence, staging interval, inoculation
+    ratio, temperature, and aeration conditions were used for the Ensifer sp. S2-8-1/Bacillus subtilis SYC consortium?
   kind: KNOWLEDGE_GAP
   status: OPEN
   attaches_to:
   - growth_media#cattle manure wastewater
   - environmental_factors#staged consortium assembly
-  rationale: The PubMed abstract names the two strains, staged design, cattle manure wastewater feedstock, and day-12 outcome,
-    but it does not expose the full staging or medium protocol needed to reproduce the fermentation.
+  rationale: The PubMed abstract names the two strains, staged design, cattle manure wastewater feedstock, and day-12
+    outcome, but it does not expose the full staging or medium protocol needed to reproduce the fermentation.
   posed_by: codex
   posed_date: '2026-09-22'
+- discussion_id: syc_transcripts_and_endpoint_mediation
+  prompt: Does the S2-8-1 transcript response causally mediate the separately reported broth and maize endpoints?
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  attaches_to:
+  - ecological_interactions#Staged cattle-manure wastewater valorization
+  - ecological_interactions#SYC rhizosphere nitrification and maize promotion
+  - ecological_interactions#S2-8-1 nitrogen and cytokinin-related gene upregulation
+  rationale: The accessible abstract reports comparative transcript abundance and suggests coordinated pathway activation.
+    It does not isolate the transcript changes as causal mediators. Keep the observed endpoints separate, the transcript
+    node scoped only to Ensifer, and no downstream arrows. Exact full-text methods were not read.
+  evidence:
+  - reference: PMID:42341825
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Comparative metatranscriptomic analysis revealed significant upregulation of heterotrophic ammonia
+      oxidation-related genes (CYP450) and cytokinin-related genes (miaA and LOG) in S2-8-1 under SYC conditions
+    explanation: Supports reported transcript upregulation specifically in S2-8-1, not direct pathway activity or
+      causal mediation of other endpoints.
 metals_present: []
 rare_earth_elements_present: []
 metal_relevance: NOT_APPLICABLE
@@ -228,11 +264,20 @@ curation_history:
 - timestamp: '2026-09-22T09:18:04Z'
   curator: codex
   action: ADD_COMMUNITY_RECORD
-  changes: Added a staged two-member Ensifer sp. S2-8-1 and Bacillus subtilis cattle-manure wastewater SynCom from PMID:42341825.
+  changes: Added a staged two-member Ensifer sp. S2-8-1 and Bacillus subtilis cattle-manure wastewater SynCom from
+    PMID:42341825.
   llm_assisted: true
 - timestamp: '2026-09-22T09:24:41Z'
   curator: codex
   action: FIX_ADVERSARIAL_REVIEW_FINDINGS
-  changes: Removed unsupported cross-feeder roles, reclassified soil-maize pot evidence as in vivo, and narrowed the metatranscriptomic
-    interaction to observed S2-8-1 gene upregulation under SYC conditions.
+  changes: Removed unsupported cross-feeder roles, reclassified soil-maize pot evidence as in vivo, and narrowed
+    the metatranscriptomic interaction to observed S2-8-1 gene upregulation under SYC conditions.
+  llm_assisted: true
+- timestamp: '2026-10-08T01:27:46Z'
+  curator: codex
+  action: REVIEW_CAUSAL_GRAPH
+  changes: Retain tested broth-density comparison without universal stability or reciprocal-benefit claims.; Preserve
+    positive maize-pot endpoints and the water-control dry-matter comparator without inferred mediator arrows.;
+    Restrict the transcript observation to canonical Ensifer S2-8-1 and distinguish it from protein activity, flux
+    or causal mediation. Issue#1826; reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
   llm_assisted: true
diff --git a/reports/causal_graph_review/README.md b/reports/causal_graph_review/README.md
index ada6f42be..560a8ca1a 100644
--- a/reports/causal_graph_review/README.md
+++ b/reports/causal_graph_review/README.md
@@ -1236,3 +1236,27 @@ Primary read and access limits are recorded; no raw-data reanalysis, new topolog
 or Edison spend. Repairs #1816-#1819 await protected-main merge; identity #1820
 and non-graph #1821 stay open. Self-review is not independent approval or
 corpus completion.
+
+## Batch105: Endpoints And Mechanism Boundaries
+
+[Decisions](decisions/20261008-four-records-batch105.yaml),
+[validation](validation-20261008-batch105.json),
+[cache provenance](cache-provenance-20261008-batch105.json) and
+[self-adversarial review](adversarial-review-20261008-batch105.yaml) cover the
+space-habitat, phenanthrene-carbon, lignin-dimer and staged cattle-manure records.
+All nine nodes remain; one existing direction is explicitly hypothetical and
+one substrate-range restatement arrow is removed. Reduced colony recovery does
+not establish reciprocal competition or definitive viability loss. Soil carbon
+stocks are distinct from fixation flux, muconate conversion from gallate
+potential, and Ensifer-specific transcript abundance from proven mediation.
+Positive observed outcomes and their comparison groups are retained.
+The whole lignin abstract supports six linkage classes; the three retained
+class snippets are representative, not exhaustive quotations.
+All caches and non-graph raw blocks remain unchanged, not recertified.
+Space-habitat primary body coverage is bounded; the other three reviews are
+abstract-limited. No new topology, provider spend or biological optimization
+procedures are introduced. Repairs #1823-#1826 await protected-main merge;
+non-graph #1827 stays open. Prior #847 concerns interaction typing, not
+environmental grounding; the new issue and review metadata were corrected
+without changing old histories. Self-review is not independent approval or
+corpus completion.
diff --git a/reports/causal_graph_review/adversarial-review-20261008-batch105.yaml b/reports/causal_graph_review/adversarial-review-20261008-batch105.yaml
new file mode 100644
index 000000000..ec1735ff2
--- /dev/null
+++ b/reports/causal_graph_review/adversarial-review-20261008-batch105.yaml
@@ -0,0 +1,244 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5d8eb3bd131fbf5c259038a2d45de27a39de0c72
+scope:
+- kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
+- kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
+- kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
+- kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
+decision_ledger: reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+validation_report: reports/causal_graph_review/validation-20261008-batch105.json
+findings:
+- issue: 1823
+  severity: P2
+  status: addressed_in_this_change
+  finding: Separate space-habitat cultivability result from categorical competition
+  disposition: Close only after protected-main merge.
+- issue: 1824
+  severity: P2
+  status: addressed_in_this_change
+  finding: Separate phenanthrene SynCom carbon stocks from fixation flux
+  disposition: Close only after protected-main merge.
+- issue: 1825
+  severity: P2
+  status: addressed_in_this_change
+  finding: Qualify lignin-dimer coupling and distinguish muconate results from gallate potential
+  disposition: Close only after protected-main merge.
+- issue: 1826
+  severity: P2
+  status: addressed_in_this_change
+  finding: Scope staged manure SynCom transcript evidence to Ensifer S2-8-1
+  disposition: Close only after protected-main merge.
+- issue: 1827
+  severity: P2
+  status: open_non_graph_follow_up
+  finding: Audit abundance and functional-role evidence in Sphingobium and manure SynCom records
+  disposition: Separate non-graph curation required.
+adversarial_checks:
+- 'Whole original targets and all changed graph/discussion diffs reviewed. All9 original nodes and2 directions have
+  dispositions: retain9nodes and1 qualified existing direction, remove1 substrate-range restatement arrow, rename3nodes.
+  No new topology or provider spend.'
+- 'Challenge removal versus lost evidence: retain positive colony-recovery, phenanthrene removal, soil carbon-content,
+  lignin-conversion, broth-density, maize-pot and transcript observations. Removing categorical mechanism labels
+  does not reject the source results.'
+- 'Space habitat: reduced B. subtilis CFU is cultivability, not definitive viability loss or reciprocal negative
+  effects. The canonical B. subtilis participant remains. Genomic potential is not confirmed metabolite activity.
+  Prior accession repair771 preserved; no new survival, stress-tolerance, biofilm, resistance, virulence, culture
+  or disinfection optimization details.'
+- 'Phenanthrene: soil carbon stocks and modeled guild associations are not measured fixation flux or traced carbon
+  transfer. Keep positive lettuce-pot endpoints with IN_VIVO evidence and partial statistical interpretation. Existing
+  random-forest/PLS-PM methods are preserved without invented software versions. Prior847/848 changes remain; those
+  open issues are not duplicated.'
+- 'Lignin: the source describes coculture systems plural, not demonstrated simultaneous products in one formulation.
+  Preserve observed muconate conversion separately from gallate potential and reuse the existing local CHEBI16918
+  descriptor. Whole primary abstract confirms all six linkage classes; the three retained class snippets are representative
+  examples, not exhaustive quotations. Remove the background-study quotation and ecological niche label; keep the
+  existing cleavage-to-conversion direction only as HYPOTHESIZED/PARTIAL.'
+- 'Manure: preserve distinct broth-density and water-control plant comparators; keep observed transcript upregulation
+  rather than direct activity, flux or pathway mediation. Narrow the transcript node to canonical identity-only
+  Ensifer S2-8-1. No inferred transcript-to-broth or transcript-to-host edges. Earlier cross-feeder removals and
+  IN_VIVO pot classification preserved.'
+- Seventeen graph and five discussion quotations match fresh primary text and unchanged caches. Space-habitat main-text
+  coverage is bounded; three other sources are abstract-only. Wiley redirected to an abstract/access page; OUP and
+  the phenanthrene DOI requests returned Internal Error, not a verified HTTP403. No global full-text absence claim,
+  bypass, cache import, supplement/figure-pixel or raw-data certification.
+- Four guarded writes and four append-only histories;456 other records/all923 caches and prior history/decision
+  files byte-identical. Non-graph raw blocks unchanged. Ensifer-only transcript scope does not change the global
+  community-level census because other whole-consortium observations remain. No census threshold, schema or runtime-rule
+  changes.
+- Eight focused tests and951 combined regressions pass. Four full-record schema/strict/term/reference/snippet checks
+  and four histories validate. Network equals56 baseline warnings with zero structural defects. Deterministic rendering
+  and exact HTML parser cover456pages/1373descriptions/550arrows, not screenshots. Plain just-lint passed; explicit-runtime
+  no-incremental mypy additionally checked.
+- Repairs1823-1826 addressed but remain open until protected-main merge; non-graph1827 remains open. Existing license949,
+  loader1703, DOIcache1091, denied and unansweredEdison scopes are not resolved. Self-review is not independent
+  approval; no artificial CI, protection bypass or premature cleanup.
+- Corpus334reviewed/76pending/50needs_research is not completion. Postcommit docs-current and exact-head publication
+  require separate receipts, not preasserted here.
+verification:
+  combined_regressions: 951 passed in 379.05s (0:06:19)
+  new_regression_tests: 8
+  total_recorded_gate_outputs: 42
+  primary_graph_snippet_proof:
+    graph_quotations: 17
+    new_discussion_quotations: 5
+    fresh_primary_literal_matches: 22
+    all_cached_literal_matches: 22
+    retained_nodes: 9
+    removed_nodes: 0
+    retained_arrows: 1
+    removed_arrows: 1
+    new_nodes_or_directions: 0
+    scope: All reviewed quotations match fresh primary text and unchanged existing caches literally after normalization;
+      entailment separately reviewed. Phenanthrene, lignin and manure abstracts only; space-habitat source has bounded
+      main-text coverage. No cache text or audit exception.
+  references: Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091
+    remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total
+    checks counts issues,not executed checks. Loader1703 not certified.
+  snippet_counts_by_record:
+    kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml:
+      MATCH: 20
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml:
+      MATCH: 17
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml:
+      MATCH: 23
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+    kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml:
+      MATCH: 17
+      RENDERING: 0
+      ASSEMBLED: 0
+      WEAK: 0
+      MISMATCH: 0
+      NOCONTENT: 0
+  full_corpus_snippet_audit:
+    counts:
+      records: 460
+      total: 8956
+      categories:
+        MATCH: 8820
+        RENDERING: 20
+        ASSEMBLED: 1
+        WEAK: 0
+        MISMATCH: 39
+        NOCONTENT: 76
+    caveat: Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.
+  network:
+    existing_findings_preserved: 56
+    added_findings: {}
+    removed_findings: {}
+    interpretation: One substrate-range restatement arrow removed; all nine nodes retained with qualified mechanisms
+      and one scoped transcript node; all56existing warnings unchanged and zero structural defects. No audit rules
+      changed.
+  tested_file_sha256:
+    reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml: 3d64b6bccead35688461e4485e84ed02d2118a45ffc71bb36a99c579f02a56d9
+    tests/test_causal_review_batch105.py: 253024f0a23a9313cbb2dd062051e60e7a5299895c1cb6ba2bf626666cf4c8e2
+    tests/test_participating_taxa.py: 0685ac6f4a721680ccb3967614b1411c59f553ccc45d485582d11126abfa9f9a
+    tests/test_community_level_connectivity_credit.py: 383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c
+    reports/causal_graph_review/cache-provenance-20261008-batch105.json: eca35700399c0be5808426ebbd9e899e3549d787825d9d95c34a9b888abc1d06
+    kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml: 0304999156eeec1556a337ff0138a6bfce205c38b9d5a8010051d864949a2a7f
+    kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml: e2555ecc152f3bbdbb5c2d557a17fc46da135500092494e0379c73fbb85c117a
+    kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml: fa5b1abb2f9493bb52263f1041fe4075028d57daf40abe7cd804edd6c65aa05c
+    kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml: ece6ced257acf7538a072ee6fb940f73d96f0f36d83a6e1eae1514356884ab12
+  unchanged_records: 456
+  unchanged_caches: 923
+  immutable_prior_history_and_decision_files: 812
+  cache_changes: []
+  edison:
+    required_for_this_repair: false
+    required_for_unresolved_extensions: false
+    provider_submissions: 0
+    credits_spent: 0
+    dry_runs: []
+    repair_scope: Qualify existing observation/mechanism boundaries and narrow member scope; retain one qualified
+      existing direction and remove one restatement. No new mechanisms or directions.
+  post_commit_docs_current: Separate publication gate, not preasserted.
+participant_census:
+  measurements:
+    baseline:
+      records: 460
+      with_community_level: 403
+      mixed: 128
+      community_level_only: 275
+      taxa: 1544
+      credited_solely_by_the_rule: 1270
+    current:
+      records: 460
+      with_community_level: 403
+      mixed: 128
+      community_level_only: 275
+      taxa: 1544
+      credited_solely_by_the_rule: 1270
+  delta:
+    records: 0
+    with_community_level: 0
+    mixed: 0
+    community_level_only: 0
+    taxa: 0
+    credited_solely_by_the_rule: 0
+  interpretation: Manure transcript node gains identity-only Ensifer scope. Other community-level observations still
+    encompass the consortium, so the global census is unchanged. No census threshold or runtime rule changes.
+corpus:
+  records: 460
+  nodes: 1387
+  edges: 558
+  review_status_counts:
+    needs_research: 50
+    pending: 76
+    reviewed: 334
+lint_limitation: Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.
+lint_environment:
+  path: /private/tmp/communitymech-batch100/lint-env
+  scope: Temporary Python3.13 lint environment reuses validation runtime and locked mypy1.19.1/stubs/scikit-learn1.8.0/pacmap0.9.1
+    for static checks; not a complete embedding runtime. Project dependencies unchanged.
+limitations:
+- 'Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural
+  defects. Four whole records and all9 original nodes/2 directions reviewed; all9 nodes and one qualified direction
+  retained, one restatement arrow removed, three renames. No new topology or Edison submission/spend.'
+- Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery
+  and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure pixels
+  or raw-data certification.
+- Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing
+  abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access
+  page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full bodies
+  or supplements read, no bypass; no global assertion of full-text absence.
+- Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All
+  retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports or
+  license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher notices
+  retained.
+- 'Space habitat: preserve reduced recoverable B. subtilis CFU and canonical participant; remove COMPETITION because
+  reciprocal negative effects are not established. Cultivability is not definitive viability loss; genomic potential
+  is not confirmed activity. No new stress-survival, resistance, virulence, biofilm, culture or disinfection optimization
+  procedures or genetic designs.'
+- 'Phenanthrene: retain positive lettuce-pot removal and carbon-content endpoints with IN_VIVO provenance. Carbon
+  stocks and statistical guild associations do not establish carbon-fixation flux or traced transfer. Existing model
+  methods retained without invented software versions; causal interpretation PARTIAL. Prior847/848 interaction-typing
+  and provenance fixes preserved.'
+- 'Lignin: source systems plural; retain designed pairwise cleavage/conversion coupling and existing arrow as HYPOTHESIZED/PARTIAL.
+  Remove background-study evidence and categorical cross-feeding/niche-partitioning. Retain observed muconate conversion
+  and qualified gallate potential, not simultaneous production by one formulation. Reuse existing local CHEBI16918
+  gallate descriptor; keep substrate-range node without its restatement arrow.'
+- 'Manure: retain broth and positive plant observations with their distinct comparators. Scope transcript upregulation
+  to identity-only Ensifer S2-8-1. Transcript abundance is not protein activity, flux or proven mediation; no new
+  arrows. Preserve earlier cross-feeder-role removals and IN_VIVO pot classification. Full protocols not certified.'
+- Graph issues1823-1826 addressed here and remain open until protected-main merge; non-graph1827 remains open. Fresh
+  all-state title/body dedup matches771/847/848. Hidden/ignored local search excludes.git/docs/site/references_cache
+  with relevant caches separately covered. PRs/comments not exhaustively searched. Abundance, functional roles,
+  broad source-formulation text and protocol blocks remain separately scoped.
+- Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw
+  block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or
+  corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted.
diff --git a/reports/causal_graph_review/cache-provenance-20261008-batch105.json b/reports/causal_graph_review/cache-provenance-20261008-batch105.json
new file mode 100644
index 000000000..9e449d156
--- /dev/null
+++ b/reports/causal_graph_review/cache-provenance-20261008-batch105.json
@@ -0,0 +1,134 @@
+{
+  "changes": [],
+  "unchanged_cache_files": 923,
+  "primary_artifacts": {
+    "/private/tmp/communitymech-batch105/baseline.json": "cc7fef283bf49b67d5c3e8b0edc947012b71370b73db9cb25458cdf2ddfcba45",
+    "/private/tmp/communitymech-batch105/dedup-local-current.txt": "037e30d7f1b0ce11a2549fa6d6c75e39a6f4db6e208b16636024dd5f59547188",
+    "/private/tmp/communitymech-batch105/issue-dedup-current.json": "83c3bbd2eb342c8704a7dc42d5521a6ed2048817e9780a9df8eece5434cd16da",
+    "/private/tmp/communitymech-batch105/lignin-metadata.json": "d66d4f9f22950368363517a79b4619479749f70e3960a718e6761af78b37f3bd",
+    "/private/tmp/communitymech-batch105/lignin-primary.txt": "0d14a9faeb798fcc1c752695dc5dce2c69fe9b8e9bd4bdeec388480125a5a17d",
+    "/private/tmp/communitymech-batch105/manure-metadata.json": "590d2e83dd3d0403da375f13811c565802f0c952ef22ef1a34c5c37da0eda32b",
+    "/private/tmp/communitymech-batch105/manure-primary.txt": "e0323f52c06d476379635c23a180fd919b75ee3183142d54e160f6363f896285",
+    "/private/tmp/communitymech-batch105/phenanthrene-metadata.json": "f1ce256f7915a72a661a220e9f39e5404911bf693a89f25fcc7d2d0dab971e50",
+    "/private/tmp/communitymech-batch105/phenanthrene-primary.txt": "454a182a7d0ecdab2e585d8122d3f48c2d46b0ed7ed17a1990bdad369d5a4e11",
+    "/private/tmp/communitymech-batch105/primary-manifest.json": "65cf37f6b534c9fa426603097c5fa6fd79e327449b07741933a6b5a3d09c61dc",
+    "/private/tmp/communitymech-batch105/space-metadata.json": "baf4e412a0c4b811860759b6b3f37858f44f3939ff8a1a22f5f043144d08bf84",
+    "/private/tmp/communitymech-batch105/space-primary.txt": "5bd9cd763bf160b068693b0d59203267bdf46bde1904d288835b409862f99648",
+    "/private/tmp/communitymech-batch105/space-primary.xml": "aeff0a81952a082f19fb10ea55f7f9dbb7a0050bf124ad74e20f2ce1a40c3443",
+    "references_cache/PMID_36030484.md": "3e24765eec279e51e901b45dde5e55b9f38e0d084057d7d4a2d0bb90aa3ff0de",
+    "references_cache/PMID_41967346.txt": "a19795680b6181bc527ebd3318bc404d9ea467a9ccac1f62b2c2cffef0cfc168",
+    "references_cache/PMID_42341825.txt": "a4e640e63bca23c67aa87994c53c09642f9c2c62920f71e576cb4dc64bb9c21e",
+    "references_cache/PMID_42577390.md": "9473c68e543cdd3bd59af3190f1f7c4fc560e9f364d55d653c5427da0f13dc9c"
+  },
+  "source_access": {
+    "retrieval_manifest": {
+      "space": {
+        "reference": "PMID:42577390",
+        "title": "Community matters: stress tolerance and survival of &lt;i&gt;Bacillus subtilis&lt;/i&gt; and &lt;i&gt;Staphylococcus capitis&lt;/i&gt; in a synthetic space habitat consortium.",
+        "pmid": "42577390",
+        "pmcid": "PMC13454065",
+        "doi": "10.3389/fmicb.2026.1869903",
+        "publication_types": {
+          "pubType": [
+            "research-article",
+            "Journal Article"
+          ]
+        },
+        "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13454065/fullTextXML",
+        "source": "/private/tmp/communitymech-batch105/space-primary.xml",
+        "source_sha256": "aeff0a81952a082f19fb10ea55f7f9dbb7a0050bf124ad74e20f2ce1a40c3443",
+        "metadata": "/private/tmp/communitymech-batch105/space-metadata.json",
+        "extracted_body": "/private/tmp/communitymech-batch105/space-primary.txt",
+        "body_sha256": "5bd9cd763bf160b068693b0d59203267bdf46bde1904d288835b409862f99648",
+        "body_lines": 1388,
+        "scope": "Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.",
+        "license": "Copyright \u00a9 2026 Kr\u00e4mer, Ly-Sauerbrey, Maier, Kadler, Rehm, Walkenfort, Neidh\u00f6fer, Leuko, Schwengers, Hasenberg, Timofeev, Janssen, Beblo-Vranesevic and D\u00f6scher-Siems.This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.",
+        "fulltext_error": null
+      },
+      "phenanthrene": {
+        "reference": "PMID:41967346",
+        "title": "SynCom improves carbon fixation capacity in phenanthrene-contaminated soils by reshaping microbial communities.",
+        "pmid": "41967346",
+        "pmcid": null,
+        "doi": "10.1016/j.jenvman.2026.129643",
+        "publication_types": {
+          "pubType": [
+            "Journal Article"
+          ]
+        },
+        "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41967346+AND+SRC%3AMED&format=json&resultType=core",
+        "source": "/private/tmp/communitymech-batch105/phenanthrene-metadata.json",
+        "source_sha256": "f1ce256f7915a72a661a220e9f39e5404911bf693a89f25fcc7d2d0dab971e50",
+        "metadata": "/private/tmp/communitymech-batch105/phenanthrene-metadata.json",
+        "extracted_body": "/private/tmp/communitymech-batch105/phenanthrene-primary.txt",
+        "body_sha256": "454a182a7d0ecdab2e585d8122d3f48c2d46b0ed7ed17a1990bdad369d5a4e11",
+        "body_lines": 15,
+        "scope": "Abstract only; complete main body not retrieved through EuropePMC.",
+        "license": "See publisher",
+        "fulltext_error": null
+      },
+      "lignin": {
+        "reference": "PMID:36030484",
+        "title": "Developing Rhodococcus opacus and Sphingobium sp. coculture systems for valorization of lignin-derived dimers.",
+        "pmid": "36030484",
+        "pmcid": null,
+        "doi": "10.1002/bit.28215",
+        "publication_types": {
+          "pubType": [
+            "Research Support, Non-U.S. Gov't",
+            "Journal Article"
+          ]
+        },
+        "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A36030484+AND+SRC%3AMED&format=json&resultType=core",
+        "source": "/private/tmp/communitymech-batch105/lignin-metadata.json",
+        "source_sha256": "d66d4f9f22950368363517a79b4619479749f70e3960a718e6761af78b37f3bd",
+        "metadata": "/private/tmp/communitymech-batch105/lignin-metadata.json",
+        "extracted_body": "/private/tmp/communitymech-batch105/lignin-primary.txt",
+        "body_sha256": "0d14a9faeb798fcc1c752695dc5dce2c69fe9b8e9bd4bdeec388480125a5a17d",
+        "body_lines": 15,
+        "scope": "Abstract only; complete main body not retrieved through EuropePMC.",
+        "license": "See publisher",
+        "fulltext_error": null
+      },
+      "manure": {
+        "reference": "PMID:42341825",
+        "title": "Staged microbial consortium valorizes cattle manure wastewater and promotes maize growth.",
+        "pmid": "42341825",
+        "pmcid": null,
+        "doi": "10.1093/jambio/lxag151",
+        "publication_types": {
+          "pubType": [
+            "Journal Article"
+          ]
+        },
+        "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42341825+AND+SRC%3AMED&format=json&resultType=core",
+        "source": "/private/tmp/communitymech-batch105/manure-metadata.json",
+        "source_sha256": "590d2e83dd3d0403da375f13811c565802f0c952ef22ef1a34c5c37da0eda32b",
+        "metadata": "/private/tmp/communitymech-batch105/manure-metadata.json",
+        "extracted_body": "/private/tmp/communitymech-batch105/manure-primary.txt",
+        "body_sha256": "e0323f52c06d476379635c23a180fd919b75ee3183142d54e160f6363f896285",
+        "body_lines": 18,
+        "scope": "Abstract only; complete main body not retrieved through EuropePMC.",
+        "license": "See publisher",
+        "fulltext_error": null
+      }
+    },
+    "actual_read_scope": [
+      "Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure pixels or raw-data certification.",
+      "Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full bodies or supplements read, no bypass; no global assertion of full-text absence.",
+      "Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports or license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher notices retained."
+    ]
+  },
+  "limitations": [
+    "Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Four whole records and all9 original nodes/2 directions reviewed; all9 nodes and one qualified direction retained, one restatement arrow removed, three renames. No new topology or Edison submission/spend.",
+    "Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure pixels or raw-data certification.",
+    "Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full bodies or supplements read, no bypass; no global assertion of full-text absence.",
+    "Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports or license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher notices retained.",
+    "Space habitat: preserve reduced recoverable B. subtilis CFU and canonical participant; remove COMPETITION because reciprocal negative effects are not established. Cultivability is not definitive viability loss; genomic potential is not confirmed activity. No new stress-survival, resistance, virulence, biofilm, culture or disinfection optimization procedures or genetic designs.",
+    "Phenanthrene: retain positive lettuce-pot removal and carbon-content endpoints with IN_VIVO provenance. Carbon stocks and statistical guild associations do not establish carbon-fixation flux or traced transfer. Existing model methods retained without invented software versions; causal interpretation PARTIAL. Prior847/848 interaction-typing and provenance fixes preserved.",
+    "Lignin: source systems plural; retain designed pairwise cleavage/conversion coupling and existing arrow as HYPOTHESIZED/PARTIAL. Remove background-study evidence and categorical cross-feeding/niche-partitioning. Retain observed muconate conversion and qualified gallate potential, not simultaneous production by one formulation. Reuse existing local CHEBI16918 gallate descriptor; keep substrate-range node without its restatement arrow.",
+    "Manure: retain broth and positive plant observations with their distinct comparators. Scope transcript upregulation to identity-only Ensifer S2-8-1. Transcript abundance is not protein activity, flux or proven mediation; no new arrows. Preserve earlier cross-feeder-role removals and IN_VIVO pot classification. Full protocols not certified.",
+    "Graph issues1823-1826 addressed here and remain open until protected-main merge; non-graph1827 remains open. Fresh all-state title/body dedup matches771/847/848. Hidden/ignored local search excludes.git/docs/site/references_cache with relevant caches separately covered. PRs/comments not exhaustively searched. Abundance, functional roles, broad source-formulation text and protocol blocks remain separately scoped.",
+    "Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted."
+  ]
+}
diff --git a/reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml b/reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
new file mode 100644
index 000000000..f70888581
--- /dev/null
+++ b/reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
@@ -0,0 +1,566 @@
+reviewer: codex
+review_mode: source_based_self_adversarial_review
+independent_approval: false
+base_commit: 5d8eb3bd131fbf5c259038a2d45de27a39de0c72
+baseline_commit: 5d8eb3bd131fbf5c259038a2d45de27a39de0c72
+base_tree: fb89729566c9f3cbbb9237c3fcbde18e7cf52e59
+pre_source_baseline_sha256: cc7fef283bf49b67d5c3e8b0edc947012b71370b73db9cb25458cdf2ddfcba45
+issues:
+- 1823
+- 1824
+- 1825
+- 1826
+unresolved_research_issues: []
+unresolved_non_graph_issues:
+- 1827
+issue_deduplication:
+  all_state_issue_titles_and_bodies: 1076
+  matching_issues:
+  - 771
+  - 847
+  - 848
+  ignored_hidden_local_search: true
+source_access:
+  retrieval_manifest:
+    space:
+      reference: PMID:42577390
+      title: 'Community matters: stress tolerance and survival of &lt;i&gt;Bacillus subtilis&lt;/i&gt; and &lt;i&gt;Staphylococcus
+        capitis&lt;/i&gt; in a synthetic space habitat consortium.'
+      pmid: '42577390'
+      pmcid: PMC13454065
+      doi: 10.3389/fmicb.2026.1869903
+      publication_types:
+        pubType:
+        - research-article
+        - Journal Article
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13454065/fullTextXML
+      source: /private/tmp/communitymech-batch105/space-primary.xml
+      source_sha256: aeff0a81952a082f19fb10ea55f7f9dbb7a0050bf124ad74e20f2ce1a40c3443
+      metadata: /private/tmp/communitymech-batch105/space-metadata.json
+      extracted_body: /private/tmp/communitymech-batch105/space-primary.txt
+      body_sha256: 5bd9cd763bf160b068693b0d59203267bdf46bde1904d288835b409862f99648
+      body_lines: 1388
+      scope: Complete main body retrieved, not yet read; no figure-pixel/supplement/raw-data review implied.
+      license: "Copyright \xA9 2026 Kr\xE4mer, Ly-Sauerbrey, Maier, Kadler, Rehm, Walkenfort, Neidh\xF6fer, Leuko,\
+        \ Schwengers, Hasenberg, Timofeev, Janssen, Beblo-Vranesevic and D\xF6scher-Siems.This is an open-access\
+        \ article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution\
+        \ or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s)\
+        \ are credited and that the original publication in this journal is cited, in accordance with accepted academic\
+        \ practice. No use, distribution or reproduction is permitted which does not comply with these terms."
+      fulltext_error: null
+    phenanthrene:
+      reference: PMID:41967346
+      title: SynCom improves carbon fixation capacity in phenanthrene-contaminated soils by reshaping microbial
+        communities.
+      pmid: '41967346'
+      pmcid: null
+      doi: 10.1016/j.jenvman.2026.129643
+      publication_types:
+        pubType:
+        - Journal Article
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A41967346+AND+SRC%3AMED&format=json&resultType=core
+      source: /private/tmp/communitymech-batch105/phenanthrene-metadata.json
+      source_sha256: f1ce256f7915a72a661a220e9f39e5404911bf693a89f25fcc7d2d0dab971e50
+      metadata: /private/tmp/communitymech-batch105/phenanthrene-metadata.json
+      extracted_body: /private/tmp/communitymech-batch105/phenanthrene-primary.txt
+      body_sha256: 454a182a7d0ecdab2e585d8122d3f48c2d46b0ed7ed17a1990bdad369d5a4e11
+      body_lines: 15
+      scope: Abstract only; complete main body not retrieved through EuropePMC.
+      license: See publisher
+      fulltext_error: null
+    lignin:
+      reference: PMID:36030484
+      title: Developing Rhodococcus opacus and Sphingobium sp. coculture systems for valorization of lignin-derived
+        dimers.
+      pmid: '36030484'
+      pmcid: null
+      doi: 10.1002/bit.28215
+      publication_types:
+        pubType:
+        - Research Support, Non-U.S. Gov't
+        - Journal Article
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A36030484+AND+SRC%3AMED&format=json&resultType=core
+      source: /private/tmp/communitymech-batch105/lignin-metadata.json
+      source_sha256: d66d4f9f22950368363517a79b4619479749f70e3960a718e6761af78b37f3bd
+      metadata: /private/tmp/communitymech-batch105/lignin-metadata.json
+      extracted_body: /private/tmp/communitymech-batch105/lignin-primary.txt
+      body_sha256: 0d14a9faeb798fcc1c752695dc5dce2c69fe9b8e9bd4bdeec388480125a5a17d
+      body_lines: 15
+      scope: Abstract only; complete main body not retrieved through EuropePMC.
+      license: See publisher
+      fulltext_error: null
+    manure:
+      reference: PMID:42341825
+      title: Staged microbial consortium valorizes cattle manure wastewater and promotes maize growth.
+      pmid: '42341825'
+      pmcid: null
+      doi: 10.1093/jambio/lxag151
+      publication_types:
+        pubType:
+        - Journal Article
+      url: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID%3A42341825+AND+SRC%3AMED&format=json&resultType=core
+      source: /private/tmp/communitymech-batch105/manure-metadata.json
+      source_sha256: 590d2e83dd3d0403da375f13811c565802f0c952ef22ef1a34c5c37da0eda32b
+      metadata: /private/tmp/communitymech-batch105/manure-metadata.json
+      extracted_body: /private/tmp/communitymech-batch105/manure-primary.txt
+      body_sha256: e0323f52c06d476379635c23a180fd919b75ee3183142d54e160f6363f896285
+      body_lines: 18
+      scope: Abstract only; complete main body not retrieved through EuropePMC.
+      license: See publisher
+      fulltext_error: null
+  actual_read_scope:
+  - Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery
+    and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure
+    pixels or raw-data certification.
+  - Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing
+    abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access
+    page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full
+    bodies or supplements read, no bypass; no global assertion of full-text absence.
+  - Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All
+    retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports
+    or license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher
+    notices retained.
+primary_artifacts:
+  /private/tmp/communitymech-batch105/baseline.json: cc7fef283bf49b67d5c3e8b0edc947012b71370b73db9cb25458cdf2ddfcba45
+  /private/tmp/communitymech-batch105/dedup-local-current.txt: 037e30d7f1b0ce11a2549fa6d6c75e39a6f4db6e208b16636024dd5f59547188
+  /private/tmp/communitymech-batch105/issue-dedup-current.json: 83c3bbd2eb342c8704a7dc42d5521a6ed2048817e9780a9df8eece5434cd16da
+  /private/tmp/communitymech-batch105/lignin-metadata.json: d66d4f9f22950368363517a79b4619479749f70e3960a718e6761af78b37f3bd
+  /private/tmp/communitymech-batch105/lignin-primary.txt: 0d14a9faeb798fcc1c752695dc5dce2c69fe9b8e9bd4bdeec388480125a5a17d
+  /private/tmp/communitymech-batch105/manure-metadata.json: 590d2e83dd3d0403da375f13811c565802f0c952ef22ef1a34c5c37da0eda32b
+  /private/tmp/communitymech-batch105/manure-primary.txt: e0323f52c06d476379635c23a180fd919b75ee3183142d54e160f6363f896285
+  /private/tmp/communitymech-batch105/phenanthrene-metadata.json: f1ce256f7915a72a661a220e9f39e5404911bf693a89f25fcc7d2d0dab971e50
+  /private/tmp/communitymech-batch105/phenanthrene-primary.txt: 454a182a7d0ecdab2e585d8122d3f48c2d46b0ed7ed17a1990bdad369d5a4e11
+  /private/tmp/communitymech-batch105/primary-manifest.json: 65cf37f6b534c9fa426603097c5fa6fd79e327449b07741933a6b5a3d09c61dc
+  /private/tmp/communitymech-batch105/space-metadata.json: baf4e412a0c4b811860759b6b3f37858f44f3939ff8a1a22f5f043144d08bf84
+  /private/tmp/communitymech-batch105/space-primary.txt: 5bd9cd763bf160b068693b0d59203267bdf46bde1904d288835b409862f99648
+  /private/tmp/communitymech-batch105/space-primary.xml: aeff0a81952a082f19fb10ea55f7f9dbb7a0050bf124ad74e20f2ce1a40c3443
+  references_cache/PMID_36030484.md: 3e24765eec279e51e901b45dde5e55b9f38e0d084057d7d4a2d0bb90aa3ff0de
+  references_cache/PMID_41967346.txt: a19795680b6181bc527ebd3318bc404d9ea467a9ccac1f62b2c2cffef0cfc168
+  references_cache/PMID_42341825.txt: a4e640e63bca23c67aa87994c53c09642f9c2c62920f71e576cb4dc64bb9c21e
+  references_cache/PMID_42577390.md: 9473c68e543cdd3bd59af3190f1f7c4fc560e9f364d55d653c5427da0f13dc9c
+primary_graph_snippet_count: 17
+snippet_checks:
+- record: Space_Habitat_SevenMember_Stress_Tolerance_SynCom
+  node: Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
+  evidence_index: 0
+  reference: PMID:42577390
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/space-primary.txt
+  cache_artifact: references_cache/PMID_42577390.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Space_Habitat_SevenMember_Stress_Tolerance_SynCom
+  node: Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
+  evidence_index: 1
+  reference: PMID:42577390
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/space-primary.txt
+  cache_artifact: references_cache/PMID_42577390.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom
+  node: SynCom phenanthrene removal in lettuce pots
+  evidence_index: 0
+  reference: PMID:41967346
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/phenanthrene-primary.txt
+  cache_artifact: references_cache/PMID_41967346.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom
+  node: SynCom soil carbon endpoints and modeled guild associations
+  evidence_index: 0
+  reference: PMID:41967346
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/phenanthrene-primary.txt
+  cache_artifact: references_cache/PMID_41967346.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom
+  node: SynCom soil carbon endpoints and modeled guild associations
+  evidence_index: 1
+  reference: PMID:41967346
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/phenanthrene-primary.txt
+  cache_artifact: references_cache/PMID_41967346.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling
+  evidence_index: 0
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Reported Lignin-Dimer Conversion Outcomes
+  evidence_index: 0
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Reported Lignin-Dimer Conversion Outcomes
+  evidence_index: 1
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Lignin-Dimer Linkage-Class Substrate Range
+  evidence_index: 0
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Lignin-Dimer Linkage-Class Substrate Range
+  evidence_index: 1
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: Lignin-Dimer Linkage-Class Substrate Range
+  evidence_index: 2
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: Staged cattle-manure wastewater valorization
+  evidence_index: 0
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: Staged cattle-manure wastewater valorization
+  evidence_index: 1
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: SYC rhizosphere nitrification and maize promotion
+  evidence_index: 0
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: SYC rhizosphere nitrification and maize promotion
+  evidence_index: 1
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: SYC rhizosphere nitrification and maize promotion
+  evidence_index: 2
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: S2-8-1 nitrogen and cytokinin-related gene upregulation
+  evidence_index: 0
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+discussion_snippet_checks:
+- record: Space_Habitat_SevenMember_Stress_Tolerance_SynCom
+  node: space_cultivability_not_reciprocal_competition
+  evidence_index: 0
+  reference: PMID:42577390
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/space-primary.txt
+  cache_artifact: references_cache/PMID_42577390.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Space_Habitat_SevenMember_Stress_Tolerance_SynCom
+  node: space_cultivability_not_reciprocal_competition
+  evidence_index: 1
+  reference: PMID:42577390
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/space-primary.txt
+  cache_artifact: references_cache/PMID_42577390.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom
+  node: phenanthrene_carbon_stocks_and_inferred_drivers
+  evidence_index: 0
+  reference: PMID:41967346
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/phenanthrene-primary.txt
+  cache_artifact: references_cache/PMID_41967346.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture
+  node: lignin_coupling_and_formulation_limits
+  evidence_index: 0
+  reference: PMID:36030484
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/lignin-primary.txt
+  cache_artifact: references_cache/PMID_36030484.md
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+- record: Staged_Cattle_Manure_Ensifer_Bacillus_SynCom
+  node: syc_transcripts_and_endpoint_mediation
+  evidence_index: 0
+  reference: PMID:42341825
+  cache_matched: true
+  independent_primary_match: true
+  matched_artifact: /private/tmp/communitymech-batch105/manure-primary.txt
+  cache_artifact: references_cache/PMID_42341825.txt
+  scope: Literal normalized match to fresh primary text and pre-existing cache; entailment separately reviewed.
+cache_changes: []
+edison:
+  required_for_this_repair: false
+  required_for_unresolved_extensions: false
+  provider_submissions: 0
+  credits_spent: 0
+  dry_runs: []
+  repair_scope: Qualify existing observation/mechanism boundaries and narrow member scope; retain one qualified
+    existing direction and remove one restatement. No new mechanisms or directions.
+limitations:
+- 'Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural
+  defects. Four whole records and all9 original nodes/2 directions reviewed; all9 nodes and one qualified direction
+  retained, one restatement arrow removed, three renames. No new topology or Edison submission/spend.'
+- Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery
+  and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure pixels
+  or raw-data certification.
+- Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing
+  abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access
+  page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full bodies
+  or supplements read, no bypass; no global assertion of full-text absence.
+- Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All
+  retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports or
+  license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher notices
+  retained.
+- 'Space habitat: preserve reduced recoverable B. subtilis CFU and canonical participant; remove COMPETITION because
+  reciprocal negative effects are not established. Cultivability is not definitive viability loss; genomic potential
+  is not confirmed activity. No new stress-survival, resistance, virulence, biofilm, culture or disinfection optimization
+  procedures or genetic designs.'
+- 'Phenanthrene: retain positive lettuce-pot removal and carbon-content endpoints with IN_VIVO provenance. Carbon
+  stocks and statistical guild associations do not establish carbon-fixation flux or traced transfer. Existing model
+  methods retained without invented software versions; causal interpretation PARTIAL. Prior847/848 interaction-typing
+  and provenance fixes preserved.'
+- 'Lignin: source systems plural; retain designed pairwise cleavage/conversion coupling and existing arrow as HYPOTHESIZED/PARTIAL.
+  Remove background-study evidence and categorical cross-feeding/niche-partitioning. Retain observed muconate conversion
+  and qualified gallate potential, not simultaneous production by one formulation. Reuse existing local CHEBI16918
+  gallate descriptor; keep substrate-range node without its restatement arrow.'
+- 'Manure: retain broth and positive plant observations with their distinct comparators. Scope transcript upregulation
+  to identity-only Ensifer S2-8-1. Transcript abundance is not protein activity, flux or proven mediation; no new
+  arrows. Preserve earlier cross-feeder-role removals and IN_VIVO pot classification. Full protocols not certified.'
+- Graph issues1823-1826 addressed here and remain open until protected-main merge; non-graph1827 remains open. Fresh
+  all-state title/body dedup matches771/847/848. Hidden/ignored local search excludes.git/docs/site/references_cache
+  with relevant caches separately covered. PRs/comments not exhaustively searched. Abundance, functional roles,
+  broad source-formulation text and protocol blocks remain separately scoped.
+- Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw
+  block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or
+  corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted.
+records:
+- path: kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml
+  id: CommunityMech:000339
+  original_sha256: dbb830353fcd0357f47df423b2258e9e06f87d1909cb84186a2cfa0d4e67d1ad
+  record_sha256: 0304999156eeec1556a337ff0138a6bfce205c38b9d5a8010051d864949a2a7f
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+  summary: Retain reduced B. subtilis colony recovery and its canonical participant; remove categorical competition
+    and distinguish cultivability from definitive viability loss.
+  node_decisions:
+  - node: Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation
+    rationale: Retain reduced B. subtilis colony recovery and its canonical participant; remove categorical competition
+      and distinguish cultivability from definitive viability loss.
+  removed_node_decisions: []
+  renamed_nodes: {}
+  edges_before: []
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions: []
+  references:
+  - PMID:42577390
+  issues:
+  - 1823
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Space_Habitat_SevenMember_Stress_Tolerance_SynCom/2026-10-08T012746Z-codex-2f9387.yaml
+- path: kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml
+  id: CommunityMech:000362
+  original_sha256: 18132fca169325f8c760a8c996a2d7fc882e516144f3a2a977c524b185899367
+  record_sha256: e2555ecc152f3bbdbb5c2d557a17fc46da135500092494e0379c73fbb85c117a
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+  summary: Retain positive lettuce-pot PHE outcomes with IN_VIVO provenance and no inferred exchange.; Retain carbon-content
+    measurements and qualify modeled drivers; remove carbon-dioxide/fixation annotations not established by stock
+    endpoints.
+  node_decisions:
+  - node: SynCom phenanthrene removal in lettuce pots
+    rationale: Retain positive lettuce-pot PHE outcomes with IN_VIVO provenance and no inferred exchange.
+  - node: SynCom soil carbon endpoints and modeled guild associations
+    rationale: Retain carbon-content measurements and qualify modeled drivers; remove carbon-dioxide/fixation annotations
+      not established by stock endpoints.
+  removed_node_decisions: []
+  renamed_nodes:
+    SynCom soil carbon restoration: SynCom soil carbon endpoints and modeled guild associations
+  edges_before: []
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions: []
+  references:
+  - PMID:41967346
+  issues:
+  - 1824
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom/2026-10-08T012747Z-codex-83fd7a.yaml
+- path: kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml
+  id: CommunityMech:000267
+  original_sha256: b9b3f065b918d17001a23b96660440448540e3a22aed4a4d9dd56f59a64645d0
+  record_sha256: fa5b1abb2f9493bb52263f1041fe4075028d57daf40abe7cd804edd6c65aa05c
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+  summary: Retain designed pairwise cleavage/conversion coupling and its existing direction as HYPOTHESIZED/PARTIAL;
+    remove the background-study quotation and categorical cross-feeding.; Preserve muconate conversion separately
+    from gallate potential across source systems; correct the graph gallate identity using the existing local descriptor.;
+    Retain reported dimer substrate coverage; remove niche-partitioning classification and the product restatement
+    arrow.
+  node_decisions:
+  - node: Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling
+    rationale: Retain designed pairwise cleavage/conversion coupling and its existing direction as HYPOTHESIZED/PARTIAL;
+      remove the background-study quotation and categorical cross-feeding.
+  - node: Reported Lignin-Dimer Conversion Outcomes
+    rationale: Preserve muconate conversion separately from gallate potential across source systems; correct the
+      graph gallate identity using the existing local descriptor.
+  - node: Lignin-Dimer Linkage-Class Substrate Range
+    rationale: Retain reported dimer substrate coverage; remove niche-partitioning classification and the product
+      restatement arrow.
+  removed_node_decisions: []
+  renamed_nodes:
+    Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling: Designed Lignin-Dimer Cleavage and Monomer-Conversion
+      Coupling
+    Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate: Reported Lignin-Dimer Conversion Outcomes
+  edges_before:
+  - &id001
+    source: Lignin-Dimer Cleavage Feeds Aromatic Monomer Funneling
+    target: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
+    description: 'Sphingobium cleavage of lignin-derived dimers supplies the monomers that R. opacus funnels into
+      cis,cis-muconate and gallate in the designed coculture.
+
+      '
+  - source: Lignin-Dimer Linkage-Class Substrate Range
+    target: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
+    description: 'Activity across beta-O-4, 4-O-5, and beta-5 dimer linkage classes broadens the substrate pool
+      that the Sphingobium-Rhodococcus coculture can funnel into cis,cis-muconate and gallate.
+
+      '
+  edges_after:
+  - &id002
+    source: Designed Lignin-Dimer Cleavage and Monomer-Conversion Coupling
+    target: Reported Lignin-Dimer Conversion Outcomes
+    description: 'HYPOTHESIZED/PARTIAL: dimer cleavage is the designed upstream step supplying substrates for monomer
+      conversion in the source coculture systems. The abstract implies this coupling but does not trace the transferred
+      intermediate, isolate its causal contribution, or demonstrate simultaneous muconate/gallate production by
+      one formulation.'
+  retained_edge_decisions:
+  - before: *id001
+    after: *id002
+    rationale: Existing source-grounded direction retained without extension.
+  removed_edge_decisions:
+  - source: Lignin-Dimer Linkage-Class Substrate Range
+    target: Funneling of Lignin-Derived Dimers to cis,cis-Muconate and Gallate
+    description: 'Activity across beta-O-4, 4-O-5, and beta-5 dimer linkage classes broadens the substrate pool
+      that the Sphingobium-Rhodococcus coculture can funnel into cis,cis-muconate and gallate.
+
+      '
+    rationale: Substrate-range evidence restates the conversion endpoint, not a separate causal driver; preserve
+      the supported observation independently.
+  references:
+  - PMID:36030484
+  issues:
+  - 1825
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture/2026-10-08T012747Z-codex-3f6f74.yaml
+- path: kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml
+  id: CommunityMech:000418
+  original_sha256: 6f3c1c71a30aa0e286010702e7d23d1e764409b76117cac7aa41ea89fd01de09
+  record_sha256: ece6ced257acf7538a072ee6fb940f73d96f0f36d83a6e1eae1514356884ab12
+  status: reviewed
+  outcome: changed
+  review_file: reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml
+  scope: Whole record and every existing node/direction reviewed; no new-mechanism discovery or non-graph certification.
+  summary: Retain tested broth-density comparison without universal stability or reciprocal-benefit claims.; Preserve
+    positive maize-pot endpoints and the water-control dry-matter comparator without inferred mediator arrows.;
+    Restrict the transcript observation to canonical Ensifer S2-8-1 and distinguish it from protein activity, flux
+    or causal mediation.
+  node_decisions:
+  - node: Staged cattle-manure wastewater valorization
+    rationale: Retain tested broth-density comparison without universal stability or reciprocal-benefit claims.
+  - node: SYC rhizosphere nitrification and maize promotion
+    rationale: Preserve positive maize-pot endpoints and the water-control dry-matter comparator without inferred
+      mediator arrows.
+  - node: S2-8-1 nitrogen and cytokinin-related gene upregulation
+    rationale: Restrict the transcript observation to canonical Ensifer S2-8-1 and distinguish it from protein activity,
+      flux or causal mediation.
+  removed_node_decisions: []
+  renamed_nodes: {}
+  edges_before: []
+  edges_after: []
+  retained_edge_decisions: []
+  removed_edge_decisions: []
+  references:
+  - PMID:42341825
+  issues:
+  - 1826
+  allowed_changed_fields:
+  - curation_history
+  - discussions
+  - ecological_interactions
+  curation_events_added: 1
+  history_files:
+  - history/records/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom/2026-10-08T012747Z-codex-9305dd.yaml
diff --git a/reports/causal_graph_review/inventory.tsv b/reports/causal_graph_review/inventory.tsv
index 5c99a7f64..60bbc9634 100644
--- a/reports/causal_graph_review/inventory.tsv
+++ b/reports/causal_graph_review/inventory.tsv
@@ -380,10 +380,10 @@ kb/communities/Soy_Sauce_Temporal_SevenSpecies_SynCom.yaml	CommunityMech:000378
 kb/communities/Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml	CommunityMech:000129	910dca8d32101e38a264c98de709523702b9694243f9096fc6c76198700e4a34	3	0	63.3	reports/causal_graph_review/decisions/20261008-four-records-batch104.yaml	reviewed
 kb/communities/Soybean_N_Fixation_sfSynCom.yaml	CommunityMech:000064	528d240b6bc712b116dcbf22ed43f9fce72b32e0b11af95390bbd1fcc46b0290	0	0	0.0	reports/causal_graph_review/decisions/20261008-four-records-batch104.yaml	needs_research
 kb/communities/Soymilk_Mixed_Starter_Metabolic_Division_SynCom.yaml	CommunityMech:000448	92ca77225b4f1d02d0a82fa19a4dfea8a509fce5e8e9ce669adc3608450debf4	2	0	57.5	reports/causal_graph_review/decisions/20261008-four-records-batch104.yaml	reviewed
-kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml	CommunityMech:000339	dbb830353fcd0357f47df423b2258e9e06f87d1909cb84186a2cfa0d4e67d1ad	1	0	55.7		pending
-kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml	CommunityMech:000362	18132fca169325f8c760a8c996a2d7fc882e516144f3a2a977c524b185899367	2	0	60.0		pending
-kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml	CommunityMech:000267	b9b3f065b918d17001a23b96660440448540e3a22aed4a4d9dd56f59a64645d0	3	2	100.0		pending
-kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml	CommunityMech:000418	6f3c1c71a30aa0e286010702e7d23d1e764409b76117cac7aa41ea89fd01de09	3	0	61.7		pending
+kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml	CommunityMech:000339	0304999156eeec1556a337ff0138a6bfce205c38b9d5a8010051d864949a2a7f	1	0	45.7	reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml	reviewed
+kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml	CommunityMech:000362	e2555ecc152f3bbdbb5c2d557a17fc46da135500092494e0379c73fbb85c117a	2	0	57.5	reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml	reviewed
+kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml	CommunityMech:000267	fa5b1abb2f9493bb52263f1041fe4075028d57daf40abe7cd804edd6c65aa05c	3	1	80.0	reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml	reviewed
+kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml	CommunityMech:000418	ece6ced257acf7538a072ee6fb940f73d96f0f36d83a6e1eae1514356884ab12	3	0	61.7	reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml	reviewed
 kb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml	CommunityMech:000326	9aa79042fb33eac69fefdf66b0bd3a02057bd8cdb0e861e449ac2204dfb93a6e	6	2	100.0		pending
 kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml	CommunityMech:000254	c61a85e2234af044ee022537059e465eb1571d50a78a5430cc9fc532aef48285	4	4	100.0		pending
 kb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml	CommunityMech:000335	29276efda4a5ebd299c0284da81aab5388909fed51cb0c32c276c79c00b2dc4a	4	2	100.0		pending
diff --git a/reports/causal_graph_review/summary.json b/reports/causal_graph_review/summary.json
index 1b3d71292..d46932eb4 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": 1387,
-  "edges": 559,
+  "edges": 558,
   "records_without_nodes": 10,
   "records_without_edges": 181,
   "review_status_counts": {
     "needs_research": 50,
-    "pending": 80,
-    "reviewed": 330
+    "pending": 76,
+    "reviewed": 334
   },
   "structural_defects": [],
   "network_audit": [
diff --git a/reports/causal_graph_review/validation-20261008-batch105.json b/reports/causal_graph_review/validation-20261008-batch105.json
new file mode 100644
index 000000000..d6c8dda8c
--- /dev/null
+++ b/reports/causal_graph_review/validation-20261008-batch105.json
@@ -0,0 +1,1098 @@
+{
+  "base_commit": "5d8eb3bd131fbf5c259038a2d45de27a39de0c72",
+  "scope": [
+    "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+    "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml",
+    "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml",
+    "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml"
+  ],
+  "results": [
+    {
+      "check": "focused",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch105.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/focused.log",
+      "log_sha256": "828fd1c753f0d6b415611c4a591e642943e428401f70db669ecf0faa89efff6f",
+      "output_tail": "........                                                                 [100%]\n8 passed in 1.47s\n"
+    },
+    {
+      "check": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch105/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-strict.tsv",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-strict.log",
+      "log_sha256": "10591e20bfa9cb05ad09b2851e9c216cc5a38010b2a70d423221d6362d5039d7",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch105/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-batch105/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-strict.tsv\n"
+    },
+    {
+      "check": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-references.log",
+      "log_sha256": "38b196605eb8e95e7c509d2ebab229a47de1fa25ea4037605a2d91810d39d007",
+      "output_tail": "Validating kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.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/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.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": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-snippets.log",
+      "log_sha256": "32d5c17677a000100a0b22db07734e7af95b7e2b40f82a74ed21b581b1a6d4f5",
+      "output_tail": "# 20 evidence snippets scanned across 1 files\n  MATCH      20\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": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-rank.log",
+      "log_sha256": "2d6248d2abca0ff122878c5b6899afe6fdd4913de202e7d3620a272040844365",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000339\",\n    \"name\": \"Space Habitat Seven-Member Stress-Tolerance SynCom\",\n    \"score\": 45.7,\n    \"taxonomy\": 7,\n    \"connected_taxa\": 1,\n    \"disconnected_taxa\": 6,\n    \"ecological_interactions\": 1,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 2,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_interactions\",\n      \"downstream\",\n      \"metabolites_or_biological_processes\",\n      \"interaction_type\",\n      \"disconnected_taxa\"\n    ],\n    \"path\": \"kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Space_Habitat_SevenMember_Stress_Tolerance_SynCom-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Space_Habitat_SevenMember_Stress_Tolerance_SynCom/2026-10-08T012746Z-codex-2f9387.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Space_Habitat_SevenMember_Stress_Tolerance_SynCom-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch105/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-strict.tsv",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-strict.log",
+      "log_sha256": "32929c5c35993d41c7a9d17b48f42350f5c37ca6adf63c8f6f148f9d6b852ce4",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch105/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-batch105/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-strict.tsv\n"
+    },
+    {
+      "check": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-references.log",
+      "log_sha256": "e146f2cce655577347856cead675b14edd568ce04e5f04220a4ce826b8d75054",
+      "output_tail": "Validating kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.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/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.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": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-snippets.log",
+      "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+      "output_tail": "# 17 evidence snippets scanned across 1 files\n  MATCH      17\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": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-rank.log",
+      "log_sha256": "619c5928b22c7a31d5658d9b9175b671c0318323750b2b51a4ccddc171da5ea4",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000362\",\n    \"name\": \"Sphingobium-Nitrososphaera Phenanthrene-Carbon SynCom\",\n    \"score\": 57.5,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 2,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 3,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_interactions\",\n      \"downstream\",\n      \"metabolites_or_biological_processes\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom/2026-10-08T012747Z-codex-83fd7a.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch105/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-strict.tsv",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-strict.log",
+      "log_sha256": "16e3325b3959485fc2bde258aed31ede9e11b82ed37ad992fcb48de1d4ca13eb",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch105/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-batch105/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-strict.tsv\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-references.log",
+      "log_sha256": "8dbe2b971d454474ebaf24a7125164a0d99ae21f98d41267bb2f1215052ddcd1",
+      "output_tail": "Validating kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n",
+      "explained_output_tail": "Validating kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml against schema src/communitymech/schema/communitymech.yaml\nCache directory: references_cache\n\nValidation Summary:\n  Total checks: 0\n  All validations passed!\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-snippets.log",
+      "log_sha256": "06a536479395cd60c7eab504952fd1ebaea7cd4609924c29d687dbc4183c3686",
+      "output_tail": "# 23 evidence snippets scanned across 1 files\n  MATCH      23\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": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-rank.log",
+      "log_sha256": "9fcb9604f291ac48bc73669d0f03c39b62aa5f405136487d07bfdac7eb3b7c6f",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000267\",\n    \"name\": \"Sphingobium-Rhodococcus Lignin-Dimer Valorization Coculture\",\n    \"score\": 80.0,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 1,\n    \"interaction_evidence\": 6,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"additional_downstream\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture/2026-10-08T012747Z-codex-3f6f74.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture-history-0.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-schema",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-schema.log",
+      "log_sha256": "de6087f4be8c0adc015333597cd864406ad889bbde42d9ee20db0df5932bb2de",
+      "output_tail": "No issues found\n"
+    },
+    {
+      "check": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-strict",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/python3",
+        "scripts/validate_strict.py",
+        "--workers",
+        "1",
+        "--out",
+        "/private/tmp/communitymech-batch105/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-strict.tsv",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-strict.log",
+      "log_sha256": "6b471251b93fa5dd03abfc2da1e141a380b5f7d75365389085a23f6fe4f75041",
+      "output_tail": "Validating 1 files with 1 workers; schema=/private/tmp/communitymech-causal-batch105/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-batch105/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-strict.tsv\n"
+    },
+    {
+      "check": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-terms",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/neDBQyZXv0RYv8B1GH0dI/bin/linkml-term-validator",
+        "validate-data",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--labels"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-terms.log",
+      "log_sha256": "23acda1c1d3194d12bc947d897d07de83f4a076a9d93c135148885108530e018",
+      "output_tail": "\u2705 Validation passed\n"
+    },
+    {
+      "check": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-references",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-reference-validator",
+        "validate",
+        "data",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
+        "-s",
+        "src/communitymech/schema/communitymech.yaml",
+        "--config",
+        "conf/reference_validator.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-references.log",
+      "log_sha256": "bd43d16bf57f8401791a799ab5e569c18c87f9cd7a3003c3605fd52a35d0f68f",
+      "output_tail": "Validating kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.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/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.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": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-snippets",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/evidence_snippet_audit.py",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
+        "--list-mismatch",
+        "--list-nocontent",
+        "--list-rendering",
+        "--list-assembled"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-snippets.log",
+      "log_sha256": "5f0e8a5be45b94195ee5599498c60e06ff8db089c85d0bf23969aa37351ca96e",
+      "output_tail": "# 17 evidence snippets scanned across 1 files\n  MATCH      17\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": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-rank",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "scripts/rank_causal_graph_readiness.py",
+        "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
+        "--format",
+        "json"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-rank.log",
+      "log_sha256": "56bf6d7d2fba62a12834471a2201eae02add633c167ebd1a8e4fe0d688abf95b",
+      "output_tail": "[\n  {\n    \"rank\": 1,\n    \"id\": \"CommunityMech:000418\",\n    \"name\": \"Staged Ensifer-Bacillus Cattle-Manure Wastewater SynCom\",\n    \"score\": 61.7,\n    \"taxonomy\": 2,\n    \"connected_taxa\": 2,\n    \"disconnected_taxa\": 0,\n    \"ecological_interactions\": 3,\n    \"downstream_edges\": 0,\n    \"interaction_evidence\": 6,\n    \"dangling_downstream\": 0,\n    \"self_downstream\": 0,\n    \"missing\": [\n      \"downstream\",\n      \"metabolites_or_biological_processes\",\n      \"interaction_type\"\n    ],\n    \"path\": \"kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml\"\n  }\n]\n"
+    },
+    {
+      "check": "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-history-0",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/linkml-validate",
+        "-s",
+        "src/communitymech/schema/history.yaml",
+        "--target-class",
+        "HistoryRecord",
+        "history/records/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom/2026-10-08T012747Z-codex-9305dd.yaml"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom-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-batch105/verification/inventory.log",
+      "log_sha256": "9adbe78316e7d89f4b6e8b76ee30dce9d94ff0e8e7f8646c28c6a1d27373bc93",
+      "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\": 1387,\n  \"edges\": 558,\n  \"records_without_nodes\": 10,\n  \"records_without_edges\": 181,\n  \"review_status_counts\": {\n    \"needs_research\": 50,\n    \"pending\": 76,\n    \"reviewed\": 334\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-batch105/verification/network.log",
+      "log_sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097",
+      "output_tail": "      \"total_genomes\": 17191,\n            \"is_reclassified\": false,\n            \"mapping_source\": \"kg-microbe NCBI2GTDB.tsv.gz; GTDB release latest (built 2026-07-25)\"\n          },\n          \"notes\": \"The eLife panel denotes this P. aeruginosa mutant as strain 5; represented at species level for ontology stability.\"\n        },\n        \"strain_designation\": {\n          \"strain_name\": \"mexZ\"\n        },\n        \"abundance_value\": \"Full-factorial SynCom panel member 5\",\n        \"evidence\": [\n          {\n            \"reference\": \"PMID:42153623\",\n            \"supports\": \"SUPPORT\",\n            \"evidence_source\": \"IN_VITRO\",\n            \"snippet\": \"Strains 1\\u20138 (as labeled in the main text) correspond, in order, to mutants pAOV, PA14, NfxB, ParR- CAZ, mexZ, OrfN, NfxB- CAZ, and MDR6- CAZ\",\n            \"explanation\": \"Maps the source's strain numbers to the eight P. aeruginosa mutant labels.\"\n          }\n        ]\n      },\n      \"message\": \"Taxon 'Pseudomonas aeruginosa mexZ' 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": "just-network-json",
+      "command": [
+        "just",
+        "audit-network-json"
+      ],
+      "exit_code": 2,
+      "expected_exit_codes": [
+        2
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/just-network-json.log",
+      "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"
+    },
+    {
+      "check": "rank-all",
+      "command": [
+        "just",
+        "rank-causal-graphs"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/rank-all.log",
+      "log_sha256": "21cb9bbd7625ba23cdc808ff9c37390a0ba4ff425463db162871a5f39f389837",
+      "output_tail": "\n401\t100.0\tkb/communities/Rhodopseudomonas_Ecoli_CrossFeeding_Coculture.yaml\tCommunityMech:000092\tRhodopseudomonas-E. coli Cross-Feeding Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n402\t100.0\tkb/communities/Rice_Acid_Soil_Bioinoculant_SynCom.yaml\tCommunityMech:000109\tRice Acid Soil Bioinoculant SynCom\t1\t1\t0\t4\t4\t4\t\t0\t0\n403\t100.0\tkb/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.yaml\tCommunityMech:000326\tStaphylococcus-Candida Context-Dependent Biofilm Coculture\t2\t2\t0\t6\t2\t13\t\t0\t0\n404\t100.0\tkb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml\tCommunityMech:000254\tStordalen Mire Methylotrophic Methanogenesis Community\t3\t3\t0\t4\t4\t9\t\t0\t0\n405\t100.0\tkb/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.yaml\tCommunityMech:000335\tStreptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium\t4\t4\t0\t4\t2\t5\t\t0\t0\n406\t100.0\tkb/communities/Subsurface_Carboxydocella_CO_Aquifer_Community.yaml\tCommunityMech:000251\tSubsurface Carboxydocella CO-Oxidation Aquifer Community\t1\t1\t0\t5\t2\t5\t\t0\t0\n407\t100.0\tkb/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.yaml\tCommunityMech:000312\tSuillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom\t3\t3\t0\t4\t3\t4\t\t0\t0\n408\t100.0\tkb/communities/Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml\tCommunityMech:000222\tSulfide Spring Autotrophic CPR-Hosting Biofilm\t3\t3\t0\t3\t2\t4\t\t0\t0\n409\t100.0\tkb/communities/SynComBac10_Chicken_Intestinal_SynCom.yaml\tCommunityMech:000127\tSynComBac10 Chicken Intestinal SynCom\t3\t3\t0\t3\t2\t3\t\t0\t0\n410\t100.0\tkb/communities/SynCom_ARC_Peanut_Aflatoxin_Nodulation.yaml\tCommunityMech:000314\tSynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community\t5\t5\t0\t3\t2\t3\t\t0\t0\n411\t100.0\tkb/communities/SynCom_BsBv_Cigar_Tobacco_Leaf_Fermentation.yaml\tCommunityMech:000278\tSynCom BsBv Cigar Tobacco Leaf Fermentation\t2\t2\t0\t3\t2\t3\t\t0\t0\n412\t100.0\tkb/communities/SynCom_Chlorella_sorokiniana_Biogas_Slurry_Coupling_System.yaml\tCommunityMech:000285\tSynCom + Chlorella sorokiniana Biogas-slurry Coupling System\t2\t2\t0\t5\t3\t5\t\t0\t0\n413\t100.0\tkb/communities/SynCom_MetG2_Rhizobacteria_Sugarcane_Stress_Resilience.yaml\tCommunityMech:000302\tSynCom MetG2 Rhizobacteria Sugarcane Stress Resilience\t2\t2\t0\t3\t2\t4\t\t0\t0\n414\t100.0\tkb/communities/SynCom_Sesame_Flavor_Baijiu_Fuqu_13Genus.yaml\tCommunityMech:000283\tSesame-flavor Baijiu Fuqu SynCom (13-genus)\t13\t13\t0\t3\t2\t3\t\t0\t0\n415\t100.0\tkb/communities/SynCom_Y_Agrobacterium_Bacillus_Biofilm_Biocontrol_Coculture.yaml\tCommunityMech:000272\tSynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture\t2\t2\t0\t4\t2\t6\t\t0\t0\n416\t100.0\tkb/communities/Synechococcus_Azotobacter_Photoproduction_Mutualism.yaml\tCommunityMech:000207\tSynechococcus-Azotobacter Photoproduction Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n417\t100.0\tkb/communities/Synechococcus_Bacillus_SPC.yaml\tCommunityMech:000065\tSynechococcus-Bacillus Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n418\t100.0\tkb/communities/Synechococcus_Ecoli_SPC.yaml\tCommunityMech:000066\tSynechococcus-E.coli Synthetic Photosynthetic Consortium\t2\t2\t0\t3\t2\t4\t\t0\t0\n419\t100.0\tkb/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml\tCommunityMech:000198\tSynechococcus-Halomonas Light-Driven PHB Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n420\t100.0\tkb/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml\tCommunityMech:000167\tSynechococcus-Pseudomonas Phototrophic PHA and DNT 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Consortium\t2\t2\t0\t3\t3\t5\t\t0\t0\n426\t100.0\tkb/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml\tCommunityMech:000189\tSyntrophomonas-Methanococcus Butyrate Growth Coordination Coculture\t2\t2\t0\t3\t2\t6\t\t0\t0\n427\t100.0\tkb/communities/Syntrophomonas_Methanospirillum_Syntrophy.yaml\tCommunityMech:000070\tSyntrophomonas-Methanospirillum Syntrophic Consortium\t2\t2\t0\t3\t3\t7\t\t0\t0\n428\t100.0\tkb/communities/Syntrophus_Benzoate_Degrader.yaml\tCommunityMech:000071\tSyntrophus Benzoate Degrader\t2\t2\t0\t3\t2\t6\t\t0\t0\n429\t100.0\tkb/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml\tCommunityMech:000187\tSyntrophus-Methanospirillum Gentianae Benzoate Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n430\t100.0\tkb/communities/THOR_Rhizosphere_Model_Community.yaml\tCommunityMech:000079\tTHOR Rhizosphere Model Community\t3\t3\t0\t4\t2\t5\t\t0\t0\n431\t100.0\tkb/communities/TYQ1_Nematode_Biocontrol_SynCom.yaml\tCommunityMech:000072\tTYQ1 Nematode Biocontrol SynCom\t8\t8\t0\t4\t4\t4\t\t0\t0\n432\t100.0\tkb/communities/Teosinte_Maize_Biofertilizer_SynCom7.yaml\tCommunityMech:000100\tTeosinte-Derived Maize Biofertilizer SynCom7\t4\t4\t0\t6\t2\t12\t\t0\t0\n433\t100.0\tkb/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml\tCommunityMech:000259\tThalassiosira-Marinobacter Marine Snow Coculture\t2\t2\t0\t4\t2\t10\t\t0\t0\n434\t100.0\tkb/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml\tCommunityMech:000162\tThalassiosira-Ruegeria Phycosphere Coculture\t2\t2\t0\t3\t2\t4\t\t0\t0\n435\t100.0\tkb/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml\tCommunityMech:000182\tThermacetogenium-Methanothermobacter Acetate Oxidation Coculture\t2\t2\t0\t3\t2\t8\t\t0\t0\n436\t100.0\tkb/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml\tCommunityMech:000282\tThermophilic Lignocellulose-degrading Composting SynCom\t5\t5\t0\t3\t2\t3\t\t0\t0\n437\t100.0\tkb/communities/Thermophilic_Pyrite_QS_Consortium.yaml\tCommunityMech:000073\tThermophilic Pyrite Quorum Sensing Consortium\t3\t3\t0\t6\t2\t14\t\t0\t0\n438\t100.0\tkb/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml\tCommunityMech:000186\tThermotoga-Methanocaldococcus Hyperthermophilic Syntrophy\t2\t2\t0\t3\t2\t8\t\t0\t0\n439\t100.0\tkb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml\tCommunityMech:000239\tThiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community\t3\t3\t0\t3\t2\t3\t\t0\t0\n440\t100.0\tkb/communities/Tinto_River_Iron_Cycling_Community.yaml\tCommunityMech:000074\tTinto River Iron Cycling Community\t6\t6\t0\t5\t3\t6\t\t0\t0\n441\t100.0\tkb/communities/Tobacco_Chemotactic_Biocontrol_SynCom.yaml\tCommunityMech:000106\tTobacco Chemotactic Biocontrol SynCom\t2\t2\t0\t3\t2\t4\t\t0\t0\n442\t100.0\tkb/communities/Tomato_Oxylipin_SynCom3.yaml\tCommunityMech:000107\tTomato Oxylipin-Protective SynCom3\t3\t3\t0\t3\t2\t4\t\t0\t0\n443\t100.0\tkb/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml\tCommunityMech:000112\tTribromophenol Anaerobic Bioremediation SynCom\t3\t3\t0\t4\t3\t5\t\t0\t0\n444\t100.0\tkb/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml\tCommunityMech:000188\tTrichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture\t3\t3\t0\t3\t2\t6\t\t0\t0\n445\t100.0\tkb/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml\tCommunityMech:000205\tTrichoderma-E. coli Cellulosic Isobutanol Coculture\t2\t2\t0\t3\t2\t5\t\t0\t0\n446\t100.0\tkb/communities/Trichoderma_Lactate_Platform.yaml\tCommunityMech:000075\tTrichoderma Lactate Platform for SCFA Production\t3\t3\t0\t3\t2\t3\t\t0\t0\n447\t100.0\tkb/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml\tCommunityMech:000270\tTrichoderma-Streptomyces Filamentous Cellulose Coculture\t2\t2\t0\t3\t2\t7\t\t0\t0\n448\t100.0\tkb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml\tCommunityMech:000147\tTrichodesmium-Alteromonas Marine Consortium\t3\t3\t0\t3\t2\t5\t\t0\t0\n449\t100.0\tkb/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml\tCommunityMech:000337\tTropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy\t3\t3\t0\t4\t2\t9\t\t0\t0\n450\t100.0\tkb/communities/Urine_Nitrification_SynCom.yaml\tCommunityMech:000117\tUrine Nitrification Synthetic Microbial Community\t5\t5\t0\t3\t2\t5\t\t0\t0\n451\t100.0\tkb/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml\tCommunityMech:000213\tVariovorax-Cryptococcus Vitamin Cross-Feeding Microcosm\t2\t2\t0\t3\t2\t4\t\t0\t0\n452\t100.0\tkb/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml\tCommunityMech:000328\tWaste-Sludge Electro-Fermentation Biofilm-Suspension Community\t5\t5\t0\t4\t2\t6\t\t0\t0\n453\t100.0\tkb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml\tCommunityMech:000098\tWatermelon Rhizosphere Fusarium-Protective SynCom8\t2\t2\t0\t3\t2\t7\t\t0\t0\n454\t100.0\tkb/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml\tCommunityMech:000255\tWetland Oxygen-Sulfate Greenhouse Gas Microcosm Community\t3\t3\t0\t3\t2\t6\t\t0\t0\n455\t100.0\tkb/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.yaml\tCommunityMech:000118\tWheat Straw Biogas Pretreatment SynCom\t4\t4\t0\t3\t2\t4\t\t0\t0\n456\t100.0\tkb/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml\tCommunityMech:000354\tYarrowia lipolytica Division-of-Labor Lipid Consortium\t2\t2\t0\t3\t2\t3\t\t0\t0\n457\t100.0\tkb/communities/Yogurt_TwoSpecies_Starter_Culture.yaml\tCommunityMech:000164\tYogurt Two-Species Starter Culture\t2\t2\t0\t4\t2\t9\t\t0\t0\n458\t100.0\tkb/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml\tCommunityMech:000210\tZymomonas-E. coli Exometabolomics-Designed Obligate Mutualism\t2\t2\t0\t3\t2\t6\t\t0\t0\n459\t100.0\tkb/communities/hCom2_Complex_Gut_Microbiome.yaml\tCommunityMech:000123\thCom2 Complex Gut Microbiome\t1\t1\t0\t3\t2\t3\t\t0\t0\n460\t100.0\tkb/communities/mCAFEs_Brachypodium_RCC.yaml\tCommunityMech:000078\tm-CAFEs Brachypodium Reduced Complexity Consortia\t10\t10\t0\t6\t2\t11\t\t0\t0\nPYTHONPATH=src uv run python scripts/rank_causal_graph_readiness.py \n"
+    },
+    {
+      "check": "render",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "communitymech.render"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/render.log",
+      "log_sha256": "660b742273cfab2becad4f9475c0a0be314228538c96dd7658fa0d06541cf383",
+      "output_tail": "unitymech-causal-batch105/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch105/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch105/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch105/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-batch105/verification/render-repeat.log",
+      "log_sha256": "660b742273cfab2becad4f9475c0a0be314228538c96dd7658fa0d06541cf383",
+      "output_tail": "unitymech-causal-batch105/docs/communities/Synechococcus_Bacillus_SPC.html\n  \u2713 Synechococcus_Ecoli_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Ecoli_SPC.html\n  \u2713 Synechococcus_Halomonas_Light_Driven_PHB_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.html\n  \u2713 Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Pseudomonas_PhotoPHA_DNT_Coculture.html\n  \u2713 Synechococcus_Saccharomyces_SPC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Saccharomyces_SPC.html\n  \u2713 Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechococcus_Shewanella_Dlactate_Biophotovoltaic_Consortium.html\n  \u2713 Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html\n  \u2713 Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html\n  \u2713 Synthetic_Periphyton_Freshwater_Biofilm.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Synthetic_Periphyton_Freshwater_Biofilm.html\n  \u2713 Syntrophobacter_Methanobacterium_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophobacter_Methanobacterium_Syntrophy.html\n  \u2713 Syntrophobacter_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophobacter_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophomonas_Methanococcus_Butyrate_Growth_Coordination_Coculture.html\n  \u2713 Syntrophomonas_Methanospirillum_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophomonas_Methanospirillum_Syntrophy.html\n  \u2713 Syntrophus_Benzoate_Degrader.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophus_Benzoate_Degrader.html\n  \u2713 Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Syntrophus_Methanospirillum_Gentianae_Benzoate_Coculture.html\n  \u2713 TCP_NonDehalogenimonas_Groundwater_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/TCP_NonDehalogenimonas_Groundwater_Consortium.html\n  \u2713 THOR_Rhizosphere_Model_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/THOR_Rhizosphere_Model_Community.html\n  \u2713 TYQ1_Nematode_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/TYQ1_Nematode_Biocontrol_SynCom.html\n  \u2713 Teosinte_Maize_Biofertilizer_SynCom7.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Teosinte_Maize_Biofertilizer_SynCom7.html\n  \u2713 Thalassiosira_Marinobacter_Marine_Snow_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thalassiosira_Marinobacter_Marine_Snow_Coculture.html\n  \u2713 Thalassiosira_Ruegeria_Phycosphere_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thalassiosira_Ruegeria_Phycosphere_Coculture.html\n  \u2713 Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html\n  \u2713 Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html\n  \u2713 Thermophilic_ExSitu_Biomethanation_Mixed_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html\n  \u2713 Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_Lignocellulose_Composting_SynCom_Biosanitization.html\n  \u2713 Thermophilic_Pyrite_QS_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermophilic_Pyrite_QS_Consortium.html\n  \u2713 Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thermotoga_Methanocaldococcus_Hyperthermophilic_Syntrophy.html\n  \u2713 Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.html\n  \u2713 Tinto_River_Iron_Cycling_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tinto_River_Iron_Cycling_Community.html\n  \u2713 Tobacco_Chemotactic_Biocontrol_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tobacco_Chemotactic_Biocontrol_SynCom.html\n  \u2713 Tomato_Oxylipin_SynCom3.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tomato_Oxylipin_SynCom3.html\n  \u2713 Tribromophenol_Anaerobic_Bioremediation_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tribromophenol_Anaerobic_Bioremediation_SynCom.html\n  \u2713 Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichococcus_Syntrophomonas_Methanospirillum_Butyrate_Coculture.html\n  \u2713 Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Ecoli_Cellulosic_Isobutanol_Coculture.html\n  \u2713 Trichoderma_Lactate_Platform.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Lactate_Platform.html\n  \u2713 Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichoderma_Streptomyces_Filamentous_Cellulose_Coculture.html\n  \u2713 Trichodesmium_Alteromonas_Marine_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Trichodesmium_Alteromonas_Marine_Consortium.html\n  \u2713 Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Tropidoatractus_Magnetotacticus_Tripartite_Syntrophy.html\n  \u2713 Urine_Nitrification_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Urine_Nitrification_SynCom.html\n  \u2713 Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Variovorax_Cryptococcus_Vitamin_Mutualism_Microcosm.html\n  \u2713 Viili_Fungus_Bacterium_EPS_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Viili_Fungus_Bacterium_EPS_SynCom.html\n  \u2713 Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Waste_Sludge_Electrofermentation_Biofilm_Suspension_Community.html\n  \u2713 Watermelon_Rhizosphere_Fusarium_SynCom8.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.html\n  \u2713 Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wetland_Oxygen_Sulfate_GHG_Microcosm_Community.html\n  \u2713 Wheat_Consortium_C1.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Consortium_C1.html\n  \u2713 Wheat_Consortium_C6.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Consortium_C6.html\n  \u2713 Wheat_CrownRot_SixStrain_CrossKingdom_SMC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_CrownRot_SixStrain_CrossKingdom_SMC.html\n  \u2713 Wheat_CrownRot_TB_CrossKingdom_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html\n  \u2713 Wheat_DT_Rhizosphere_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_DT_Rhizosphere_SynCom.html\n  \u2713 Wheat_Straw_Biogas_Pretreatment_SynCom.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_Straw_Biogas_Pretreatment_SynCom.html\n  \u2713 Wheat_SynCom_SASW01_Drought_Inoculant.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wheat_SynCom_SASW01_Drought_Inoculant.html\n  \u2713 Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wine_Yeast_FiveSpecies_Strain_Substitution_Consortium.html\n  \u2713 Wine_Yeast_ThreeSpecies_Contact_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wine_Yeast_ThreeSpecies_Contact_Consortium.html\n  \u2713 Wolffia_Mankai_Endosphere_Cobamide_Guild.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wolffia_Mankai_Endosphere_Cobamide_Guild.html\n  \u2713 Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Wollastonite_Ramichloridium_Talaromyces_Fungal_Consortium.html\n  \u2713 Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Yarrowia_lipolytica_Division_of_Labor_Lipid_Consortium.html\n  \u2713 Yogurt_TwoSpecies_Starter_Culture.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Yogurt_TwoSpecies_Starter_Culture.html\n  \u2713 Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/Zymomonas_Ecoli_Exometabolomics_Obligate_Mutualism.html\n  \u2713 hCom2_Complex_Gut_Microbiome.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/hCom2_Complex_Gut_Microbiome.html\n  \u2713 mCAFEs_Brachypodium_RCC.yaml \u2192 /private/tmp/communitymech-causal-batch105/docs/communities/mCAFEs_Brachypodium_RCC.html\n\n\u2705 Rendered 456 communities to /private/tmp/communitymech-causal-batch105/docs/communities\n  \u2713 Generated browser at /private/tmp/communitymech-causal-batch105/docs/browser.html\n  \u2713 Generated landing at /private/tmp/communitymech-causal-batch105/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-batch104')),('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-batch105/verification/connectivity-survey.log",
+      "log_sha256": "38a12f49cbc88c7b8677195d203bbd2c525ef38242aa0ab91633314f37a45aa7",
+      "output_tail": "{\"baseline\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}, \"current\": {\"records\": 460, \"with_community_level\": 403, \"mixed\": 128, \"community_level_only\": 275, \"taxa\": 1544, \"credited_solely_by_the_rule\": 1270}}\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_batch100.py",
+        "tests/test_causal_review_batch101.py",
+        "tests/test_causal_review_batch102.py",
+        "tests/test_causal_review_batch103.py",
+        "tests/test_causal_review_batch104.py",
+        "tests/test_causal_review_batch105.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_batch63.py",
+        "tests/test_causal_review_batch64.py",
+        "tests/test_causal_review_batch65.py",
+        "tests/test_causal_review_batch66.py",
+        "tests/test_causal_review_batch67.py",
+        "tests/test_causal_review_batch68.py",
+        "tests/test_causal_review_batch69.py",
+        "tests/test_causal_review_batch7.py",
+        "tests/test_causal_review_batch70.py",
+        "tests/test_causal_review_batch71.py",
+        "tests/test_causal_review_batch72.py",
+        "tests/test_causal_review_batch73.py",
+        "tests/test_causal_review_batch74.py",
+        "tests/test_causal_review_batch75.py",
+        "tests/test_causal_review_batch76.py",
+        "tests/test_causal_review_batch77.py",
+        "tests/test_causal_review_batch78.py",
+        "tests/test_causal_review_batch79.py",
+        "tests/test_causal_review_batch8.py",
+        "tests/test_causal_review_batch80.py",
+        "tests/test_causal_review_batch81.py",
+        "tests/test_causal_review_batch82.py",
+        "tests/test_causal_review_batch83.py",
+        "tests/test_causal_review_batch84.py",
+        "tests/test_causal_review_batch85.py",
+        "tests/test_causal_review_batch86.py",
+        "tests/test_causal_review_batch87.py",
+        "tests/test_causal_review_batch88.py",
+        "tests/test_causal_review_batch89.py",
+        "tests/test_causal_review_batch9.py",
+        "tests/test_causal_review_batch90.py",
+        "tests/test_causal_review_batch91.py",
+        "tests/test_causal_review_batch92.py",
+        "tests/test_causal_review_batch93.py",
+        "tests/test_causal_review_batch94.py",
+        "tests/test_causal_review_batch95.py",
+        "tests/test_causal_review_batch96.py",
+        "tests/test_causal_review_batch97.py",
+        "tests/test_causal_review_batch98.py",
+        "tests/test_causal_review_batch99.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-batch105/verification/regressions.log",
+      "log_sha256": "c92533158955254397d50b1ac57403c143a99d8f49304f1eda0a2771ee3e6b20",
+      "output_tail": "........................................................................ [  7%]\n........................................................................ [ 15%]\n........................................................................ [ 22%]\n........................................................................ [ 30%]\n........................................................................ [ 37%]\n........................................................................ [ 45%]\n........................................................................ [ 52%]\n........................................................................ [ 60%]\n........................................................................ [ 68%]\n........................................................................ [ 75%]\n........................................................................ [ 83%]\n........................................................................ [ 90%]\n........................................................................ [ 98%]\n...............                                                          [100%]\n951 passed in 379.05s (0:06:19)\n"
+    },
+    {
+      "check": "just-lint",
+      "command": [
+        "just",
+        "lint"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0,
+        2
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/just-lint.log",
+      "log_sha256": "446571cf674ab5481dcdbf13072eaf64f44a809f1daa61c149abd299bd11bf9c",
+      "output_tail": "All checks passed!\nSuccess: no issues found in 49 source files\nuv run black --check src/ tests/ scripts/\nAll done! \u2728 \ud83c\udf70 \u2728\n358 files would be left unchanged.\nuv run ruff check src/ tests/ scripts/\nwarning: Invalid `# noqa` directive on scripts/gtdb_ground.py:74: expected code to consist of uppercase letters followed by digits only (e.g. `F401`)\nuv run mypy src/\n"
+    },
+    {
+      "check": "mypy-explicit-runtime",
+      "command": [
+        "/private/tmp/communitymech-batch100/lint-env/bin/mypy",
+        "--no-incremental",
+        "--python-executable",
+        "/private/tmp/communitymech-batch100/lint-env/bin/python",
+        "src/"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/mypy-explicit-runtime.log",
+      "log_sha256": "b1fdd8413863455c6896d811c9ab42dc9256d679a668643bb18df2318c3bc875",
+      "output_tail": "Success: no issues found in 49 source files\n"
+    },
+    {
+      "check": "audit-snippets-all",
+      "command": [
+        "just",
+        "audit-snippets"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/audit-snippets-all.log",
+      "log_sha256": "0b1a06355c79d860babe8763bde20ad1a80bd154381b651ca0bcb1270413d441",
+      "output_tail": "# 8956 evidence snippets scanned across 460 files\n  MATCH      8820\n  RENDERING  20\n  ASSEMBLED  1\n  WEAK       0\n  MISMATCH   39\n  NOCONTENT  76\n\n# Files with MISMATCH/WEAK (content present but snippet absent) \u2014 fabrication suspects\n  19 (19 hard)  kb/communities/DCPP_DBS4_DCP4_DCP11d_Degradation_SynCom.yaml\n  15 (15 hard)  kb/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.yaml\n   3 (3 hard)  kb/communities/Coscinodiscus_Synthetic_Community.yaml\n   1 (1 hard)  kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml\n   1 (1 hard)  kb/communities/Shewanella_Geobacter_Exoelectrogenic_Biofilm_Community.yaml\nuv run python scripts/evidence_snippet_audit.py \n"
+    },
+    {
+      "check": "diff-check",
+      "command": [
+        "git",
+        "diff",
+        "--check"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/diff-check.log",
+      "log_sha256": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
+      "output_tail": ""
+    },
+    {
+      "check": "metadata-focused-recheck",
+      "command": [
+        "/Users/marcin/.cache/uv/archive-v0/l58VlyFvdmnkl0CcAx5Gk/bin/python3",
+        "-m",
+        "pytest",
+        "-q",
+        "tests/test_causal_review_batch105.py"
+      ],
+      "exit_code": 0,
+      "expected_exit_codes": [
+        0
+      ],
+      "log": "/private/tmp/communitymech-batch105/verification/metadata-focused-recheck.log",
+      "log_sha256": "7a61f8399ee727504c4a7c38a83adab2783e64d82eaa38d44a3492f2c92060f5",
+      "output_tail": "........                                                                 [100%]\n8 passed in 1.72s\n"
+    }
+  ],
+  "limitations": [
+    "Fresh both-root baseline before source reads: 460 records, 923 caches, 56 existing warnings, zero structural defects. Four whole records and all9 original nodes/2 directions reviewed; all9 nodes and one qualified direction retained, one restatement arrow removed, three renames. No new topology or Edison submission/spend.",
+    "Fresh EuropePMC XML retrieved for space habitat. Results lines462-558 and Discussion lines731-819 read for colony-recovery and interpretation context. This is bounded main-text reading, not whole-paper methods, supplements, figure pixels or raw-data certification.",
+    "Phenanthrene, lignin and manure primary abstracts independently retrieved and read whole, alongside whole existing abstract caches. No PMCID supplied for these three. Wiley full-text request redirected to the abstract/access page; OUP and the phenanthrene DOI web requests returned Internal Error with no HTTP code reported. No full bodies or supplements read, no bypass; no global assertion of full-text absence.",
+    "Large space-habitat cache used for normalized claim matching, not exhaustive duplicated full-text review. All retained graph and new discussion quotations match fresh primary text and unchanged caches. No cache imports or license949/loader1703/DOI-case1091 certification. Space-habitat metadata identifies CC BY; other publisher notices retained.",
+    "Space habitat: preserve reduced recoverable B. subtilis CFU and canonical participant; remove COMPETITION because reciprocal negative effects are not established. Cultivability is not definitive viability loss; genomic potential is not confirmed activity. No new stress-survival, resistance, virulence, biofilm, culture or disinfection optimization procedures or genetic designs.",
+    "Phenanthrene: retain positive lettuce-pot removal and carbon-content endpoints with IN_VIVO provenance. Carbon stocks and statistical guild associations do not establish carbon-fixation flux or traced transfer. Existing model methods retained without invented software versions; causal interpretation PARTIAL. Prior847/848 interaction-typing and provenance fixes preserved.",
+    "Lignin: source systems plural; retain designed pairwise cleavage/conversion coupling and existing arrow as HYPOTHESIZED/PARTIAL. Remove background-study evidence and categorical cross-feeding/niche-partitioning. Retain observed muconate conversion and qualified gallate potential, not simultaneous production by one formulation. Reuse existing local CHEBI16918 gallate descriptor; keep substrate-range node without its restatement arrow.",
+    "Manure: retain broth and positive plant observations with their distinct comparators. Scope transcript upregulation to identity-only Ensifer S2-8-1. Transcript abundance is not protein activity, flux or proven mediation; no new arrows. Preserve earlier cross-feeder-role removals and IN_VIVO pot classification. Full protocols not certified.",
+    "Graph issues1823-1826 addressed here and remain open until protected-main merge; non-graph1827 remains open. Fresh all-state title/body dedup matches771/847/848. Hidden/ignored local search excludes.git/docs/site/references_cache with relevant caches separately covered. PRs/comments not exhaustively searched. Abundance, functional roles, broad source-formulation text and protocol blocks remain separately scoped.",
+    "Four guarded writes and append-only histories;456 other records and all923 caches unchanged. Every unrelated raw block preserved. No schema/runtime/audit rule changes. Self-adversarial review is not independent approval or corpus completion. DeniedAM_AB000444 and unanswered Edison scopes untouched. Validation/publication not preasserted."
+  ],
+  "reference_validator_version": "0.1.7",
+  "snippet_counts_by_record": {
+    "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml": {
+      "MATCH": 20,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml": {
+      "MATCH": 17,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml": {
+      "MATCH": 23,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    },
+    "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml": {
+      "MATCH": 17,
+      "RENDERING": 0,
+      "ASSEMBLED": 0,
+      "WEAK": 0,
+      "MISMATCH": 0,
+      "NOCONTENT": 0
+    }
+  },
+  "unchanged_record_files": 456,
+  "unchanged_cache_files": 923,
+  "unchanged_raw_blocks": 68,
+  "cache_changes": [],
+  "edison": {
+    "required_for_this_repair": false,
+    "required_for_unresolved_extensions": false,
+    "provider_submissions": 0,
+    "credits_spent": 0,
+    "dry_runs": [],
+    "repair_scope": "Qualify existing observation/mechanism boundaries and narrow member scope; retain one qualified existing direction and remove one restatement. No new mechanisms or directions."
+  },
+  "primary_artifacts": {
+    "/private/tmp/communitymech-batch105/baseline.json": "cc7fef283bf49b67d5c3e8b0edc947012b71370b73db9cb25458cdf2ddfcba45",
+    "/private/tmp/communitymech-batch105/dedup-local-current.txt": "037e30d7f1b0ce11a2549fa6d6c75e39a6f4db6e208b16636024dd5f59547188",
+    "/private/tmp/communitymech-batch105/issue-dedup-current.json": "83c3bbd2eb342c8704a7dc42d5521a6ed2048817e9780a9df8eece5434cd16da",
+    "/private/tmp/communitymech-batch105/lignin-metadata.json": "d66d4f9f22950368363517a79b4619479749f70e3960a718e6761af78b37f3bd",
+    "/private/tmp/communitymech-batch105/lignin-primary.txt": "0d14a9faeb798fcc1c752695dc5dce2c69fe9b8e9bd4bdeec388480125a5a17d",
+    "/private/tmp/communitymech-batch105/manure-metadata.json": "590d2e83dd3d0403da375f13811c565802f0c952ef22ef1a34c5c37da0eda32b",
+    "/private/tmp/communitymech-batch105/manure-primary.txt": "e0323f52c06d476379635c23a180fd919b75ee3183142d54e160f6363f896285",
+    "/private/tmp/communitymech-batch105/phenanthrene-metadata.json": "f1ce256f7915a72a661a220e9f39e5404911bf693a89f25fcc7d2d0dab971e50",
+    "/private/tmp/communitymech-batch105/phenanthrene-primary.txt": "454a182a7d0ecdab2e585d8122d3f48c2d46b0ed7ed17a1990bdad369d5a4e11",
+    "/private/tmp/communitymech-batch105/primary-manifest.json": "65cf37f6b534c9fa426603097c5fa6fd79e327449b07741933a6b5a3d09c61dc",
+    "/private/tmp/communitymech-batch105/space-metadata.json": "baf4e412a0c4b811860759b6b3f37858f44f3939ff8a1a22f5f043144d08bf84",
+    "/private/tmp/communitymech-batch105/space-primary.txt": "5bd9cd763bf160b068693b0d59203267bdf46bde1904d288835b409862f99648",
+    "/private/tmp/communitymech-batch105/space-primary.xml": "aeff0a81952a082f19fb10ea55f7f9dbb7a0050bf124ad74e20f2ce1a40c3443",
+    "references_cache/PMID_36030484.md": "3e24765eec279e51e901b45dde5e55b9f38e0d084057d7d4a2d0bb90aa3ff0de",
+    "references_cache/PMID_41967346.txt": "a19795680b6181bc527ebd3318bc404d9ea467a9ccac1f62b2c2cffef0cfc168",
+    "references_cache/PMID_42341825.txt": "a4e640e63bca23c67aa87994c53c09642f9c2c62920f71e576cb4dc64bb9c21e",
+    "references_cache/PMID_42577390.md": "9473c68e543cdd3bd59af3190f1f7c4fc560e9f364d55d653c5427da0f13dc9c"
+  },
+  "immutable_prior_history_and_decision_files": 812,
+  "primary_graph_snippet_proof": {
+    "graph_quotations": 17,
+    "new_discussion_quotations": 5,
+    "fresh_primary_literal_matches": 22,
+    "all_cached_literal_matches": 22,
+    "retained_nodes": 9,
+    "removed_nodes": 0,
+    "retained_arrows": 1,
+    "removed_arrows": 1,
+    "new_nodes_or_directions": 0,
+    "scope": "All reviewed quotations match fresh primary text and unchanged existing caches literally after normalization; entailment separately reviewed. Phenanthrene, lignin and manure abstracts only; space-habitat source has bounded main-text coverage. No cache text or audit exception."
+  },
+  "network_delta": {
+    "existing_findings_preserved": 56,
+    "added_findings": {},
+    "removed_findings": {},
+    "interpretation": "One substrate-range restatement arrow removed; all nine nodes retained with qualified mechanisms and one scoped transcript node; all56existing warnings unchanged and zero structural defects. No audit rules changed."
+  },
+  "render_determinism": true,
+  "published_description_coverage": {
+    "pages": 456,
+    "nodes": 1373,
+    "arrows": 550
+  },
+  "render_scope": "Deterministic rendering and exact HTML-description parser, not browser screenshots; postcommit docs-current separately required.",
+  "participant_census": {
+    "measurements": {
+      "baseline": {
+        "records": 460,
+        "with_community_level": 403,
+        "mixed": 128,
+        "community_level_only": 275,
+        "taxa": 1544,
+        "credited_solely_by_the_rule": 1270
+      },
+      "current": {
+        "records": 460,
+        "with_community_level": 403,
+        "mixed": 128,
+        "community_level_only": 275,
+        "taxa": 1544,
+        "credited_solely_by_the_rule": 1270
+      }
+    },
+    "delta": {
+      "records": 0,
+      "with_community_level": 0,
+      "mixed": 0,
+      "community_level_only": 0,
+      "taxa": 0,
+      "credited_solely_by_the_rule": 0
+    },
+    "interpretation": "Manure transcript node gains identity-only Ensifer scope. Other community-level observations still encompass the consortium, so the global census is unchanged. No census threshold or runtime rule changes."
+  },
+  "lint_limitation": "Plain just-lint passed; explicit-runtime no-incremental mypy additionally checked.",
+  "lint_environment": {
+    "path": "/private/tmp/communitymech-batch100/lint-env",
+    "scope": "Temporary Python3.13 lint environment reuses validation runtime and locked mypy1.19.1/stubs/scikit-learn1.8.0/pacmap0.9.1 for static checks; not a complete embedding runtime. Project dependencies unchanged."
+  },
+  "full_corpus_snippet_counts": {
+    "records": 460,
+    "total": 8956,
+    "categories": {
+      "MATCH": 8820,
+      "RENDERING": 20,
+      "ASSEMBLED": 1,
+      "WEAK": 0,
+      "MISMATCH": 39,
+      "NOCONTENT": 76
+    }
+  },
+  "full_corpus_snippet_audit_caveat": "Both-root informational audit exit0 is not clean-corpus certification; literal matches are not entailment.",
+  "corpus": {
+    "scope": "Every YAML under kb/communities and data/isolates; filesystem discovery includes hidden/ignored files.",
+    "records": 460,
+    "nodes": 1387,
+    "edges": 558,
+    "records_without_nodes": 10,
+    "records_without_edges": 181,
+    "review_status_counts": {
+      "needs_research": 50,
+      "pending": 76,
+      "reviewed": 334
+    },
+    "structural_defects": []
+  },
+  "tested_file_sha256": {
+    "reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml": "3d64b6bccead35688461e4485e84ed02d2118a45ffc71bb36a99c579f02a56d9",
+    "tests/test_causal_review_batch105.py": "253024f0a23a9313cbb2dd062051e60e7a5299895c1cb6ba2bf626666cf4c8e2",
+    "tests/test_participating_taxa.py": "0685ac6f4a721680ccb3967614b1411c59f553ccc45d485582d11126abfa9f9a",
+    "tests/test_community_level_connectivity_credit.py": "383a0f5904085a5cda800b5102923fc99301831f5769d8d4821e000773d2ea4c",
+    "reports/causal_graph_review/cache-provenance-20261008-batch105.json": "eca35700399c0be5808426ebbd9e899e3549d787825d9d95c34a9b888abc1d06",
+    "kb/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml": "0304999156eeec1556a337ff0138a6bfce205c38b9d5a8010051d864949a2a7f",
+    "kb/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.yaml": "e2555ecc152f3bbdbb5c2d557a17fc46da135500092494e0379c73fbb85c117a",
+    "kb/communities/Sphingobium_Rhodococcus_Lignin_Dimer_Valorization_Coculture.yaml": "fa5b1abb2f9493bb52263f1041fe4075028d57daf40abe7cd804edd6c65aa05c",
+    "kb/communities/Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml": "ece6ced257acf7538a072ee6fb940f73d96f0f36d83a6e1eae1514356884ab12"
+  },
+  "pre_research_baseline": {
+    "base_commit": "5d8eb3bd131fbf5c259038a2d45de27a39de0c72",
+    "base_tree": "fb89729566c9f3cbbb9237c3fcbde18e7cf52e59",
+    "research_worktree": "/private/tmp/communitymech-causal-batch104",
+    "checks": [
+      {
+        "name": "rank",
+        "command": [
+          "just",
+          "rank-causal-graphs"
+        ],
+        "exit_code": 0,
+        "expected_exit_code": 0,
+        "log": "/private/tmp/communitymech-batch105/baseline-rank.log",
+        "sha256": "87d98273ed34b3fb001881714f935b3921f774bbdb1c7b6091d0c4c5d75143e7"
+      },
+      {
+        "name": "just-network",
+        "command": [
+          "just",
+          "audit-network-json"
+        ],
+        "exit_code": 2,
+        "expected_exit_code": 2,
+        "log": "/private/tmp/communitymech-batch105/baseline-just-network.log",
+        "sha256": "8595db43420d3f0a01c57acd6ad733a531a72e962486d20b4e1c2840dda55bff"
+      },
+      {
+        "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-batch105/baseline-network.log",
+        "sha256": "8febc2a966f5c2b51cd59095a8877c8773cd1e9383e5214bcdc3832c5858c097"
+      },
+      {
+        "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-batch105/baseline-downstream.log",
+        "sha256": "6a1f0e1789315e27d0dfa2d2a7eba83fb675a9e2ce38aa438177fa29effa32ff"
+      }
+    ],
+    "baseline_sha256": "cc7fef283bf49b67d5c3e8b0edc947012b71370b73db9cb25458cdf2ddfcba45"
+  },
+  "reference_validator_caveat": "Four full-record CLI and local snippet checks executed on macOS,not Linux; DOI-cache casing issue1091 remains. Literal matches do not establish entailment; per-source read and access limits are recorded. CLI Total checks counts issues,not executed checks. Loader1703 not certified.",
+  "status": "verified_existing_graph_repairs_with_source_access_limits",
+  "total_recorded_gate_outputs": 42,
+  "review_metadata_correction": {
+    "reason": "Fresh issue body confirms847 removed unsupported mutualism typing, not environmental grounding. Corrected the new issue1824 body and uncommitted ledger/provenance wording; canonical records and all histories unchanged.",
+    "prior_validation_sha256": "ebd232ee64b13ab29deecb4fa310cacf45ea35be1b630e68e32f62ad4cd9964c",
+    "source": "https://github.com/CultureBotAI/CommunityMech/issues/847",
+    "raw_gate_logs_unchanged": true,
+    "focused_recheck_passed": true
+  }
+}
diff --git a/tests/test_causal_review_batch105.py b/tests/test_causal_review_batch105.py
new file mode 100644
index 000000000..d1111ed3b
--- /dev/null
+++ b/tests/test_causal_review_batch105.py
@@ -0,0 +1,120 @@
+"""Guard observation/mechanism, comparator and member-scope boundaries."""
+
+import hashlib
+from pathlib import Path
+
+import yaml
+
+ROOT = Path(__file__).resolve().parents[1]
+LEDGER = ROOT / "reports/causal_graph_review/decisions/20261008-four-records-batch105.yaml"
+
+
+def records():
+    ledger = yaml.safe_load(LEDGER.read_text())
+    rows = ledger["records"]
+    return ledger, rows, [yaml.safe_load((ROOT / r["path"]).read_text()) for r in rows]
+
+
+def test_colony_recovery_does_not_assert_competition_or_viability_loss():
+    _, _, docs = records()
+    (node,) = docs[0]["ecological_interactions"]
+    assert "interaction_type" not in node and not node.get("downstream")
+    assert "not definitive loss of viability" in node["description"]
+    assert "reciprocal negative effects" in node["description"]
+    assert node["participating_taxa"][0]["preferred_term"] == "Bacillus subtilis W2-B1-K4"
+    assert len(node["evidence"]) == 2
+    assert "confirmed metabolite activity" in docs[0]["discussions"][-1]["evidence"][1]["snippet"]
+
+
+def test_phenanthrene_pot_outcomes_keep_observed_support():
+    _, _, docs = records()
+    removal, carbon = docs[1]["ecological_interactions"]
+    assert "90.02%" in removal["description"] and "81.07%" in removal["description"]
+    for node in [removal, carbon]:
+        assert node["evidence"][0]["supports"] == "SUPPORT"
+        assert node["evidence"][0]["evidence_source"] == "IN_VIVO"
+        assert not node.get("downstream")
+
+
+def test_carbon_stocks_and_models_do_not_become_fixation_flux():
+    _, _, docs = records()
+    carbon = docs[1]["ecological_interactions"][1]
+    assert "metabolites" not in carbon and "biological_processes" not in carbon
+    assert "do not themselves quantify carbon-fixation flux" in carbon["description"]
+    model = carbon["evidence"][1]
+    assert model["supports"] == "PARTIAL" and model["evidence_source"] == "COMPUTATIONAL"
+    provenance = model["computational_provenance"]
+    assert provenance["prediction_type"] == "STATISTICAL_INFERENCE"
+    assert [t["tool_name"] for t in provenance["tools"]] == [
+        "random forest model",
+        "partial least-squares path modeling",
+    ]
+    assert all("version" not in t for t in provenance["tools"])
+
+
+def test_lignin_conversion_preserves_gallate_qualification_and_identity():
+    _, _, docs = records()
+    coupling, conversion, substrates = docs[2]["ecological_interactions"]
+    assert len(coupling["evidence"]) == 1
+    assert coupling["evidence"][0]["supports"] == "PARTIAL"
+    assert "HYPOTHESIZED:" in coupling["description"]
+    assert "simultaneous production" in conversion["description"]
+    assert "showed potential" in conversion["evidence"][1]["snippet"]
+    assert conversion["metabolites"][1]["term"] == {"id": "CHEBI:16918", "label": "gallate"}
+    assert all("interaction_type" not in n for n in [coupling, conversion, substrates])
+
+
+def test_lignin_retains_only_the_qualified_existing_causal_direction():
+    _, _, docs = records()
+    coupling, conversion, substrates = docs[2]["ecological_interactions"]
+    (edge,) = coupling["downstream"]
+    assert edge["target"] == conversion["name"]
+    assert edge["description"].startswith("HYPOTHESIZED/PARTIAL:")
+    assert not conversion.get("downstream") and not substrates.get("downstream")
+    assert "substrate-range evidence" in substrates["description"]
+
+
+def test_manure_comparators_and_member_transcripts_stay_separate():
+    _, _, docs = records()
+    doc = docs[3]
+    broth, plant, transcripts = doc["ecological_interactions"]
+    assert "monoculture, simultaneous co-culture" in broth["description"]
+    assert "41.4% versus the water control" in plant["description"]
+    assert all(e["evidence_source"] == "IN_VIVO" for e in plant["evidence"])
+    assert transcripts["participating_taxa"] == [
+        {k: doc["taxonomy"][0]["taxon_term"][k] for k in ["preferred_term", "term"]}
+    ]
+    assert "not demonstrated protein activity" in transcripts["description"]
+    assert all(not n.get("downstream") for n in doc["ecological_interactions"])
+
+
+def test_all_original_nodes_and_directions_have_dispositions():
+    ledger, rows, docs = records()
+    assert sum(len(r["node_decisions"]) for r in rows) == 9
+    assert sum(len(r["removed_node_decisions"]) for r in rows) == 0
+    assert sum(len(r["renamed_nodes"]) for r in rows) == 3
+    assert sum(len(r["retained_edge_decisions"]) for r in rows) == 1
+    assert sum(len(r["removed_edge_decisions"]) for r in rows) == 1
+    for row, doc in zip(rows, docs, strict=True):
+        assert hashlib.sha256((ROOT / row["path"]).read_bytes()).hexdigest() == row["record_sha256"]
+        assert row["status"] == "reviewed"
+        assert row["curation_events_added"] == len(row["history_files"]) == 1
+        assert (ROOT / row["history_files"][0]).is_file()
+        assert doc["curation_history"][-1]["llm_assisted"]
+    assert ledger["primary_graph_snippet_count"] == len(ledger["snippet_checks"]) == 17
+    assert len(ledger["discussion_snippet_checks"]) == 5
+    assert all(
+        c["cache_matched"] and c["independent_primary_match"]
+        for c in ledger["snippet_checks"] + ledger["discussion_snippet_checks"]
+    )
+
+
+def test_followups_and_provider_scope_are_not_silently_resolved():
+    ledger, _, _ = records()
+    assert ledger["issues"] == [1823, 1824, 1825, 1826]
+    assert ledger["unresolved_non_graph_issues"] == [1827]
+    assert ledger["unresolved_research_issues"] == []
+    assert not ledger["independent_approval"]
+    assert ledger["cache_changes"] == []
+    assert ledger["edison"]["provider_submissions"] == ledger["edison"]["credits_spent"] == 0
+    assert ledger["issue_deduplication"]["matching_issues"] == [771, 847, 848]
diff --git a/tests/test_participating_taxa.py b/tests/test_participating_taxa.py
index f8fdc7ad7..e8bc07d16 100644
--- a/tests/test_participating_taxa.py
+++ b/tests/test_participating_taxa.py
@@ -411,6 +411,7 @@ def test_a_curie_is_ambiguous_where_members_share_an_id(example):
     "Soybean_Chlorophyll_Selected_Biofertilizer_SynCom.yaml",
     "Soymilk_Mixed_Starter_Metabolic_Division_SynCom.yaml",
     "Space_Habitat_SevenMember_Stress_Tolerance_SynCom.yaml",
+    "Staged_Cattle_Manure_Ensifer_Bacillus_SynCom.yaml",
     "Sulfide_Spring_Autotrophic_CPR_Biofilm.yaml",
     "SynComBac10_Chicken_Intestinal_SynCom.yaml",
     "SynCom_Pseudomonas_Rahnella_Artemisia_Phytoremediation.yaml",