Bound wetland cross-feeding and magnetite claims (batch66)

docs/communities/MWF001_FourSpecies_CrossFeeding_Consortium.html

@@ -618,7 +618,7 @@ <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 MWF001 Four-Species Cross-Feeding Consortium</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, niche partitioning).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -631,8 +631,8 @@ <h2>Ecological Interactions</h2>
                     </div>
                     <div class="legend-item">
                         <svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
-                             aria-hidden="true" data-symbol="symbolSquare2"
-                             data-color="#1212ed"></svg> Niche partitioning
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -643,11 +643,23 @@ <h2>Ecological Interactions</h2>
                     <h3>Cross-fed metabolic byproduct partitioning</h3>
                     <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">The four MWF001 strains coexisted because they generated and partitioned metabolic byproducts that supported cross-feeding beyond the externally supplied carbon source.</p>
+                <p class="prewrap interaction-description">PARTIAL - partner spent-media growth and persistence of primary-carbon-source nonusers support byproduct cross-feeding in MWF001. All four strains grew better in partner spent medium than their own, but exact exchanged compounds and donor-recipient fluxes were not chemically resolved. Unchanged stationary OD does not establish complete primary-substrate depletion; the greater-than-10-percent residual-resource exclusion described in Methods applies to simulations, not an equivalent experimental chemical assay. Generic consumer-resource models support coexistence through byproduct availability and differential resource affinities, not exact four-strain pathways. Fresh-medium pair effects were positive or negative depending on partner and condition, so reciprocal benefit is not universal.</p>
 
 
 
 
+                <p><strong>Participating Taxa:</strong>
+
+                    Agrobacterium tumefaciens MWF001,
+
+                    Comamonas testosteroni MWF001,
+
+                    Microbacterium liquefaciens MWF001,
+
+                    Ochrobactrum anthropi MWF001
+
+                </p>
+
 
 
 
@@ -665,7 +677,7 @@ <h4>Evidence</h4>
                             <a href="https://pubmed.ncbi.nlm.nih.gov/42752228/"
                                class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42752228</a>
 
-                            - SUPPORT (IN_VITRO)
+                            - PARTIAL (IN_VITRO)
                         </div>
 
                         <div class="snippet">"experimental assays and consumer-resource modeling showed that the coexistence was explained by cross-feeding and niche partitioning of metabolic byproducts"</div>
@@ -692,12 +704,23 @@ <h4>Evidence</h4>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Robust coexistence across simple nutrient environments</h3>
-                    <span class="interaction-type">NICHE_PARTITIONING</span>
                 </div>
-                <p class="prewrap interaction-description">All four members survived eight serial batch transfers across the first 31 single- or paired-resource M9 media tested, despite several media supplying only one carbon source.</p>
+                <p class="prewrap interaction-description">All four strains remained detectable through eight 72-hour growth-and-dilution cycles in 31 carbon-supplied conditions, including 16 single-resource environments. These finite observations support broad conditional persistence, not asymptotic stability or a measured niche-partitioning mechanism. Additional 5X-malate conditions lost Comamonas after the first transfer; Microbacterium did not persist without carbon. The initial batch panel used 1/100 transfers except 1/10 for citrate and inosine, with the first citrate transfer at 1/100. Separate four-day chemostats on four single carbon sources also retained all four strains. The canonical participants preserve the source roster and prior unresolved taxonomic mappings, not independently recertified identities.</p>
+
+
+
 
+                <p><strong>Participating Taxa:</strong>
 
+                    Agrobacterium tumefaciens MWF001,
 
+                    Comamonas testosteroni MWF001,
+
+                    Microbacterium liquefaciens MWF001,
+
+                    Ochrobactrum anthropi MWF001
+
+                </p>
 
 
 
@@ -733,7 +756,7 @@ <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>
@@ -748,6 +771,21 @@ <h3>
 
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    How strongly does byproduct partitioning support the observed coexistence?
+                </h3>
+                <p class="prewrap">The complete primary text supports considering a PARTIAL arrow from cross-feeding/byproduct partitioning to coexistence, with generic-model, residual-substrate and exact-metabolite limits. This new causal structure is tracked in #1575: the free one-community Edison causal dry run passed, but the paid run and report review are not complete. Keep needs_research rather than calling the sparse graph complete. Preserve the existing exact-byproduct gap and #1127/#1128 safeguards. Protocol and source inconsistencies remain under #1574. Original figure pixels, separate supplements, raw data and executable models were not audited.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Cross-fed metabolic byproduct partitioning</code>, <code>ecological_interactions#Robust coexistence across simple nutrient environments</code></p>
+
+
+
+
             </div>
 
         </section>
@@ -1228,11 +1266,28 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Agrobacterium tumefaciens MWF001",
+
+                "Comamonas testosteroni MWF001",
+
+                "Microbacterium liquefaciens MWF001",
+
+                "Ochrobactrum anthropi MWF001"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {
             var intId = "interaction:1";
-            var intType = "NICHE_PARTITIONING";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
             var processes = [];
@@ -1252,6 +1307,23 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Agrobacterium tumefaciens MWF001",
+
+                "Comamonas testosteroni MWF001",
+
+                "Microbacterium liquefaciens MWF001",
+
+                "Ochrobactrum anthropi MWF001"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
 

docs/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.html

@@ -748,7 +748,7 @@ <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 Magnetite Sulfate-Stress Anaerobic Microbiome</title>
-                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding, syntrophy).</desc>
+                    <desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (cross-feeding).</desc>
                 </svg>
                 <div class="network-legend">
                     <div class="legend-item">
@@ -761,8 +761,8 @@ <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="symbolTriangle"
-                             data-color="#7f30cf"></svg> Syntrophy
+                             aria-hidden="true" data-symbol="symbolTriangle2"
+                             data-color="#929caa"></svg> Other
                     </div>
                 </div>
             </div>
@@ -771,13 +771,23 @@ <h2>Ecological Interactions</h2>
             <div class="interaction-card">
                 <div class="interaction-header">
                     <h3>Magnetite-enhanced methanogenesis under sulfate stress</h3>
-                    <span class="interaction-type">SYNTROPHY</span>
                 </div>
-                <p class="prewrap interaction-description">Adding 10 g/L magnetite to the 0.6 g/L sulfate condition relieved the sulfate-associated methane-production penalty, reduced sulfide stress through precipitation, and increased CH4 production by 19% relative to the sulfate-only treatment without eliminating sulfate-reducer activity.
-</p>
+                <p class="prewrap interaction-description">At 0.6 g/L sulfate, 10 g/L magnetite increased cumulative methane by 19% relative to the sulfate-only treatment in five-day batch assays, without reducing sulfate consumption. This is partial improvement, not full sulfate-free recovery or rescue at 1.2 g/L sulfate. Separate abiotic tests showed sulfide removal and sulfur retained on magnetite, but elemental analysis did not resolve sulfur species and no abiotic hydrogen accumulation was detected. These results support toxicity mitigation as a contributing interpretation; they do not isolate its mediation of the methane response or demonstrate syntrophy or direct interspecies electron transfer. The four guilds identify an incomplete community context, not all organisms contributing to the bulk endpoints.</p>
+
+
+
+
+                <p><strong>Participating Taxa:</strong>
 
+                    Methanoculleus methanogenic MAGs,
+
+                    putative sulfate-reducing MAGs,
+
+                    Limnochordia homoacetogenic MAGs,
 
+                    Dethiobacteria syntrophic acetate-oxidizing MAGs
 
+                </p>
 
 
 
@@ -860,8 +870,7 @@ <h4>Evidence</h4>
                     <h3>Acetate-centered four-guild redox cycling</h3>
                     <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">Genome-scale metabolic models for the representative methanogen, SRB, homoacetogen, and SAOB MAGs supported acetate turnover in which the homoacetogen consumes H2 and CO2 to secrete acetate, and acetate is then oxidized back to H2 and CO2 by SAOB or used by SRB as an electron donor for sulfate reduction.
-</p>
+                <p class="prewrap interaction-description">HYPOTHESIZED - condition-specific four-member GEMs predict acetate-centered exchange: a homoacetogen uses H2/CO2 and secretes acetate, a syntrophic acetate oxidizer returns H2/CO2, and a putative sulfate reducer oxidizes acetate while reducing sulfate, with the shared pool supporting hydrogenotrophic methanogenesis. Representatives are Methanoculleus DTU8, Halopseudomonas DTU25, Limnochordia DTU38 and Dethiobacteria DTU36, not every MAG in the four canonical guild placeholders. Models were gap-filled and curated for expected roles, constrained by measured reactor outputs, and analyzed using MICOM cooperative trade-off 0.7 and flux-space sampling. Agreement is stoichiometric feasibility under assumptions, not independent validation, measured partner flux or demonstrated DIET. One biological replicate per sequenced condition and relative MAG abundances cannot establish replicated absolute guild growth.</p>
 
 
 
@@ -967,8 +976,7 @@ <h4>Evidence</h4>
                     <h3>Model-predicted amino-acid and organic-acid exchange</h3>
                     <span class="interaction-type">CROSS_FEEDING</span>
                 </div>
-                <p class="prewrap interaction-description">Flux-space sampling of the community GEMs predicted exchange of glucogenic amino acids and short-chain organic acids among the four modeled guilds, with the homoacetogen, SAOB, and methanogen acting as major exchange hubs and the SRB predicted to import several amino acids.
-</p>
+                <p class="prewrap interaction-description">HYPOTHESIZED - flux-space sampling of the four representative GEMs predicts exchange of amino acids and organic acids, with the homoacetogen, acetate oxidizer and methanogen serving as modeled hubs and the putative sulfate reducer importing multiple amino acids. The reported heatmaps select mean exchange fluxes above 0.1 mmol/gDW/hour from feasible solutions; these are model summaries, not extracellular metabolomics or traced donor-recipient rates. Multiple solutions satisfy the imposed constraints, and regulation, protein capacity and kinetics are not resolved. These exchanges could support alternative metabolic routes, but actual necessity, universal mutualism and specific partner transfers remain untested.</p>
 
 
 
@@ -1075,7 +1083,7 @@ <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>
@@ -1114,6 +1122,21 @@ <h3>
                 </details>
 
 
+            </div>
+
+            <div class="discussion">
+                <h3>
+                    <span class="role-badge">KNOWLEDGE_GAP</span>
+                    <span class="role-badge">OPEN</span>
+                    Which processes mediate magnetite-associated methane improvement?
+                </h3>
+                <p class="prewrap">Keep zero arrows and preserve #914 backward-edge removal. Separate abiotic sulfide removal, replicated bulk methane response and single-replicate compositional metagenomics. Feasibility of role-curated and output-constrained GEMs does not independently verify partner flux. Retain the existing direct-DIET knowledge gap, #913 putative-SRB caveats and #915 restriction to MAGN_0.6. Myxococcota DTU51 lacks sulfate-reduction genes; do not silently promote it to a validated reducer. Source metadata and identity limits remain under #1574. Complete primary main text and figure captions read, not original figure pixels, separate supplements, raw data or executable models.</p>
+
+                <p class="muted small">Attaches to: <code>ecological_interactions#Magnetite-enhanced methanogenesis under sulfate stress</code>, <code>ecological_interactions#Acetate-centered four-guild redox cycling</code>, <code>ecological_interactions#Model-predicted amino-acid and organic-acid exchange</code></p>
+
+
+
+
             </div>
 
         </section>
@@ -1508,7 +1531,7 @@ <h4 style="color: var(--text);">Evidence</h4>
 
         (function() {
             var intId = "interaction:0";
-            var intType = "SYNTROPHY";
+            var intType = "UNKNOWN";
             var metabolites = [];
 
 
@@ -1542,6 +1565,23 @@ <h4 style="color: var(--text);">Evidence</h4>
 
 
 
+            var participantKeys = [
+
+                "Methanoculleus methanogenic MAGs",
+
+                "putative sulfate-reducing MAGs",
+
+                "Limnochordia homoacetogenic MAGs",
+
+                "Dethiobacteria syntrophic acetate-oxidizing MAGs"
+
+            ];
+            participantKeys.forEach(function(key) {
+                if (taxonNodeIds[key]) {
+                    links.push({ source: taxonNodeIds[key], target: intId });
+                }
+            });
+
         })();
 
         (function() {

history/records/MUCC_Freshwater_Wetland_Methane_Network_Community/2026-10-06T230847Z-codex-95d09c.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/MUCC_Freshwater_Wetland_Methane_Network_Community.yaml
+  slug: MUCC_Freshwater_Wetland_Methane_Network_Community
+session:
+  id: 2026-10-06T230847Z-codex-95d09c
+  timestamp: '2026-10-06T23:08:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1571
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Bound wetland co-occurrence and Methanoregula predictions to observational and
+    genomic evidence.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml

history/records/MWF001_FourSpecies_CrossFeeding_Consortium/2026-10-06T230847Z-codex-73e39c.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/MWF001_FourSpecies_CrossFeeding_Consortium.yaml
+  slug: MWF001_FourSpecies_CrossFeeding_Consortium
+session:
+  id: 2026-10-06T230847Z-codex-73e39c
+  timestamp: '2026-10-06T23:08:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1572
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Qualify MWF001 cross-feeding and finite coexistence; keep causal extension research
+    open.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml

history/records/Magnetite_Sulfate_Stress_Anaerobic_Microbiome/2026-10-06T230847Z-codex-cac4a6.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: kb/communities/Magnetite_Sulfate_Stress_Anaerobic_Microbiome.yaml
+  slug: Magnetite_Sulfate_Stress_Anaerobic_Microbiome
+session:
+  id: 2026-10-06T230847Z-codex-cac4a6
+  timestamp: '2026-10-06T23:08:47Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: unspecified
+    agent_tool: codex
+links:
+  issues:
+  - https://github.com/CultureBotAI/CommunityMech/issues/1573
+events:
+- type: EDIT
+  outcome: changed
+  sections:
+  - interactions
+  - discussions
+  summary: Separate magnetite methane response from unvalidated DIET and constrained model
+    flux.
+  details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-wetland-crossfeeding-batch66.yaml