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Bound inferred support and community outcome causality (batch92) #1749

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50 changes: 42 additions & 8 deletions docs/communities/QY2S1_Dehalogenimonas_BFR_Bioremediation_Consortium.html
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Expand Up @@ -665,16 +665,16 @@ <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 QY2-S1 Dehalogenimonas-Rich Brominated-Flame-Retardant Consortium</title>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction (syntrophy).</desc>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
<span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -683,9 +683,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Fermenter-Methanogen Support for Dehalogenimonas RDase Activity</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Dominant Clostridium and Sedimentibacter fermenters and Methanoculleus methanogens form a syntrophic support network that can supply H2, carbon, and cofactors required for Dehalogenimonas reductive dehalogenase activity during BDE 99 and beta-TBCO organohalide respiration.</p>
<p class="prewrap interaction-description">HYPOTHESIZED: The authors propose that Clostridium and Sedimentibacter fermenters support Dehalogenimonas through hydrogen, carbon and cofactors. Methanoculleus is discussed as a hydrogen consumer that may indirectly favour fermentation, not as a demonstrated hydrogen donor. The QY2-S1 assays measured pollutant transformation and genus-level abundance, not partner-specific metabolite flux or product-removal feedback. The proposed support network is retained without categorical SYNTROPHY.</p>



Expand Down Expand Up @@ -726,7 +725,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42511722/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42511722</a>

- SUPPORT (IN_VITRO)
- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"This robust consortium forms a synergistic metabolic network, where fermentative bacteria and methanogens provide essential electron donors (H2), carbon source, and other growth cofactors, required for the RDase activity of the core OHRB, Dehalogenimonas"</div>
Expand Down Expand Up @@ -778,7 +777,7 @@ <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>
Expand All @@ -793,6 +792,41 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which partner exchanges and product-removal feedback, if any, support Dehalogenimonas in QY2-S1?
</h3>
<p class="prewrap">Section 2.3 proposes indirect methanogen support through hydrogen consumption. Absolute 16S abundance and pollutant/product kinetics do not isolate that feedback or demonstrate the proposed carbon/cofactor provision. Current SYNTROPHY does not assert obligacy; the missing criterion is demonstrated product-removal feedback. The positive transformation and co-exposure inhibition results remain unchanged outside this node.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Fermenter-Methanogen Support for Dehalogenimonas RDase Activity</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/42511722/" rel="nofollow noreferrer">PMID:42511722</a>


</div>
<p class="snippet small prewrap">By maintaining extremely low H2 partial pressures, methanogens prevent the feedback inhibition of fermentation</p>
<p class="muted small prewrap">Identifies the authors proposed feedback explanation, not a measured partner-specific perturbation or flux.</p>
</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -1234,7 +1268,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:0";
var intType = "SYNTROPHY";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down
30 changes: 24 additions & 6 deletions docs/communities/Quinoa_SCDY1_Salt_Stress_SynCom.html
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Expand Up @@ -813,16 +813,16 @@ <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 Quinoa SCDY1 Salt-Stress 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 (mutualism).</desc>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
<span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -831,9 +831,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>SCDY1 Arabidopsis salt-stress growth promotion</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">SCDY1 improved Arabidopsis root elongation and biomass under moderate sodium-chloride stress, with the clearest overall response at 120 mM NaCl.</p>
<p class="prewrap interaction-description">SCDY1 improved Arabidopsis root elongation and biomass under moderate sodium-chloride stress, with the clearest overall response at 120 mM NaCl. This is a host-growth outcome, not evidence of reciprocal fitness benefits to the plant and bacterial members.</p>



Expand Down Expand Up @@ -871,6 +870,25 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Does SCDY1 confer reciprocal fitness benefits, and which mechanisms mediate the plant-growth response?
</h3>
<p class="prewrap">The cited preprint abstract supports plant growth under salt stress and recovery of a subset of bacteria; recoverability alone does not establish bacterial benefit or unaffected fitness. Host transcriptional and root-hair responses are not demonstrated causal mediators. The complete preprint body was not retrieved in this review, so missing access is not evidence that additional controls are absent. The independently retrieved accepted journal abstract corroborates the endpoint, but does not supersede the historical preprint evidence. No COMMENSALISM substitution or previously removed recovery/epidermal node is added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#SCDY1 Arabidopsis salt-stress growth promotion</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1139,7 +1157,7 @@ <h2>Environmental Factors</h2>

(function() {
var intId = "interaction:0";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];

var processes = [];
Expand Down
63 changes: 43 additions & 20 deletions docs/communities/RH1_Glyphosate_Streptomyces_Consortium.html
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Expand Up @@ -657,16 +657,16 @@ <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 RH1 Glyphosate Streptomyces 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 (mutualism).</desc>
<desc id="network-svg-desc">Bipartite graph where circle nodes represent taxa and each ecological interaction is drawn as a distinct non-circular symbol, with colour repeating the same distinction.</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
<span class="legend-swatch legend-circle" style="background: #7a7a7a;"></span> Taxon
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -675,9 +675,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>RH1 glyphosate biodegradation</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The four Streptomyces members were compatible in the antagonism assay and, as the RH1 mixed culture, degraded glyphosate at all tested initial concentrations. At 50 mg/L glyphosate, RH1 exceeded the previously reported single-strain removal and TOC-reduction rates. Pairwise exchange metabolites and glyphosate-catabolic genes were not directly resolved.</p>
<p class="prewrap interaction-description">The four Streptomyces members were compatible in the antagonism assay and, as the RH1 mixed culture, degraded glyphosate at all tested initial concentrations. At 50 mg/L glyphosate, RH1 exceeded the previously reported single-strain removal and TOC-reduction rates. Pairwise exchange metabolites and glyphosate-catabolic genes were not directly resolved. Compatibility and greater aggregate performance do not establish reciprocal fitness benefits among the four members.</p>



Expand Down Expand Up @@ -707,16 +706,6 @@ <h3>RH1 glyphosate biodegradation</h3>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> RH1 total organic carbon reduction
<p class="prewrap causal-description">Glyphosate transformation by the mixed RH1 culture reduced TOC after 15 days at 50 mg/L initial glyphosate.</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -768,9 +757,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>RH1 total organic carbon reduction</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">At 50 mg/L initial glyphosate, the RH1 consortium removed 91.03% of measured total organic carbon over the 15-day incubation, supporting substantial transformation of glyphosate-derived organic carbon.</p>
<p class="prewrap interaction-description">At 50 mg/L initial glyphosate, RH1 showed a 91.03% decrease in measured total organic carbon after 15 days. TOC was measured after centrifugation and filtration. This positive processed-sample endpoint does not distinguish mineralization from biomass incorporation or other carbon partitioning, and does not independently establish a direct glyphosate-transformation-to-TOC causal link.</p>



Expand Down Expand Up @@ -817,7 +805,7 @@ <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>
Expand Down Expand Up @@ -854,6 +842,41 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
How are member fitness benefits and glyphosate-derived carbon partitioned in RH1?
</h3>
<p class="prewrap">The negative antagonism test demonstrates compatibility, not MUTUALISM. The single-strain comparisons cite earlier work, and consortium-level growth/removal does not measure each member benefit. Glyphosate removal, ATR-FTIR changes and TOC decline remain positive observations, but centrifuged/filtered TOC does not resolve mineralization versus biomass or other partitioning. The stoichiometric reaction is predicted, not an empirical carbon balance. The direct arrow between the two outcome nodes is removed while both endpoints and the existing unresolved-gene discussion are preserved.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#RH1 glyphosate biodegradation</code>, <code>ecological_interactions#RH1 total organic carbon reduction</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/42582159/" rel="nofollow noreferrer">PMID:42582159</a>


</div>
<p class="snippet small prewrap">After 15 days of incubation, samples were centrifuged, filtered, and diluted before analysis</p>
<p class="muted small prewrap">Methods 2.4 delimit the measured TOC fraction; this preparation does not itself resolve the missing carbon fate.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1355,7 +1378,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:0";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down Expand Up @@ -1387,7 +1410,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:1";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down
26 changes: 26 additions & 0 deletions .../QY2S1_Dehalogenimonas_BFR_Bioremediation_Consortium/2026-10-07T144612Z-codex-187f33.yaml
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@@ -0,0 +1,26 @@
history_version: 1
target:
kind: record
path: kb/communities/QY2S1_Dehalogenimonas_BFR_Bioremediation_Consortium.yaml
slug: QY2S1_Dehalogenimonas_BFR_Bioremediation_Consortium
session:
id: 2026-10-07T144612Z-codex-187f33
timestamp: '2026-10-07T14:46:12Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1746
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Qualify the existing support network as HYPOTHESIZED/PARTIAL, distinguish proposed
methanogen hydrogen consumption from donor provision, and remove categorical SYNTROPHY
without requiring obligacy.
details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch92.yaml
26 changes: 26 additions & 0 deletions history/records/Quinoa_SCDY1_Salt_Stress_SynCom/2026-10-07T144612Z-codex-71fc10.yaml
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@@ -0,0 +1,26 @@
history_version: 1
target:
kind: record
path: kb/communities/Quinoa_SCDY1_Salt_Stress_SynCom.yaml
slug: Quinoa_SCDY1_Salt_Stress_SynCom
session:
id: 2026-10-07T144612Z-codex-71fc10
timestamp: '2026-10-07T14:46:12Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1747
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain supported SCDY1 plant growth and its SUPPORT evidence; remove MUTUALISM
because the cited evidence does not establish reciprocal benefit, and record the abstract-only
access boundary.
details: Source-based self-adversarial review; reports/causal_graph_review/decisions/20261007-four-records-batch92.yaml
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