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Qualify cross-study and omics claims in four community graphs (batch106) #1835

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143 changes: 73 additions & 70 deletions docs/communities/Staphylococcus_Candida_Context_Dependent_Biofilm_Coculture.html
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238 changes: 132 additions & 106 deletions docs/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.html
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96 changes: 70 additions & 26 deletions docs/communities/Streptomyces_A2_A5_A11_M7_Pesticide_Consortium.html
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Original file line number Diff line number Diff line change
Expand Up @@ -634,16 +634,16 @@ <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 Streptomyces A2-A5-A11-M7 Pesticide-Bioremediation 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 @@ -652,10 +652,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Non-antagonistic community-level growth enhancement</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The four strains showed no detectable antagonism in the reported screen, and the A2-A5-A11-M7 mixed culture accumulated more biomass than the corresponding pure cultures in pesticide-supplemented minimal medium. Pairwise directions and exchanged metabolites were not resolved.
</p>
<p class="prewrap interaction-description">The exact four-strain mixture showed non-antagonism and greater aggregate biomass than the corresponding pure cultures in the reported pesticide experiment. These observations do not measure reciprocal benefit to each member. The 2013 paper includes other mixtures, including a six-member immobilized system whose results are not assigned to this four-member record.</p>



Expand Down Expand Up @@ -713,7 +711,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41678860/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41678860</a>

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

<div class="snippet">"revealing their metabolic versatility and potential cooperative work, fundamental for the degradation of xenobiotic compounds."</div>
Expand All @@ -726,11 +724,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>C1 Distributed Atrazine Catabolism</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>C1 Herbicide-Catabolism Gene Detection</h3>
</div>
<p class="prewrap interaction-description">Every Streptomyces member of C1 carried at least one gene encoding an herbicide-degradation enzyme, supporting atrazine catabolic capacity distributed across the exact A2-A5-A11-M7 consortium.
</p>
<p class="prewrap interaction-description">The 2026 source detected at least one herbicide-catabolism-associated gene in each C1 member. This supports distributed genetic potential, not measured expression, enzyme activity or a demonstrated contribution of each member to removal.</p>



Expand Down Expand Up @@ -765,8 +761,7 @@ <h3>C1 Distributed Atrazine Catabolism</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> C1 Atrazine Growth and Removal
<p class="prewrap causal-description">Distributed herbicide-catabolism genes provide the mechanistic basis for C1 growth on and removal of atrazine as a sole carbon or nitrogen source.
</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: the detected catabolic genes could underlie the reported C1 atrazine growth/removal phenotype. The accessible abstract reports gene presence and community outcomes but does not isolate gene activity or member-specific contributions as causal mediators.</p>
</div>

</div>
Expand Down Expand Up @@ -796,10 +791,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>C1 Atrazine Growth and Removal</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The exact A2-A5-A11-M7 consortium grew on atrazine supplied as either the sole carbon source or sole nitrogen source while removing the herbicide from liquid cultures.
</p>
<p class="prewrap interaction-description">The exact A2-A5-A11-M7 consortium showed growth and atrazine removal in the source nutrient-role comparisons. Preserve these observed liquid-culture outcomes without treating parent-compound removal as complete mineralization or measured reciprocal partner benefit.</p>



Expand Down Expand Up @@ -834,8 +827,7 @@ <h3>C1 Atrazine Growth and Removal</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> C1 Atrazine Phytotoxicity Reversal
<p class="prewrap causal-description">Atrazine growth and removal by C1 reduces the herbicide toxicity of the treated liquid system.
</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: atrazine removal could contribute to the reported decrease in phytotoxicity after C1 treatment. The accessible abstract does not establish parent-compound depletion as the sole cause, resolve transformation-product effects or demonstrate complete mineralization.</p>
</div>

</div>
Expand Down Expand Up @@ -865,10 +857,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>C1 Atrazine Phytotoxicity Reversal</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Liquid cultures treated with the C1 consortium were detoxified enough to reverse the measured phytotoxicity of atrazine, especially when atrazine was supplied as the carbon source.
</p>
<p class="prewrap interaction-description">The source phytotoxicity tests found that C1 treatment reversed the measured herbicide toxicity, with differing outcomes across the nutrient-role comparisons. Preserve this positive tested endpoint without attributing it exclusively to parent-compound depletion or generalizing it to all toxicity endpoints.</p>



Expand Down Expand Up @@ -925,6 +915,60 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

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

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Do the detected genes and atrazine removal independently establish the mechanisms of C1 performance and reduced phytotoxicity?
</h3>
<p class="prewrap">Retain the exact four-member observations. Aggregate biomass and compatibility are not reciprocal benefit. Gene detection does not establish expression or flux, and treatment-associated phytotoxicity reversal does not isolate its mediator. Keep the two existing directions qualified; do not transfer six-member immobilized-culture results. The 2026 abstract and bounded 2013 results were read, not full methods or all source formulations.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Non-antagonistic community-level growth enhancement</code>, <code>ecological_interactions#C1 Herbicide-Catabolism Gene Detection</code>, <code>ecological_interactions#C1 Atrazine Growth and Removal</code>, <code>ecological_interactions#C1 Atrazine Phytotoxicity Reversal</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/41678860/" rel="nofollow noreferrer">PMID:41678860</a>


</div>
<p class="snippet small prewrap">the presence of at least one of the genes that encode enzymes involved in the herbicide degradation was detected in all C1 members.</p>
<p class="muted small prewrap">Supports distribution of herbicide-catabolic potential across all four consortium members.</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/41678860/" rel="nofollow noreferrer">PMID:41678860</a>


</div>
<p class="snippet small prewrap">Phytotoxicity tests demonstrated the ability of C1 to reverse the herbicide toxicity, especially with atrazine as a carbon source.</p>
<p class="muted small prewrap">Supports the reported post-treatment phytotoxicity endpoint, not an isolated depletion-mediated causal mechanism.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1675,7 +1719,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1709,7 +1753,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1726,7 +1770,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "C1 Distributed Atrazine Catabolism",
label: "C1 Herbicide-Catabolism Gene Detection",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1741,7 +1785,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:2";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down Expand Up @@ -1773,7 +1817,7 @@ <h4 style="color: var(--text);">Evidence</h4>

(function() {
var intId = "interaction:3";
var intType = "MUTUALISM";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down
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