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Separate observed outcomes from causal inference (batch88) #1731

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138 changes: 94 additions & 44 deletions docs/communities/Propanotrophic_Chlorinated_Ethene_Cometabolism_Enrichment.html
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Original file line number Diff line number Diff line change
Expand Up @@ -754,36 +754,28 @@ <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 Propanotrophic Chlorinated Ethene Cometabolism Enrichment Cultures</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, 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">
<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="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="symbolTimes"
data-color="#a91919"></svg> Competition
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Propane-Cometabolic TCE Degradation by Rhodococcus</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>TCE Removal in Rhodococcus-Dominated Enrichments</h3>
</div>
<p class="prewrap interaction-description">Rhodococcus opacus and R. wratislaviensis populations dominate TCE-amended enrichments and degrade TCE while propane is supplied as the growth substrate. The Rhodococcus MAGs carry the group-5 propane monooxygenase operon (prmABCD); functional gene analysis identified both group 5 and putative group 6 propane monooxygenases in the community but expression was not examined, so the specific enzyme responsible for TCE oxidation in vivo is not directly demonstrated.</p>
<p class="prewrap interaction-description">Propane-enriched mixed cultures sustained TCE degradation and were dominated by Rhodococcus; recovered MAGs were classified as R. opacus or R. wratislaviensis. PARTIAL: abundance and monooxygenase genes do not assign the measured community transformation to a particular taxon or enzyme. Gene expression was not examined.</p>


<p><strong>Source Taxon:</strong> Rhodococcus opacus</p>



<p><strong>Participating Taxa:</strong>
Expand Down Expand Up @@ -860,13 +852,10 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Propane-Cometabolic cDCE Degradation by Mycolicibacterium and Mycobacterium</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>cDCE Removal in Mycobacterium and Mycolicibacterium Enrichments</h3>
</div>
<p class="prewrap interaction-description">Mycolicibacterium dominates and Mycobacterium follows in all four cDCE-amended enrichments; both genera carry propane monooxygenase operons (with prmACDB ordering for the Mycobacterium MAGs, suggestive of group-6 SDIMOs) that drive cometabolic cDCE oxidation while propane is the growth substrate.</p>

<p class="prewrap interaction-description">Propane-enriched mixed cultures sustained cDCE degradation and were dominated by Mycobacterium and Mycolicibacterium. PARTIAL: genus abundance does not establish which organisms or enzymes performed the community transformation. The accessible abstract does not establish an interspecies transfer route.</p>

<p><strong>Source Taxon:</strong> Mycolicibacterium</p>



Expand Down Expand Up @@ -932,10 +921,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Substrate-Specific Selection Across Chlorinated Ethenes</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">cDCE, TCE, and 1,1-DCE select for taxonomically distinct propanotrophic guilds within the same starting inocula: cDCE selects for Mycolicibacterium/Mycobacterium, TCE selects for Rhodococcus, and 1,1-DCE re-selects for Pseudonocardia. This is competition mediated by differential tolerance/transformation of each chlorinated substrate rather than direct interaction between the guilds.
</p>
<p class="prewrap interaction-description">Different chlorinated substrates were associated with distinct enrichment compositions and degradation behavior. Preserve the reported substrate-dependent selection without equating environmental filtering with demonstrated competition among guilds. This record combines separate enrichment treatments, not one fixed community.</p>



Expand Down Expand Up @@ -977,15 +964,13 @@ <h3>Substrate-Specific Selection Across Chlorinated Ethenes</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Propane-Cometabolic TCE Degradation by Rhodococcus
<p class="prewrap causal-description">TCE-specific pressure selected Rhodococcus-dominated enrichments that carried group-5 propane monooxygenase operons and sustained propane-driven TCE cometabolism.
</p>
<span class="flow-arrow">→</span> TCE Removal in Rhodococcus-Dominated Enrichments
<p class="prewrap causal-description">PARTIAL: substrate-specific selection is the authors explanation for Rhodococcus-dominated communities sustaining TCE transformation. The abstract supports the treatment-linked structure/function pattern, not isolated taxon or enzyme mediation.</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Propane-Cometabolic cDCE Degradation by Mycolicibacterium and Mycobacterium
<p class="prewrap causal-description">cDCE-specific pressure selected Mycolicibacterium/Mycobacterium enrichments that dominated the cDCE-amended transfers and carried propane monooxygenase operons.
</p>
<span class="flow-arrow">→</span> cDCE Removal in Mycobacterium and Mycolicibacterium Enrichments
<p class="prewrap causal-description">PARTIAL: substrate-specific selection is the authors explanation for Mycobacterium/Mycolicibacterium-dominated communities sustaining cDCE transformation. Dominance does not identify the active organism or monooxygenase.</p>
</div>

</div>
Expand Down Expand Up @@ -1028,9 +1013,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>1,1-DCE-Driven Inhibition of Propanotrophs</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">1,1-DCE biodegradation is restricted to a subset of cultures and stalls at elevated concentrations; propane biodegradation slowed during 1,1-DCE exposure and resumed when TCE was substituted, consistent with inhibitory or toxic effects on propanotrophs at the elevated concentrations tested. The paper does not separate inhibition by the parent 1,1-DCE from inhibition by its transformation products.</p>
<p class="prewrap interaction-description">1,1-DCE removal occurred in only some enrichments, took longer over transfers and was absent at elevated concentrations. PARTIAL: these observations are consistent with inhibitory or toxic effects, not demonstrated interspecies competition or an identified toxic agent.</p>



Expand Down Expand Up @@ -1069,7 +1053,7 @@ <h3>1,1-DCE-Driven Inhibition of Propanotrophs</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Substrate-Specific Selection Across Chlorinated Ethenes
<p class="prewrap causal-description">1,1-DCE toxicity restricted which propanotrophic cultures persisted, contributing to the broader chlorinated-ethene-specific selection of distinct actinobacterial genera.</p>
<p class="prewrap causal-description">HYPOTHESIZED: inhibition could contribute to substrate-dependent selection by restricting community function. The abstract does not isolate toxicity as the cause of taxonomic replacement.</p>
</div>

</div>
Expand Down Expand Up @@ -1101,6 +1085,56 @@ <h4>Evidence</h4>

<!-- Associated Datasets -->

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

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which activities connect substrate selection to measured mixed-culture transformation?
</h3>
<p class="prewrap">Retain all four findings and three existing directions with explicit inference bounds. Only the fresh primary abstract was accessible. Monooxygenase expression was not examined; taxon dominance is not enzyme activity or partner exchange. Detailed kinetic and operon assertions outside this graph remain part of #765 after paywalled-body removal under #754. Missing access is not evidence that experiments were absent. No new nodes or directions were added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#TCE Removal in Rhodococcus-Dominated Enrichments</code>, <code>ecological_interactions#cDCE Removal in Mycobacterium and Mycolicibacterium Enrichments</code>, <code>ecological_interactions#Substrate-Specific Selection Across Chlorinated Ethenes</code>, <code>ecological_interactions#1,1-DCE-Driven Inhibition of Propanotrophs</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">COMPUTATIONAL</span>
<span class="badge small">SUPPORT</span>


<a href="https://doi.org/10.1016/j.jenvman.2026.129957" rel="noreferrer">doi:10.1016/j.jenvman.2026.129957</a>

</div>
<p class="snippet small prewrap">Functional gene analysis identified both group 5 (prmABCD) and putative group 6 propane monooxygenases</p>
<p class="muted small prewrap">Supports community monooxygenase gene content, not taxon-specific enzyme expression, activity or cross-feeding.</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://doi.org/10.1016/j.jenvman.2026.129957" rel="noreferrer">doi:10.1016/j.jenvman.2026.129957</a>

</div>
<p class="snippet small prewrap">1,1-DCE removal was absent at elevated concentrations, both trends consistent with inhibitory or toxic effects</p>
<p class="muted small prewrap">Supports restricted removal consistent with inhibition, not proof of the toxic agent or selection mechanism.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1404,7 +1438,7 @@ <h3>

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


Expand All @@ -1423,7 +1457,7 @@ <h3>

nodes.push({
id: intId,
label: "Propane-Cometabolic TCE Degradation by Rhodococcus",
label: "TCE Removal in Rhodococcus-Dominated Enrichments",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1432,18 +1466,26 @@ <h3>
});


var srcKey = "Rhodococcus opacus";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

"Rhodococcus opacus",

"Rhodococcus wratislaviensis"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

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


Expand All @@ -1462,7 +1504,7 @@ <h3>

nodes.push({
id: intId,
label: "Propane-Cometabolic cDCE Degradation by Mycolicibacterium and Mycobacterium",
label: "cDCE Removal in Mycobacterium and Mycolicibacterium Enrichments",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1471,18 +1513,26 @@ <h3>
});


var srcKey = "Mycolicibacterium";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

"Mycolicibacterium",

"Mycobacterium"

];
participantKeys.forEach(function(key) {
if (taxonNodeIds[key]) {
links.push({ source: taxonNodeIds[key], target: intId });
}
});

})();

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


Expand Down Expand Up @@ -1518,7 +1568,7 @@ <h3>

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


Expand Down
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