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Correct exact-system dechlorination and biochar causality (batch 31) #1393

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66 changes: 38 additions & 28 deletions docs/communities/Dehalococcoides_Pelobacter_Acetylene_TCE_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -585,26 +585,21 @@ <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 Dehalococcoides-Pelobacter Acetylene TCE 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, syntrophy, colonization facilitation).</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 (syntrophy).</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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -615,7 +610,7 @@ <h2>Ecological Interactions</h2>
<h3>Acetylene-Fueled Dechlorinating Coculture</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Pelobacter strain SFB93 enables a defined coculture in which acetylene is supplied as electron donor and carbon source while D. mccartyi strain 195 uses TCE as the electron acceptor for reductive dechlorination.</p>
<p class="prewrap interaction-description">SFB93 fermentation allows acetylene to supply electron donor and carbon for the defined strain-195 coculture through hydrogen and acetate provision. Strain 195 reductively dechlorinates TCE, predominantly to vinyl chloride under the reported conditions. The BAV1 coculture and the ANAS enrichment are separate systems.</p>


<p><strong>Source Taxon:</strong> Pelobacter strain SFB93</p>
Expand Down Expand Up @@ -658,8 +653,7 @@ <h3>Acetylene-Fueled Dechlorinating Coculture</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> D. mccartyi Reductive Dechlorination
<p class="prewrap causal-description">Pelobacter fermentation lets acetylene serve as the reduced substrate that fuels D. mccartyi organohalide respiration of TCE in the defined coculture.
</p>
<p class="prewrap causal-description">SFB93 acetylene fermentation supplies hydrogen and acetate that support strain-195 TCE dechlorination and growth. This positive nutritional coupling is distinct from removal of an initially inhibitory acetylene exposure; it does not assign BAV1 vinyl-chloride respiration to strain 195.</p>
</div>

</div>
Expand Down Expand Up @@ -702,17 +696,14 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>D. mccartyi Reductive Dechlorination</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">D. mccartyi strain 195 performs reductive dechlorination of TCE in the coculture; transcriptomic observations indicate that reductive dehalogenase genes such as tceA were monitored during acetylene inhibition.</p>
<p class="prewrap interaction-description">Strain 195 performs hydrogen-dependent reductive dechlorination of TCE in the coculture, predominantly producing vinyl chloride. This is the recipient phenotype, not nutrient transfer back to SFB93. In separate acetylene-inhibited strain-195 assays, unchanged tceA transcript abundance does not establish induction-mediated rescue or identify the inhibited enzyme.</p>


<p><strong>Source Taxon:</strong> Dehalococcoides mccartyi strain 195</p>



<p><strong>Target Taxon:</strong> Pelobacter strain SFB93</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -766,7 +757,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/28075122/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28075122</a>

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

<div class="snippet">"genes encoding for reductive dehalogenases"</div>
Expand All @@ -780,15 +771,16 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>SFB93-Mediated Relief of Acetylene Inhibition</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Addition of the acetylene-fermenting SFB93 partner removed acetylene inhibition of reductive dechlorination and methanogenesis in the ANAS enrichment, supporting the functional relevance of pairing acetylene metabolism with dechlorinating organisms.</p>
<p class="prewrap interaction-description">Adding SFB93 to acetylene-inhibited strain-195 cultures consumed acetylene and restored TCE reductive dechlorination in the primary study. This exact-pair rescue is distinct from the separate ANAS enrichment and its condition-dependent methanogenesis response; it is detoxification support, not demonstrated colonization facilitation.</p>


<p><strong>Source Taxon:</strong> Pelobacter strain SFB93</p>



<p><strong>Target Taxon:</strong> Dehalococcoides mccartyi strain 195</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -819,8 +811,7 @@ <h3>SFB93-Mediated Relief of Acetylene Inhibition</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> D. mccartyi Reductive Dechlorination
<p class="prewrap causal-description">Acetylene fermentation by SFB93 relieves acetylene inhibition of organohalide respiration, allowing D. mccartyi to resume reductive dechlorination in acetylene-fed cultures.
</p>
<p class="prewrap causal-description">SFB93 consumption of inhibitory acetylene permits strain 195 to resume TCE reductive dechlorination, as tested by delayed partner addition in the primary Results and Figure 2 caption. The local abstract rescue phrase concerns ANAS and alone does not establish this exact-pair result; ANAS methanogenesis is not transferred to this arrow.</p>
</div>

</div>
Expand All @@ -836,7 +827,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/28075122/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28075122</a>

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

<div class="snippet">"inhibition was removed by adding Pelobacter SFB93"</div>
Expand Down Expand Up @@ -903,6 +894,25 @@ <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 acetylene-sensitive processes limit strain-195 recovery after SFB93 addition?
</h3>
<p class="prewrap">The whole primary main body and six figure captions were read. Figure 2 reports exact strain-195 rescue after delayed SFB93 addition; the cached abstract rescue sentence instead concerns ANAS. Unchanged tceA transcription does not identify the inhibited enzyme. Distinguish the nutritional coculture, inhibited-isolate rescue and ANAS methanogenesis assays. Exact-pair body evidence is not locally snippet-verifiable. Existing non-graph evidence debt remains under #765; the curated Syntrophotalea grounding is unchanged. No figure images, Table 1 or supplements were inspected.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Acetylene-Fueled Dechlorinating Coculture</code>, <code>ecological_interactions#D. mccartyi Reductive Dechlorination</code>, <code>ecological_interactions#SFB93-Mediated Relief of Acetylene Inhibition</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1332,7 +1342,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1367,16 +1377,11 @@ <h4 style="color: var(--text);">Evidence</h4>



var tgtKey = "Pelobacter strain SFB93";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();

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


Expand Down Expand Up @@ -1409,6 +1414,11 @@ <h4 style="color: var(--text);">Evidence</h4>



var tgtKey = "Dehalococcoides mccartyi strain 195";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();


Expand Down
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