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Bound enrichment and Core-20 causal mechanisms (batch51) #1500

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35 changes: 24 additions & 11 deletions docs/communities/High_Ammonia_Biogas_0B_Butyrate_Oxidizing_Enrichment.html
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Expand Up @@ -748,7 +748,7 @@ <h2>Ecological Interactions</h2>
<h3>Syntrophic Butyrate Oxidation by MAG1</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Candidatus Syntrophothermus ammoniitolerans MAG1 is inferred to oxidize butyrate through beta-oxidation, releasing acetate and reduced electron carriers whose removal by acetate oxidizers and hydrogenotrophic methanogens makes the overall butyrate-to-methane conversion favorable.</p>
<p class="prewrap interaction-description">PARTIAL - cultivation and metagenomics support MAG1 as a putative syntrophic butyrate oxidizer. The single long-term 0B culture converted butyrate to methane, while MAG1 beta-oxidation and energy-conservation genes support the proposed organism-level role. Acetate provision to the putative MAG2 acetate oxidizer and carrier consumption by methanogens form the authors&#39; model, not measured MAG-specific flux or a selectively tested partner requirement. The source-to-target pair represents the proposed acetate branch, not transfer of every listed metabolite to MAG2.</p>


<p><strong>Source Taxon:</strong> Candidatus Syntrophothermus ammoniitolerans MAG1</p>
Expand Down Expand Up @@ -799,12 +799,12 @@ <h3>Syntrophic Butyrate Oxidation by MAG1</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Syntrophic Acetate Oxidation by MAG2 to Methanoculleus
<p class="prewrap causal-description">MAG1 produces acetate during butyrate beta-oxidation; MAG2 is then inferred to oxidize acetate with Methanoculleus consuming released H2 or formate.</p>
<p class="prewrap causal-description">PARTIAL - proposed MAG1 butyrate oxidation supplies acetate that MAG2 could oxidize while Methanoculleus consumes released hydrogen or formate, supporting the modeled coupled conversion. Bulk conversion and genomic potential do not establish this exact partner-resolved flux or the hydrogen/formate split.</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Syntrophic Acetate Oxidation by MAG2 to Methanothermobacter
<p class="prewrap causal-description">MAG1 produces acetate during butyrate beta-oxidation; MAG2 is then inferred to oxidize acetate with Methanothermobacter consuming released H2 or formate.</p>
<p class="prewrap causal-description">PARTIAL - proposed MAG1 butyrate oxidation supplies acetate that MAG2 could oxidize while Methanothermobacter consumes released hydrogen or formate, supporting the modeled coupled conversion. Bulk conversion and genomic potential do not establish this exact partner-resolved flux or the hydrogen/formate split.</p>
</div>

</div>
Expand All @@ -820,13 +820,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42527912/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42527912</a>

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

<div class="snippet">"Acetate produced during butyrate oxidation was further oxidized by syntrophic acetate-oxidizing bacteria and ultimately converted to methane by hydrogenotrophic methanogens"</div>

</li>

<li class="evidence-item">
<div>

<a href="https://pubmed.ncbi.nlm.nih.gov/42527912/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42527912</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Thereafter, the 0B culture subsequently converted butyrate to methane without substantial lag phases during the subsequent seven butyrate depletion cycles"</div>

</li>

</ul>

</div>
Expand All @@ -836,7 +849,7 @@ <h4>Evidence</h4>
<h3>Syntrophic Acetate Oxidation by MAG2 to Methanoculleus</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">The Candidatus Thermosyntrophaceticus-like MAG2 is inferred to consume acetate produced during MAG1-driven butyrate oxidation and to route electrons to H2 or formate for Candidatus Methanoculleus thermohydrogenotrophicum MAG3.</p>
<p class="prewrap interaction-description">PARTIAL - the authors infer acetate oxidation by MAG2 coupled to hydrogen- or formate-consuming Methanoculleus MAG3. MAG2 is a moderate-quality genome without a completely annotated Wood-Ljungdahl pathway; the close-relative comparison supports a hypothesis, not observation of its missing genes or active acetate flux. Methanogen genomic potential supports the proposed partner role without resolving carrier partition or proving that each partner is necessary.</p>


<p><strong>Source Taxon:</strong> Candidatus Thermosyntrophaceticus-like SAOB MAG2</p>
Expand Down Expand Up @@ -916,7 +929,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42527912/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42527912</a>

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

<div class="snippet">"members of the genera Methanoculleus and Methanothermobacter likely served as hydrogenotrophic methanogenic partners"</div>
Expand All @@ -932,7 +945,7 @@ <h4>Evidence</h4>
<h3>Syntrophic Acetate Oxidation by MAG2 to Methanothermobacter</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">The Candidatus Thermosyntrophaceticus-like MAG2 is inferred to consume acetate produced during MAG1-driven butyrate oxidation and to route electrons to H2 or formate for Methanothermobacter MAG4 and MAG5.</p>
<p class="prewrap interaction-description">PARTIAL - the authors infer acetate oxidation by MAG2 coupled to hydrogen- or formate-consuming Methanothermobacter MAG4/MAG5. MAG2 is a moderate-quality genome without a completely annotated Wood-Ljungdahl pathway; the close-relative comparison supports a hypothesis, not observation of its missing genes or active acetate flux. Methanogen genomic potential supports the proposed partner role without resolving carrier partition or proving that each partner is necessary. Late relative enrichment of Methanothermobacter does not establish an improved butyrate-conversion rate. Proposed acetate assimilation by MAG5 is distinct from acetoclastic methane production.</p>


<p><strong>Source Taxon:</strong> Candidatus Thermosyntrophaceticus-like SAOB MAG2</p>
Expand Down Expand Up @@ -1012,7 +1025,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42527912/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42527912</a>

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

<div class="snippet">"members of the genera Methanoculleus and Methanothermobacter likely served as hydrogenotrophic methanogenic partners"</div>
Expand Down Expand Up @@ -1072,9 +1085,9 @@ <h3>
<span class="role-badge">OPEN</span>
Does the moderate-quality Candidatus Thermosyntrophaceticus-like MAG2 actively perform syntrophic acetate oxidation in the 0B enrichment, and what is the division of hydrogen versus formate transfer among the MAG1, MAG2, Methanoculleus, and Methanothermobacter MAGs?
</h3>
<p class="prewrap">The 0B enrichment couples butyrate loss to methane formation, but MAG2 was reconstructed at moderate quality and a complete Wood-Ljungdahl pathway was inferred from a close relative rather than completely annotated in MAG2 itself.</p>
<p class="prewrap">The 0B enrichment couples butyrate loss to methane formation, but MAG2 was reconstructed at moderate quality and a complete Wood-Ljungdahl pathway was inferred from a close relative rather than completely annotated in MAG2 itself. All three pairwise assignments and both acetate-branch arrows remain PARTIAL. The single 0B long-term culture is distinct from replicated yeast-extract YB cultures; yeast-extract-free medium is not proof that butyrate was the only available organic carbon. Direct MAG1-to-methanogen carrier provision is another proposed route, not a new demonstrated branch here. MAG9 alternative roles, hydrogen/formate partition, MAG2 activity and partner necessity remain unresolved; isotope tracing, expression and partner perturbations would discriminate them. Below-detection relative abundance is not extinction, calculated free ammonia is not a direct measurement, and archaeal succession is not a demonstrated rate advantage. No complete mechanism expansion is claimed. Non-graph metadata is preserved, not recertified.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Syntrophic Acetate Oxidation by MAG2 to Methanoculleus</code>, <code>ecological_interactions#Syntrophic Acetate Oxidation by MAG2 to Methanothermobacter</code></p>
<p class="muted small">Attaches to: <code>ecological_interactions#Syntrophic Butyrate Oxidation by MAG1</code>, <code>ecological_interactions#Syntrophic Acetate Oxidation by MAG2 to Methanoculleus</code>, <code>ecological_interactions#Syntrophic Acetate Oxidation by MAG2 to Methanothermobacter</code></p>



Expand Down Expand Up @@ -1532,7 +1545,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("fatty acid beta-oxidation");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
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