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Repair pyrene, syntrophy and pepper causal claims (batch83) #1693

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89 changes: 69 additions & 20 deletions docs/communities/Pelagerythrobacter_Salinicola_PES_Pyrene_Degradation_SynCom.html
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Expand Up @@ -584,32 +584,32 @@ <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 Pelagerythrobacter-Salinicola PES Pyrene-Degradation 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, 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 (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="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>N7-A11 4,5-dicarboxyphenanthrene handoff</h3>
<h3>Proposed N7-A11 4,5-dicarboxyphenanthrene handoff</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Pelagerythrobacter sp. N7 initiated pyrene oxidation but accumulated 4,5-dicarboxyphenanthrene as a bottleneck product in monoculture. PES additionally accumulated downstream products including 4-carboxyphenanthrene, phthalate, salicylic acid, and gentisate, leading the authors to propose that Salinicola sp. A11 assists N7 by decarboxylating 4,5-dicarboxyphenanthrene through an hphtC-5-encoded candidate aromatic-acid decarboxylase.</p>
<p class="prewrap interaction-description">PARTIAL - N7 monoculture accumulated 4,5-dicarboxyphenanthrene, while PES contained additional downstream metabolites. The authors infer an N7-to-A11 intermediate handoff and propose hphtC-5 as a candidate A11 decarboxylase from genome annotation, structural modeling and transcripts. These observations do not directly trace intercellular flux or establish enzyme necessity or sufficiency. The published Figure 8 correction confirms the proposed direction from 4,5-dicarboxyphenanthrene to 4-carboxyphenanthrene, not its reverse.</p>


<p><strong>Source Taxon:</strong> Pelagerythrobacter sp. N7</p>
Expand Down Expand Up @@ -637,7 +637,7 @@ <h3>N7-A11 4,5-dicarboxyphenanthrene handoff</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Complete 5%-salinity pyrene removal by PES
<p class="prewrap causal-description">The proposed N7-to-A11 intermediate handoff relieves the 4,5-dicarboxyphenanthrene bottleneck observed in N7 monoculture and helps PES degrade the supplied pyrene completely within the main 10-day assay.</p>
<p class="prewrap causal-description">HYPOTHESIZED - A11-mediated transformation of the intermediate accumulated by N7 could relieve the degradation bottleneck and enable the observed PES pyrene removal. Metabolite profiles, annotation and expression support the proposed pathway but do not isolate hphtC-5-dependent intercellular transfer as the cause of the removal advantage.</p>
</div>

</div>
Expand Down Expand Up @@ -666,7 +666,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42666409/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42666409</a>

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

<div class="snippet">"enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process of 4,5-dicarboxyphenanthrene."</div>
Expand All @@ -679,10 +679,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>A11 extracellular bioemulsification of hydrophobic pyrene</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>A11-Associated Extracellular Emulsifying Activity</h3>
</div>
<p class="prewrap interaction-description">Salinicola sp. A11 secreted extracellular emulsan-like material detected in A11 and PES cell-free supernatants, but not N7 cell-free supernatant. The extracellular emulsifier was modeled as increasing hydrophobic pyrene bioavailability for the N7-centered upstream oxidation arm.</p>
<p class="prewrap interaction-description">A11 and PES cell-free supernatants formed persistent soybean-oil emulsions, unlike N7 supernatant, washed cells or fresh medium; the reported 24-hour emulsification index was 68%. A11 was grown with yeast extract, whereas N7 and PES were grown with pyrene, so this is not a substrate-matched production comparison. FTIR of crude material and genome annotation support an emulsan-like interpretation. HYPOTHESIZED - Its contribution to pyrene bioavailability and N7 degradation is proposed, not isolated by the soybean-oil assay or proof of reciprocal fitness benefit.</p>


<p><strong>Source Taxon:</strong> Salinicola sp. A11</p>
Expand Down Expand Up @@ -710,7 +709,7 @@ <h3>A11 extracellular bioemulsification of hydrophobic pyrene</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Complete 5%-salinity pyrene removal by PES
<p class="prewrap causal-description">A11 extracellular bioemulsifier production is proposed to reduce the mass transfer limitation of hydrophobic pyrene and thereby increase PES pyrene degradation efficiency.</p>
<p class="prewrap causal-description">HYPOTHESIZED - Extracellular emulsifying material attributed to A11 could increase pyrene availability and thereby improve PES removal. The measured emulsion phenotype and genomic capacity do not isolate pyrene mass transfer, the export system or the fraction of removal caused by this mechanism.</p>
</div>

</div>
Expand Down Expand Up @@ -739,7 +738,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42666409/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42666409</a>

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

<div class="snippet">"In the genome of strain A11, wza, wzb, and wzc related genes were identified"</div>
Expand All @@ -755,7 +754,7 @@ <h4>Evidence</h4>
<h3>Complete 5%-salinity pyrene removal by PES</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">In 200 mL 5%-salinity SSDM batch flasks with 50 mg/L pyrene as the sole carbon source, the two-member PES consortium approached complete pyrene removal within 10 days, whereas neither pure culture completely degraded pyrene by itself under the tested conditions.</p>
<p class="prewrap interaction-description">PES approached complete removal of 50 mg/L pyrene in 200 mL 5%-salinity SSDM within 10 days. N7 removal plateaued at 49.95% after 14 days, and A11 lacked direct PAH-degrading capability. These controlled culture observations support the consortium removal advantage. Residual-substrate HPLC and intermediate detection do not by themselves establish complete carbon mineralization, a closed carbon balance or reciprocal member-specific fitness benefits.</p>



Expand Down Expand Up @@ -850,7 +849,7 @@ <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 @@ -860,9 +859,59 @@ <h3>
</h3>
<p class="prewrap">The source detected downstream pyrene metabolites in PES, annotated hphtC-5 in the A11 genome, modeled a compatible active site, and measured hphtC-5 expression by RT-PCR. It did not purify HphtC-5 or perturb hphtC-5 genetically, so the specific enzyme assignment remains a candidate step.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#N7-A11 4,5-dicarboxyphenanthrene handoff</code></p>
<p class="muted small">Attaches to: <code>ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff</code></p>




</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which candidate enzyme and emulsifier activities cause the measured PES removal advantage?
</h3>
<p class="prewrap">Preserve positive pyrene removal, intermediate profiles and extracellular emulsification. hphtC-5 remains a candidate, as in the existing gap. Soybean-oil emulsification is not a direct pyrene-solubility or depletion/add-back test; A11 and the other cultures had different growth substrates. The correction DOI10.3389/fmicb.2026.1971230 changes structures in Figure8, not the need for causal validation. No new nodes/arrows are warranted by the inspected main text.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Proposed N7-A11 4,5-dicarboxyphenanthrene handoff</code>, <code>ecological_interactions#A11-Associated Extracellular Emulsifying Activity</code>, <code>ecological_interactions#Complete 5%-salinity pyrene removal by PES</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">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42666409/" rel="nofollow noreferrer">PMID:42666409</a>


</div>
<p class="snippet small prewrap">enzyme encoded by hphtC-5 was proposed to be the candidate decarboxylase for the decarboxylation process of 4,5-dicarboxyphenanthrene.</p>
<p class="muted small prewrap">Candidate enzyme assignment based on annotation/modeling and expression, not direct enzymatic validation.</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/42666409/" rel="nofollow noreferrer">PMID:42666409</a>


</div>
<p class="snippet small prewrap">Distinct and persistent emulsion layers were observed only in the cell-free supernatants of strain A11 and consortium PES</p>
<p class="muted small prewrap">Supports A11 and PES, but not N7 alone, as sources of extracellular emulsifying activity.</p>
</div>

</details>


</div>
Expand Down Expand Up @@ -1191,7 +1240,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "N7-A11 4,5-dicarboxyphenanthrene handoff",
label: "Proposed N7-A11 4,5-dicarboxyphenanthrene handoff",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1216,7 +1265,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1229,7 +1278,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "A11 extracellular bioemulsification of hydrophobic pyrene",
label: "A11-Associated Extracellular Emulsifying Activity",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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