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Qualify polymer, groundwater and microalgal causal mechanisms (batch 38) #1444

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127 changes: 45 additions & 82 deletions docs/communities/Ensifer_YF2_Sphingobacterium_Y2_Polyethylene_Degrading_Consortium.html
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Expand Up @@ -560,21 +560,16 @@ <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 Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading 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 (cross-feeding, 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="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="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -583,9 +578,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Metabolic division of labor in polyethylene degradation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Complementary enzymatic repertoire drives synergistic PE degradation. Ensifer YF2, the primary degrader, performs backbone cleavage via oxidases (LadA, AlkB, CYP450); Sphingobacterium Y2, enriched in esterases and lipases, metabolizes the resulting intermediates through cross-feeding.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - genomic oxidase annotations in Ensifer YF2 and esterase/lipase annotations in Sphingobacterium Y2 motivate a model in which YF2 supplies polymer-derived intermediates to Y2. The directed pair represents that conceptual model, not measured donor export, identified exchanged compounds, recipient uptake or selectively established enzyme activity on polyethylene.</p>


<p><strong>Source Taxon:</strong> Ensifer sp. YF2</p>
Expand All @@ -598,25 +592,14 @@ <h3>Metabolic division of labor in polyethylene degradation</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
alkane catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0043448"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0043448</a>)
</li>

</ul>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Synergistic enhancement of PE degradation in the dual-strain consortium
<p class="prewrap causal-description">Ensifer backbone cleavage and Sphingobacterium intermediate metabolism combine into the YF2/Y2 dual consortium&#39;s enhanced PE degradation phenotype.</p>
<p class="prewrap causal-description">HYPOTHESIZED - complementary transformation capacities could contribute to the stronger YF2/Y2 consortium phenotype. Genomic annotation and the coculture comparison do not isolate cross-feeding as the cause of that improvement.</p>
</div>

</div>
Expand All @@ -632,7 +615,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41996795/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41996795</a>

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

<div class="snippet">"YF2, encoding key oxidases (LadA, AlkB, CYP450), served as the primary degrader for backbone cleavage, while Y2, enriched with esterases and lipases, facilitated intermediate metabolism through cross-feeding."</div>
Expand All @@ -646,43 +629,25 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Synergistic enhancement of PE degradation in the dual-strain consortium</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Co-culture of Ensifer YF2 and Sphingobacterium Y2 degraded polyethylene more efficiently than either strain alone or the full three-strain combination, indicating emergent synergy from functional compatibility rather than taxonomic richness.</p>
<p class="prewrap interaction-description">The abstract reports greater polyethylene degradation by the YF2/Y2 pair than by either isolate or the screened three-strain mixture including MF1. This is a consortium-output comparison, not demonstrated reciprocal fitness benefit, an identified exchanged metabolite or a formal additive-synergy test. MF1 is a comparator, not a member of this curated pair.</p>


<p><strong>Source Taxon:</strong> Ensifer sp. YF2</p>



<p><strong>Target Taxon:</strong> Sphingobacterium sp. Y2</p>



<p><strong>Participating Taxa:</strong>

Ensifer sp. YF2,

<p><strong>Biological Processes:</strong></p>
<ul>
Sphingobacterium sp. Y2

<li>
alkane catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0043448"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0043448</a>)
</li>
</p>

</ul>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Polyethylene Oxidation and Surface Erosion
<p class="prewrap causal-description">The enhanced dual-strain consortium grows with PE as the sole carbon source and induces oxidative and physical damage to the polymer.</p>
</div>

</div>



Expand All @@ -709,9 +674,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Polyethylene Oxidation and Surface Erosion</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The Ensifer YF2 and Sphingobacterium Y2 consortium utilizes polyethylene as sole carbon source while oxidizing and eroding the polymer surface.</p>
<p class="prewrap interaction-description">The tested two-member consortium was reported to use polyethylene as the sole carbon source and to induce polymer oxidation and surface erosion. These physical and chemical endpoints do not by themselves establish complete mineralization, a measured interstrain carbon flux or a separate downstream consequence of the performance summary.</p>



Expand All @@ -728,17 +692,6 @@ <h3>Polyethylene Oxidation and Surface Erosion</h3>



<p><strong>Biological Processes:</strong></p>
<ul>

<li>
alkane catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0043448"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0043448</a>)
</li>

</ul>




Expand Down Expand Up @@ -768,6 +721,25 @@ <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 exchanged compounds and enzymes account for the YF2/Y2 polymer phenotype?
</h3>
<p class="prewrap">Retain the existing conceptual donor/recipient model and only a HYPOTHESIZED contribution to comparative performance. Remove the performance-to-surface-endpoint part/whole arrow. The available primary abstract does not expose isotope tracing, enzyme perturbations or species-resolved fitness. Preserve the exact pair and AMBIGUOUS Ensifer grounding; do not reintroduce the screened MF1 member. The publisher labels the article open access, but full-body retrieval failed in this session; this is not evidence of a paywall. Non-graph role and access/protocol claims remain #1441. No new causal structure is needed to repair the existing claims.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Metabolic division of labor in polyethylene degradation</code>, <code>ecological_interactions#Synergistic enhancement of PE degradation in the dual-strain consortium</code>, <code>ecological_interactions#Polyethylene Oxidation and Surface Erosion</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -914,15 +886,11 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("alkane catabolic process");


var evidenceCount = 1;

nodes.push({
Expand Down Expand Up @@ -952,15 +920,11 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("alkane catabolic process");


var evidenceCount = 1;

nodes.push({
Expand All @@ -974,31 +938,30 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Ensifer sp. YF2";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Sphingobacterium sp. Y2";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Ensifer sp. YF2",

"Sphingobacterium sp. Y2"

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

})();

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

var processes = [];


processes.push("alkane catabolic process");


var evidenceCount = 1;

nodes.push({
Expand Down
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