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Bound gas-rate and isotope claims; document empty peptide graph (batch72) #1613

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142 changes: 69 additions & 73 deletions docs/communities/Methylomicrobium_Chlorella_Methane_Sequestration_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 Methylomicrobium-Chlorella Methane Sequestration 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, mutualism, 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 (mutualism).</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
</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 @@ -615,8 +610,7 @@ <h2>Ecological Interactions</h2>
<h3>Methane Removal and Mutualistic Growth</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">M. alcaliphilum 20Z and Chlorella sp. HS2 form a mutualistic coculture in which methane removal and growth of both organisms increase relative to the tested controls.
</p>
<p class="prewrap interaction-description">The M. alcaliphilum 20Z/Chlorella sp. HS2 coculture enhanced growth of both members under saline conditions (&gt;3.0%), supporting the authors&#39; mutualistic-growth interpretation. Increased methane provision in enclosed bottles led to saturated methane removal. Positive growth and removal are retained, without assigning all benefits to measured reciprocal O2/CO2 transfer or implying obligatory dependence.</p>


<p><strong>Source Taxon:</strong> Chlorella sp. HS2</p>
Expand Down Expand Up @@ -671,7 +665,7 @@ <h3>Methane Removal and Mutualistic Growth</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Methane and Carbon Dioxide Mitigation
<p class="prewrap causal-description">The mutualistic O2/CO2 exchange that increases growth of both partners under methane feeds the downstream methane removal and biomass carbon-sequestration phenotype.</p>
<p class="prewrap causal-description">PARTIAL - enhanced partner growth and methane utilization contribute to greater whole-coculture biomass carbon sequestration. The exact-pair abstract supports these positive outcomes but does not isolate reciprocal gas exchange as their sole mediator; it explicitly implicates factors beyond gaseous exchange.</p>
</div>

</div>
Expand All @@ -690,7 +684,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Increased CH4 removal and growth of both microbes were observed in co-cultures."</div>
<div class="snippet">"Co-culture significantly enhanced the growth of both microbes"</div>

</li>

Expand All @@ -703,7 +697,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Co-culture significantly enhanced the growth of both microbes"</div>
<div class="snippet">"increased methane provision in enclosed serum bottles led to saturated methane removal"</div>

</li>

Expand All @@ -714,17 +708,19 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Methane and Carbon Dioxide Mitigation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The methanotroph-microalga consortium was proposed as a halotolerant platform for simultaneous methane and carbon dioxide mitigation, with methane-fed cocultures increasing carbon sequestered in biomass.
</p>
<p class="prewrap interaction-description">Methane-fed cocultures showed nearly an order of magnitude more carbon sequestered in biomass in the reported analyses. This is a whole-culture carbon endpoint and supports the proposed halotolerant CH4/CO2 mitigation platform, not a quantified methanotroph-to-Chlorella carbon flux or demonstrated operation on real wastewater.</p>




<p><strong>Source Taxon:</strong> Methylomicrobium alcaliphilum 20Z</p>
<p><strong>Participating Taxa:</strong>

Methylomicrobium alcaliphilum 20Z,

Chlorella sp. HS2

<p><strong>Target Taxon:</strong> Chlorella sp. HS2</p>
</p>



Expand Down Expand Up @@ -798,37 +794,26 @@ <h4>Evidence</h4>

</li>

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

<a href="https://doi.org/10.1016/j.mex.2022.101652"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.mex.2022.101652</a>

- PARTIAL (COMPUTATIONAL)
</div>

<div class="snippet">"Explicitly models the exchange of in situ produced O2 and CO2 within the coculture"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Saline Metabolic Coupling and pH Recovery</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">The coculture showed robust metabolic coupling under saline conditions and maintained culture pH suitable for methanotrophic growth.
</p>
<p class="prewrap interaction-description">Methane-fed saline cocultures maintained pH suitable for methanotrophic growth, alongside enhanced growth and carbon sequestration. This culture-level observation supports a favorable chemical environment; it does not establish colonization facilitation or selectively demonstrate that Chlorella-driven pH recovery causes the growth benefit.</p>


<p><strong>Source Taxon:</strong> Chlorella sp. HS2</p>


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

<p><strong>Target Taxon:</strong> Methylomicrobium alcaliphilum 20Z</p>
Methylomicrobium alcaliphilum 20Z,

Chlorella sp. HS2

</p>



Expand All @@ -852,8 +837,7 @@ <h3>Saline Metabolic Coupling and pH Recovery</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Methane and Carbon Dioxide Mitigation
<p class="prewrap causal-description">Saline pH recovery and robust methanotroph-alga metabolic coupling sustain methane-fed coculture conditions that increase methane removal and biomass carbon sequestration.
</p>
<p class="prewrap causal-description">HYPOTHESIZED - maintaining a suitable pH could sustain methanotrophic activity and thereby biomass carbon sequestration. The available exact-pair abstract reports the association, not a selective pH perturbation establishing its contribution independently of gas supply or other interactions.</p>
</div>

</div>
Expand All @@ -872,7 +856,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"robust metabolic coupling between the two microbes"</div>
<div class="snippet">"maintained a suitable cultural pH suitable for methanotrophic growth"</div>

</li>

Expand All @@ -882,36 +866,42 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1016/j.biortech.2024.130607"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1016/j.biortech.2024.130607</a>

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

<div class="snippet">"pH recovery above mild alkaline level was observed in co-cultures."</div>
<div class="snippet">"robust metabolic coupling between the two microbes"</div>

</li>

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

<a href="https://doi.org/10.20517/mrr.2023.70"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.20517/mrr.2023.70</a>
</div>

- PARTIAL (COMPUTATIONAL)
</div>

<div class="snippet">"the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture"</div>
</section>

</li>
<!-- Associated Datasets -->

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

</div>
<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which processes mediate the positive growth, pH and biomass-carbon effects in the exact 20Z/HS2 pair?
</h3>
<p class="prewrap">Preserve mutual growth enhancement, methane removal and biomass carbon sequestration. The exact-pair primary abstract was read; publisher full text returned 403, so no absence-of-controls claim is made. Both cited model papers (doi:10.1016/j.mex.2022.101652 and doi:10.20517/mrr.2023.70) actually study M. buryatense 5GB1/A. platensis. Their complete main texts support kinetic/computational context, not independent exact-pair evidence. DynamiCom nitrogen exchange is a prediction awaiting experimental validation, not an HS2 mechanism. Remove those graph evidence items without inventing new nitrogen-exchange structure. #1608 addresses graph scope.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Methane Removal and Mutualistic Growth</code>, <code>ecological_interactions#Methane and Carbon Dioxide Mitigation</code>, <code>ecological_interactions#Saline Metabolic Coupling and pH Recovery</code></p>

</section>

<!-- Associated Datasets -->


</div>

</section>

<!-- Environmental Factors -->

<section>
Expand Down Expand Up @@ -1404,7 +1394,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1423,7 +1413,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("photosynthesis");


var evidenceCount = 3;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1436,23 +1426,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Methylomicrobium alcaliphilum 20Z";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Chlorella sp. HS2";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Methylomicrobium alcaliphilum 20Z",

"Chlorella sp. HS2"

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

})();

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

var processes = [];
Expand All @@ -1461,7 +1454,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("biological process involved in interspecies interaction between organisms");


var evidenceCount = 3;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1474,17 +1467,20 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Chlorella sp. HS2";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Methylomicrobium alcaliphilum 20Z";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Methylomicrobium alcaliphilum 20Z",

"Chlorella sp. HS2"

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

})();

Expand Down
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