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Review removal evidence and social-spreading graph (batch89) #1737

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123 changes: 106 additions & 17 deletions docs/communities/Pseudomonas_Bacillus_Waxy_Oil_Biodegradation_Consortium.html
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Original file line number Diff line number Diff line change
Expand Up @@ -583,7 +583,7 @@ <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 Pseudomonas-Bacillus Waxy Oil Biodegradation 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 (cross-feeding).</desc>
</svg>
<div class="network-legend">
<div class="legend-item">
Expand All @@ -596,8 +596,8 @@ <h2>Ecological Interactions</h2>
</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 @@ -608,8 +608,7 @@ <h2>Ecological Interactions</h2>
<h3>Interfacial Remodeling and Precursor Cross-feeding</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">B. subtilis G1 uses lipopeptides and small molecules to remodel the oil-water interface, improve substrate accessibility, and supply precursors assimilated by P. aeruginosa PA12.
</p>
<p class="prewrap interaction-description">PARTIAL: the authors propose that Bacillus-mediated interface remodeling and precursor supply facilitate the partner contribution to waxy-oil conversion. Preserve this reported directed interpretation; the accessible abstract does not establish a measured transfer flux or isolate each mediator experimentally.</p>


<p><strong>Source Taxon:</strong> Bacillus subtilis G1</p>
Expand Down Expand Up @@ -648,8 +647,7 @@ <h3>Interfacial Remodeling and Precursor Cross-feeding</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Multilayer Cooperative Hydrocarbon Degradation
<p class="prewrap causal-description">Bacillus-mediated oil-water interface remodeling and precursor transfer form one layer of the cooperative network that lets the two-member consortium outperform either monoculture.
</p>
<p class="prewrap causal-description">PARTIAL: interface remodeling and precursor transfer are proposed contributors to the reported cooperative degradation model. The abstract supports this interpretation but does not establish their necessity or relative contributions.</p>
</div>

</div>
Expand Down Expand Up @@ -679,13 +677,19 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Multilayer Cooperative Hydrocarbon Degradation</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The consortium combines interface remodeling, metabolic cross-feeding, signal exchange, and redox-energy homeostasis to outperform either monoculture.
</p>
<p class="prewrap interaction-description">PARTIAL: multi-omics and molecular docking support the authors multilayer cooperation model. These analyses do not by themselves prove functional mediation by each proposed process or reciprocal fitness benefits; the measured consortium-versus-monoculture degradation advantage remains a separate positive result.</p>




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

Pseudomonas aeruginosa PA12,

Bacillus subtilis G1

</p>



Expand All @@ -709,8 +713,7 @@ <h3>Multilayer Cooperative Hydrocarbon Degradation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> High-Efficiency Waxy Oil Removal
<p class="prewrap causal-description">Interface remodeling, precursor cross-feeding, signal exchange, and redox-energy homeostasis drive high-efficiency wax removal by the two-member consortium.
</p>
<p class="prewrap causal-description">PARTIAL: the proposed cooperative processes are offered as an explanation for the observed wax-removal advantage. The abstract does not resolve which processes are necessary or sufficient for that endpoint.</p>
</div>

</div>
Expand Down Expand Up @@ -766,13 +769,19 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>High-Efficiency Waxy Oil Removal</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The PA12-G1 cooperative network improved waxy crude oil conversion, producing 85.5% wax removal within 12 days compared with lower PA12 and G1 monoculture degradation efficiencies.
</p>
<p class="prewrap interaction-description">The source reports 85.5% wax removal within 12 days, compared with lower monoculture degradation efficiencies of 52.5% and 42.0%. Preserve this positive treatment comparison without equating pollutant removal with reciprocal growth benefits or complete mineralization.</p>




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

Pseudomonas aeruginosa PA12,

Bacillus subtilis G1

</p>



Expand Down Expand Up @@ -826,6 +835,60 @@ <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 reported cooperative processes actually mediate the removal advantage?
</h3>
<p class="prewrap">All three nodes and both existing directions remain. Positive removal measurements are distinct from multi-omics and docking interpretations. Only the fresh abstract was accessible; absence of full methods is not evidence that perturbations were absent. No new biological mechanisms, strain combinations, optimization parameters or experimental designs were added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Interfacial Remodeling and Precursor Cross-feeding</code>, <code>ecological_interactions#Multilayer Cooperative Hydrocarbon Degradation</code>, <code>ecological_interactions#High-Efficiency Waxy Oil Removal</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">IN_VITRO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41905048/" rel="nofollow noreferrer">PMID:41905048</a>


</div>
<p class="snippet small prewrap">enhancing substrate accessibility and supplying precursors to PA12</p>
<p class="muted small prewrap">Supports the authors proposed substrate-access and precursor-transfer contribution, not independently verified transfer flux.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">COMPUTATIONAL</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41905048/" rel="nofollow noreferrer">PMID:41905048</a>


</div>
<p class="snippet small prewrap">Molecular docking validated the aforementioned mechanism of action</p>
<p class="muted small prewrap">This is the authors wording; docking is computational support, not independent biological validation of the whole causal mechanism.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1165,7 +1228,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1189,11 +1252,24 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas aeruginosa PA12",

"Bacillus subtilis G1"

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

})();

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


Expand Down Expand Up @@ -1221,6 +1297,19 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas aeruginosa PA12",

"Bacillus subtilis G1"

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

})();


Expand Down
103 changes: 95 additions & 8 deletions docs/communities/Pseudomonas_Klebsiella_Alcaligenes_FeII_Nitrogen_Removal_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -597,16 +597,16 @@ <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 Pseudomonas-Klebsiella-Alcaligenes Fe2+ Nitrogen-Removal 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 (niche partitioning).</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="symbolSquare2"
data-color="#1212ed"></svg> Niche partitioning
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -615,13 +615,22 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Composite nitrogen-removal metabolic network</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Pseudomonas stutzeri, Klebsiella sp., and Alcaligenes sp. were combined into a synthetic consortium spanning aerobic denitrification, facultative anaerobic denitrification, and heterotrophic nitrification-aerobic denitrification. Fe2+ chemical regulation increased nitrate-N removal efficiency relative to other iron species and shifted the metagenomic carbon and nitrogen network toward higher dissimilatory nitrate reduction to ammonium pathway abundance and lower denitrification pathway abundance.</p>
<p class="prewrap interaction-description">The three-member consortium showed higher nitrate-N removal under the reported iron-species treatment comparison and associated changes in carbon/nitrogen pathway abundance. PARTIAL: complementary named capabilities do not establish niche partitioning, member-specific contributions or measured pathway flux. The abstract labels the analysis metagenomic but calls the reported counts transcript abundance, leaving the measurement type unresolved.</p>




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

Pseudomonas stutzeri,

Klebsiella sp.,

Alcaligenes sp.

</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -682,6 +691,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42520901/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42520901</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"compared with the other iron species, the Fe2+ group achieved a 20-30% increase in nitrate-N removal efficiency"</div>

</li>

</ul>

</div>
Expand All @@ -692,7 +714,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<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 @@ -707,6 +729,56 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
What measurement supports the reported pathway shift and net nitrogen fate?
</h3>
<p class="prewrap">The nitrate-N treatment response remains a measured positive endpoint. The accessible abstract mixes metagenomic sequencing with transcript-abundance terminology; it does not resolve that inconsistency, taxon-specific partitioning or flux. Nitrate disappearance alone does not establish whole-system nitrogen loss. Full text and complete nitrogen balances were not available in this review. No new arrows or experimental protocols were added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Composite nitrogen-removal metabolic network</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">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42520901/" rel="nofollow noreferrer">PMID:42520901</a>


</div>
<p class="snippet small prewrap">Metagenomic analysis revealed that Fe2+ modulated the carbon and nitrogen metabolic networks: in the carbon metabolic network, enrichment of the por gene in the glycolytic pathway generated substantial reducing power in the form of reduced ferredoxin; concomitantly, the transcript abundance of the dissimilatory nitrate reduction to ammonium pathway increased from 775 to 802, whereas that of the denitrification pathway decreased from 1259 to 1222.</p>
<p class="muted small prewrap">Supports the source-reported abundance shift with an unresolved metagenomic/transcript terminology inconsistency, not verified transcription, reducing-power production or nitrogen flux.</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/42520901/" rel="nofollow noreferrer">PMID:42520901</a>


</div>
<p class="snippet small prewrap">compared with the other iron species, the Fe2+ group achieved a 20-30% increase in nitrate-N removal efficiency</p>
<p class="muted small prewrap">Supports Fe2+ as the iron species that increased nitrate-N removal efficiency.</p>
</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -997,7 +1069,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1012,7 +1084,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("denitrification");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand All @@ -1027,6 +1099,21 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas stutzeri",

"Klebsiella sp.",

"Alcaligenes sp."

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

})();


Expand Down
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