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Bound UFMP, GOM oil and garlic SynCom causal graphs (batch44) #1477

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188 changes: 128 additions & 60 deletions docs/communities/GLBRC_UFMP_Fermentation_Community.html
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173 changes: 119 additions & 54 deletions docs/communities/GOM_Oil_Degrading_Consortium.html
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Original file line number Diff line number Diff line change
Expand Up @@ -643,16 +643,16 @@ <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 Gulf of Mexico Oil-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 (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 @@ -661,24 +661,31 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Consortium n-Alkane Biodegradation</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The four-member Gulf of Mexico consortium degraded n-alkanes from light crude oil, one of the two GC-MS-measured contaminant classes supporting its improved crude-oil removal.</p>
<p class="prewrap interaction-description">GC-MS with an abiotic-control baseline measured C8-C38 n-alkane depletion in the four-strain consortium and individual cultures. Consortium values reached about 60% at day 30 and about 45% at day 75; chain-length fractions differed, and time-dependent abiotic loss of shorter alkanes affects these relative estimates. These measurements support hydrocarbon transformation, not complete mineralization, obligatory niche partitioning or strain-resolved in-consortium flux. Similar monoculture preferences and MetaMIS predictions do not assign the consortium result exclusively to Pseudomonas or Alcanivorax.</p>




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

Pseudomonas sp. GOM,

Halopseudomonas aestusnigri GOM5,

Paenarthrobacter sp. GOM3,

Alcanivorax sp. GOM

</p>



<p><strong>Metabolites:</strong>

alkane
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18310"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18310</a>),

dodecane
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=28817"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:28817</a>)
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18310</a>)

</p>

Expand All @@ -697,16 +704,6 @@ <h3>Consortium n-Alkane Biodegradation</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced Light Crude Oil Removal
<p class="prewrap causal-description">Consortium-scale n-alkane biodegradation contributes to improved gravimetric light-crude-oil removal by the selected four-strain consortium.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -732,12 +729,23 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Consortium Polyaromatic Hydrocarbon Biodegradation</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The selected four-strain consortium degraded 12 measured polyaromatic hydrocarbons from light crude oil alongside its n-alkane biodegradation activity.</p>
<p class="prewrap interaction-description">GC-MS monitored 12 aromatic analytes, with different susceptibilities; not all 12 were substantially biodegraded. The consortium aggregate PAH estimate reached about 16% at day 75 relative to the abiotic baseline. The main text identifies fluorene, dibenzothiophene, methylated phenanthrenes and pyrene among susceptible compounds, while others were hardly biodegraded. This does not establish generic phenanthrene degradation, complete mineralization or a necessary division of labor. The canonical four participants identify the assayed consortium, not four proven owners of each degradation reaction.</p>




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

Pseudomonas sp. GOM,

Halopseudomonas aestusnigri GOM5,

Paenarthrobacter sp. GOM3,

Alcanivorax sp. GOM

</p>



Expand All @@ -751,10 +759,6 @@ <h3>Consortium Polyaromatic Hydrocarbon Biodegradation</h3>
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=23681"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:23681</a>),

phenanthrene
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=28851"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:28851</a>),

pyrene
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=39106"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:39106</a>)
Expand All @@ -765,16 +769,6 @@ <h3>Consortium Polyaromatic Hydrocarbon Biodegradation</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced Light Crude Oil Removal
<p class="prewrap causal-description">PAH biodegradation is one measured hydrocarbon-removal activity of the consortium that reached higher total crude-oil removal than any individual member.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -799,25 +793,32 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Enhanced Light Crude Oil Removal</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Higher Gross Light Crude Oil Removal</h3>
</div>
<p class="prewrap interaction-description">The Plackett-Burman-selected Pseudomonas, Halopseudomonas, Paenarthrobacter, and Alcanivorax consortium removed more light crude oil than any constituent grown alone over the 75-day assay.</p>
<p class="prewrap interaction-description">After 75 days, gravimetric light-crude-oil removal was about 62% in the Plackett-Burman-selected four-strain consortium versus about 25-39% in individual cultures. The authors explicitly did not subtract abiotic-control removal from these gross percentages, unlike the baseline used for GC-MS biodegradation. Both monocultures and consortium started at 1e8 CFU/mL per strain, so total starting CFUs were higher in the consortium; this is not a total-inoculum-matched synergy test. Stable relative abundance after day 7 and inferred MetaMIS interactions suggest possible cooperation, not directly demonstrated niche partitioning or the mechanism of this comparative endpoint. Neither the n-alkane nor PAH percentage alone selectively explains the gross-removal advantage.</p>




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

Pseudomonas sp. GOM,

Halopseudomonas aestusnigri GOM5,

Paenarthrobacter sp. GOM3,

Alcanivorax sp. GOM

</p>



<p><strong>Metabolites:</strong>

alkane
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18310"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18310</a>),

polyaromatic hydrocarbons
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=33848"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:33848</a>)
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18310</a>)

</p>

Expand Down Expand Up @@ -852,6 +853,25 @@ <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 processes explain the consortium gross-removal advantage?
</h3>
<p class="prewrap">Equal-total-inoculum controls, abiotic-adjusted mass balance and selective partner or metabolic perturbations would separate starting cell number, hydrocarbon transformation, other removal processes and true interaction effects. The paper infers a signed network from relative-abundance time series using MetaMIS; these predictions and possible biosurfactant/cometabolic roles are not newly curated causal nodes here. Two class-to-bulk arrows are removed because neither establishes mediation of the comparative gross endpoint. Existing cache has an abstract and one Methods sentence despite a FULL TEXT marker; the publisher main body, Methods, tables and captions were read separately. Non-graph claims of significant degradation and metadata remain preserved, not certified.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Consortium n-Alkane Biodegradation</code>, <code>ecological_interactions#Consortium Polyaromatic Hydrocarbon Biodegradation</code>, <code>ecological_interactions#Higher Gross Light Crude Oil Removal</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1068,14 +1088,12 @@ <h4 style="color: var(--text);">Evidence</h4>

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


metabolites.push("alkane");

metabolites.push("dodecane");


var processes = [];

Expand All @@ -1098,20 +1116,35 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas sp. GOM",

"Halopseudomonas aestusnigri GOM5",

"Paenarthrobacter sp. GOM3",

"Alcanivorax sp. GOM"

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

})();

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


metabolites.push("fluorene");

metabolites.push("dibenzothiophene");

metabolites.push("phenanthrene");

metabolites.push("pyrene");


Expand All @@ -1132,26 +1165,41 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas sp. GOM",

"Halopseudomonas aestusnigri GOM5",

"Paenarthrobacter sp. GOM3",

"Alcanivorax sp. GOM"

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

})();

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


metabolites.push("alkane");

metabolites.push("polyaromatic hydrocarbons");


var processes = [];

var evidenceCount = 1;

nodes.push({
id: intId,
label: "Enhanced Light Crude Oil Removal",
label: "Higher Gross Light Crude Oil Removal",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1162,6 +1210,23 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Pseudomonas sp. GOM",

"Halopseudomonas aestusnigri GOM5",

"Paenarthrobacter sp. GOM3",

"Alcanivorax sp. GOM"

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

})();


Expand Down
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