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Review degradation, competition and diatom graph scope (batch90) #1743

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105 changes: 81 additions & 24 deletions docs/communities/Pseudomonas_Rhodococcus_Chloronitrobenzene_Coculture.html
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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-Rhodococcus Chloronitrobenzene 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, 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 (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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -608,7 +608,7 @@ <h2>Ecological Interactions</h2>
<h3>Pseudomonas Partial Chloronitrobenzene Transformation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">P. putida HS12 converts 3- and 4-chloronitrobenzene to chlorohydroxyacetanilide intermediates through partial reduction and acetylation, supplying compounds that the Rhodococcus partner can further degrade.</p>
<p class="prewrap interaction-description">The source reports chemically identified conversion of the substrates into intermediates subsequently degraded by the partner. PARTIAL: the sequential transformation supports the reported directed coupling, not reciprocal metabolite supply or directly traced assimilation by both partners.</p>


<p><strong>Source Taxon:</strong> Pseudomonas putida HS12</p>
Expand Down Expand Up @@ -651,8 +651,7 @@ <h3>Pseudomonas Partial Chloronitrobenzene Transformation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Rhodococcus Intermediate Degradation
<p class="prewrap causal-description">P. putida HS12 partial reduction and acetylation generate chlorohydroxyacetanilide intermediates that Rhodococcus sp. strain HS51 further degrades in the sequential two-strain pathway.
</p>
<p class="prewrap causal-description">The reported upstream transformation produces the intermediates that the downstream partner degrades, coupling the two steps. PARTIAL: the accessible abstract does not resolve every transfer or assimilation step.</p>
</div>

</div>
Expand Down Expand Up @@ -695,16 +694,19 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Rhodococcus Intermediate Degradation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Rhodococcus sp. strain HS51 degrades the chlorohydroxyacetanilide intermediates generated by P. putida HS12, completing the sequential catabolic design.</p>
<p class="prewrap interaction-description">Rhodococcus degrades the intermediates generated by Pseudomonas in the proposed two-member pathway. This is the downstream transformation step, not evidence of Rhodococcus supplying a metabolite back to Pseudomonas.</p>


<p><strong>Source Taxon:</strong> Rhodococcus sp. strain HS51</p>


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

Pseudomonas putida HS12,

Rhodococcus sp. strain HS51

<p><strong>Target Taxon:</strong> Pseudomonas putida HS12</p>
</p>



Expand All @@ -728,8 +730,7 @@ <h3>Rhodococcus Intermediate Degradation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Coculture Chloronitrobenzene Mineralization
<p class="prewrap causal-description">Rhodococcus degradation of the Pseudomonas-derived chlorohydroxyacetanilide intermediates completes the sequential pathway needed for 3- and 4-chloronitrobenzene mineralization by the coculture.
</p>
<p class="prewrap causal-description">The reported downstream intermediate degradation contributes to the proposed two-strain pathway and conditional coculture mineralization. PARTIAL: the full pathway and carbon-balance measurements were not independently inspected.</p>
</div>

</div>
Expand Down Expand Up @@ -772,9 +773,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Coculture Chloronitrobenzene Mineralization</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">The two-member coculture mineralizes 3- and 4-chloronitrobenzene in the presence of an additional carbon source.</p>
<p class="prewrap interaction-description">The primary abstract reports coculture mineralization in the presence of an additional carbon source. Preserve that conditional result. The endpoint is not itself evidence that removal of a partner product makes the upstream metabolism favourable, and a complete carbon balance was not independently audited.</p>



Expand Down Expand Up @@ -845,6 +845,60 @@ <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>
What evidence resolves transfer direction and the conditional mineralization pathway?
</h3>
<p class="prewrap">The sequential transformations and reported mineralization are preserved. The reverse-feeding label on the intermediate-degradation node was removed without reversing either graph arrow. Only the primary abstract was retrieved: XML failed after bounded retries, the article page presented a browser challenge and the open-access metadata request returned404. Missing full methods are not evidence that controls were absent. SYNTROPHY does not require obligacy in the local schema; the endpoint label is removed because pathway completion alone does not demonstrate product-removal feedback on the upstream metabolism.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Pseudomonas Partial Chloronitrobenzene Transformation</code>, <code>ecological_interactions#Rhodococcus Intermediate Degradation</code>, <code>ecological_interactions#Coculture Chloronitrobenzene Mineralization</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/10049867/" rel="nofollow noreferrer">PMID:10049867</a>


</div>
<p class="snippet small prewrap">Rhodococcus sp. strain HS51, which degrades 4- and 5-chloro-2-hydroxyacetanilides</p>
<p class="muted small prewrap">Supports HS51 as the organism degrading P. putida-derived intermediates.</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/10049867/" rel="nofollow noreferrer">PMID:10049867</a>


</div>
<p class="snippet small prewrap">This coculture was confirmed to mineralize 3- and 4-CNBs</p>
<p class="muted small prewrap">Directly supports the community-level mineralization claim.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1293,7 +1347,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1315,23 +1369,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Rhodococcus sp. strain HS51";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Pseudomonas putida HS12";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Pseudomonas putida HS12",

"Rhodococcus sp. strain HS51"

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

})();

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


Expand Down
82 changes: 73 additions & 9 deletions docs/communities/Pseudomonas_putida_PpTE_Rhodococcus_RDK17_Terephthalic_Acid_Consortium.html
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Expand Up @@ -578,7 +578,7 @@ <h2>Ecological Interactions</h2>
<h3>Exploitative competition for terephthalic acid</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Both strains utilize TPA at comparable rates in monoculture, but they compete for TPA as the shared sole carbon and energy source in coculture; Pp-TE consistently outcompetes RDK17, partly through relative growth kinetics.</p>
<p class="prewrap interaction-description">Both members use the shared substrate, and the source reports that abolishing its metabolism in Pp-TE removes dominance. This supports a metabolic contribution to competition; dominance alone does not identify that mechanism. PARTIAL: the abstract does not separately quantify resource competition and contact-inhibition contributions.</p>


<p><strong>Source Taxon:</strong> Pseudomonas putida strain Pp-TE (engineered)</p>
Expand Down Expand Up @@ -606,8 +606,7 @@ <h3>Exploitative competition for terephthalic acid</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Pp-TE Dominance During TPA Coculture
<p class="prewrap causal-description">Competition for terephthalic acid contributes to Pp-TE dominance in the two-member TPA coculture fermentations.
</p>
<p class="prewrap causal-description">The source-reported metabolic perturbation supports a contribution of substrate use to dominance, alongside contact inhibition. PARTIAL: their separate effect sizes are not resolved by the accessible abstract.</p>
</div>

</div>
Expand All @@ -630,6 +629,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42324694/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42324694</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"when TPA metabolism was abolished in Pp-TE, it lost its dominance to RDK17"</div>

</li>

</ul>

</div>
Expand All @@ -639,7 +651,7 @@ <h4>Evidence</h4>
<h3>Interference competition via type VI secretion system</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Pp-TE inhibits RDK17 through contact-dependent inhibition mediated by its type VI secretion system, which impairs RDK17 growth and reinforces Pp-TE dominance in coculture.</p>
<p class="prewrap interaction-description">The authors report assays attributing the main competitive advantage to type-VI-secretion-associated contact inhibition, with a partial contribution from relative growth kinetics. Preserve this experimental attribution; the accessible abstract does not expose the full controls or separate effect sizes.</p>


<p><strong>Source Taxon:</strong> Pseudomonas putida strain Pp-TE (engineered)</p>
Expand Down Expand Up @@ -670,8 +682,7 @@ <h3>Interference competition via type VI secretion system</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Pp-TE Dominance During TPA Coculture
<p class="prewrap causal-description">Contact-dependent growth inhibition reinforces Pp-TE dominance over RDK17 in TPA-fed cocultures.
</p>
<p class="prewrap causal-description">The source reports that contact-dependent impairment of the partner is the main contributor to dominance, alongside metabolic capability and relative kinetics. This preserves the reported causal attribution without independently certifying unreviewed methods.</p>
</div>

</div>
Expand Down Expand Up @@ -703,8 +714,7 @@ <h4>Evidence</h4>
<h3>Pp-TE Dominance During TPA Coculture</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">P. putida Pp-TE consistently dominates Rhodococcus sp. RDK17 in batch and serial-transfer cocultures supplied with terephthalic acid as the sole carbon and energy source.
</p>
<p class="prewrap interaction-description">Pp-TE consistently outcompetes RDK17 in the reported batch and serial-transfer cocultures. This is the measured population outcome; its mechanistic attribution is represented by the two upstream nodes, not inferred from dominance alone.</p>


<p><strong>Source Taxon:</strong> Pseudomonas putida strain Pp-TE (engineered)</p>
Expand Down Expand Up @@ -765,6 +775,60 @@ <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>
How are the two competitive contributions distinguished from the dominance observation?
</h3>
<p class="prewrap">All three competition nodes and both existing directions remain. The primary abstract reports contact inhibition, relative kinetics and a metabolism-loss comparison; those positive findings are retained. Full methods and quantitative decomposition were unavailable, which does not imply absent controls. No new resistance-selection details, genetic designs or experimental protocols were added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Exploitative competition for terephthalic acid</code>, <code>ecological_interactions#Interference competition via type VI secretion system</code>, <code>ecological_interactions#Pp-TE Dominance During TPA Coculture</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/42324694/" rel="nofollow noreferrer">PMID:42324694</a>


</div>
<p class="snippet small prewrap">Pp-TE consistently outcompeted RDK17 in batch and multitransfer coculture fermentations, even when RDK17 was inoculated at a significantly higher initial abundance</p>
<p class="muted small prewrap">Supports the observed competitive outcome, not by itself the mechanism of resource competition.</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/42324694/" rel="nofollow noreferrer">PMID:42324694</a>


</div>
<p class="snippet small prewrap">the dominance of Pp-TE was primarily conferred by its type VI secretion system, which impaired the growth of RDK17 via contact-dependent inhibition</p>
<p class="muted small prewrap">Contact-dependent inhibition through the Pp-TE T6SS is interference competition against RDK17.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -933,7 +997,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
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