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Bound photosynthetic graph products and electron recipients (batch110) #1864

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137 changes: 73 additions & 64 deletions docs/communities/Synechococcus_Halomonas_Light_Driven_PHB_Coculture.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 Synechococcus-Halomonas Light-Driven PHB 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, 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 (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="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
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>Photosynthetic Sucrose Transfer To Halomonas</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Engineered S. elongatus PCC 7942 cscB fixes carbon dioxide using light energy and exports sucrose that directly supports H. boliviensis growth and PHB accumulation.</p>
<p class="prewrap interaction-description">The study reports that sucrose secreted by S. elongatus CscB directly supports H. boliviensis in the light-driven consortium. CO2 is the photosynthetic substrate, not the exchanged organic carbon. The record retains its canonical LC1 identity, but the available primary abstract identifies the heterotroph only at species level; strain-specific attribution and complete medium inputs remain unverified.</p>


<p><strong>Source Taxon:</strong> Synechococcus elongatus PCC 7942 cscB</p>
Expand Down Expand Up @@ -657,8 +657,7 @@ <h3>Photosynthetic Sucrose Transfer To Halomonas</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Light-Driven Biopolymer Production
<p class="prewrap causal-description">Exported cyanobacterial sucrose is the photosynthetically derived organic carbon that H. boliviensis consumes to support PHB accumulation without added external organic carbon.
</p>
<p class="prewrap causal-description">Photosynthetically supplied sucrose supports the PHB-producing Halomonas partner. This preserves the source-supported carbon-to-product route without asserting that the abstract proves exclusion of every external organic input or a quantitative carbon balance.</p>
</div>

</div>
Expand All @@ -681,59 +680,38 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/29061492/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:29061492</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"photoautotroph/chemoheterotroph consortial design"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Light-Driven Biopolymer Production</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">H. boliviensis uses photosynthetically derived sucrose from the cyanobacterium to support stable polyhydroxybutyrate production without adding external organic carbon.</p>
<p class="prewrap interaction-description">The light-driven consortium accumulated PHB in H. boliviensis. The primary abstract reports up to 31% of heterotroph dry weight as PHB and productive coculture persistence for over five months. This is a community production endpoint, not an additional pairwise exchange or direct photosynthesis by Halomonas. Exact assay and LC1 attribution await primary Methods.</p>


<p><strong>Source Taxon:</strong> Synechococcus elongatus PCC 7942 cscB</p>


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

<p><strong>Target Taxon:</strong> Halomonas boliviensis LC1</p>
Synechococcus elongatus PCC 7942 cscB,

Halomonas boliviensis LC1

</p>

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

sucrose
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17992"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17992</a>)

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

poly(3-hydroxybutyrate)
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=53389"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:53389</a>)

</p>

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

<li>
photosynthesis
(<a href="http://amigo.geneontology.org/amigo/term/GO:0015979"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
</li>

</ul>



Expand All @@ -751,7 +729,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"stable polyhydroxybutyrate production"</div>
<div class="snippet">"Consortial H. boliviensis accumulate up to 31% of their dry-weight as PHB"</div>

</li>

Expand All @@ -764,7 +742,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"improved synthetic photoautotroph/chemoheterotroph consortial design"</div>
<div class="snippet">"cultures were continuously productive for over 5 months"</div>

</li>

Expand All @@ -775,9 +753,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Alginate-Partitioned Coculture Stabilization</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Alginate encapsulation of the S. elongatus CscB module enhances sucrose export and coculture stability, physically partitioning the sucrose-producing cyanobacterium from H. boliviensis while maintaining carbohydrate transfer that drives PHB accumulation.</p>
<p class="prewrap interaction-description">Alginate encapsulation of S. elongatus CscB increased sucrose export and improved coculture stability in the primary abstract. This is an abiotic partitioning intervention, not organism-driven colonization facilitation. The source supports these positive effects but the abstract does not isolate how much of PHB output is mediated by export versus other effects.</p>



Expand All @@ -794,10 +771,6 @@ <h3>Alginate-Partitioned Coculture Stabilization</h3>

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

alginic acid
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17548"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17548</a>),

sucrose
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=17992"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:17992</a>)
Expand All @@ -813,7 +786,7 @@ <h3>Alginate-Partitioned Coculture Stabilization</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Light-Driven Biopolymer Production
<p class="prewrap causal-description">Enhanced sucrose export and improved partitioned-coculture stability increase the reliability of cyanobacterial sucrose delivery that supports Halomonas PHB accumulation.</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: alginate-enhanced sucrose export and stability could sustain carbon delivery to the PHB producer. The abstract reports these benefits and PHB production but does not separate their causal contributions to productivity.</p>
</div>

</div>
Expand Down Expand Up @@ -858,6 +831,45 @@ <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 primary methods establish LC1 identity and the contribution of encapsulation to PHB output?
</h3>
<p class="prewrap">Fresh Europe PMC abstract and Crossref DOI metadata were checked. Publisher retrieval failed and bounded author-page/title/DOI/OSTI searches did not recover the full article. The abstract supports species-level sucrose feeding, PHB and enhanced stability, but not LC1 attribution, the complete organic-input accounting or isolated mediation. Obtain authorized primary Methods/supplements before treating these exact-system details as verified; issue #1860 remains open.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Photosynthetic Sucrose Transfer To Halomonas</code>, <code>ecological_interactions#Light-Driven Biopolymer Production</code>, <code>ecological_interactions#Alginate-Partitioned Coculture Stabilization</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VITRO</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/29061492/" rel="nofollow noreferrer">PMID:29061492</a>


</div>
<p class="snippet small prewrap">enhances the co-culture stability</p>
<p class="muted small prewrap">A positive stability finding does not resolve the missing strain and mediation details.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1208,7 +1220,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("sucrose biosynthetic process");


var evidenceCount = 2;
var evidenceCount = 1;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1237,19 +1249,15 @@ <h4 style="color: var(--text);">Evidence</h4>

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


metabolites.push("sucrose");
metabolites.push("poly(3-hydroxybutyrate)");


var processes = [];


processes.push("photosynthesis");


var evidenceCount = 2;

nodes.push({
Expand All @@ -1263,28 +1271,29 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Synechococcus elongatus PCC 7942 cscB";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Halomonas boliviensis LC1";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Synechococcus elongatus PCC 7942 cscB",

"Halomonas boliviensis LC1"

];
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 = [];


metabolites.push("alginic acid");

metabolites.push("sucrose");


Expand Down
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