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realmarcin merged 1 commit into from
Oct 6, 2026
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Review biohydrogen, minority-mediator and syngas causal graphs (batch 20) #1334

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80 changes: 33 additions & 47 deletions ...mmunities/Clostridium_Cellulovorans_Rhodopseudomonas_Cellulose_Biohydrogen_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -585,7 +585,7 @@ <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 Clostridium cellulovorans-Rhodopseudomonas palustris Cellulose Biohydrogen 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 @@ -598,8 +598,8 @@ <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 @@ -610,8 +610,7 @@ <h2>Ecological Interactions</h2>
<h3>VFA Cross-Feeding and pH Stabilization</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">C. cellulovorans degrades cellulose and releases volatile fatty acids, while R. palustris consumes some of those acids, stabilizing pH and allowing greater cellulose consumption.
</p>
<p class="prewrap interaction-description">C. cellulovorans supplies VFAs to R. palustris in illuminated cellulose-fed coculture. PARTIAL - the measured pH and substrate profiles support product-removal feedback, but do not isolate pH as its only mediator. Cellulose is the upstream substrate, not a compound directly donated to R. palustris.</p>


<p><strong>Source Taxon:</strong> Clostridium cellulovorans 743B</p>
Expand Down Expand Up @@ -660,8 +659,7 @@ <h3>VFA Cross-Feeding and pH Stabilization</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Integrated Dark and Photo Fermentation for Hydrogen
<p class="prewrap causal-description">R. palustris consumption of C. cellulovorans volatile fatty acids links cellulose-fed dark fermentation to photofermentative metabolism and the enhanced hydrogen yield.
</p>
<p class="prewrap causal-description">VFA supply supports R. palustris photofermentation. PARTIAL - acid consumption can also sustain fermenter activity through a smaller pH decline; partner fluxes and the separate contributions of these routes are not directly resolved.</p>
</div>

</div>
Expand All @@ -677,7 +675,7 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1128/AEM.00789-16"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1128/AEM.00789-16</a>

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

<div class="snippet">"genes related to biosynthesis of volatile fatty acids (VFAs) in C. cellulovorans were upregulated"</div>
Expand All @@ -690,7 +688,7 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1128/AEM.00789-16"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1128/AEM.00789-16</a>

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

<div class="snippet">"a gene that mediates organic compound catabolism in R. palustris was also upregulated"</div>
Expand All @@ -704,10 +702,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Integrated Dark and Photo Fermentation for Hydrogen</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Dark fermentation by C. cellulovorans and photofermentative metabolism by R. palustris jointly enhance hydrogen production from cellulose relative to monocultures.
</p>
<p class="prewrap interaction-description">Coculture hydrogen output exceeded C. cellulovorans monoculture output. PARTIAL - ammonium suppression supports R. palustris nitrogenase involvement in the enhancement, not a directly measured partition of all hydrogen between partners. Nitrogenase-associated proton reduction is not itself evidence of N2 fixation under the argon headspace.</p>



Expand Down Expand Up @@ -737,12 +733,6 @@ <h3>Integrated Dark and Photo Fermentation for Hydrogen</h3>
class="term-link" target="_blank" rel="noopener noreferrer">GO:0015979</a>)
</li>

<li>
nitrogen fixation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0009399"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0009399</a>)
</li>

</ul>


Expand Down Expand Up @@ -771,7 +761,7 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1128/AEM.00789-16"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1128/AEM.00789-16</a>

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

<div class="snippet">"the enhanced H 2 yield was contributed mainly by R. palustris"</div>
Expand All @@ -784,11 +774,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Transcriptomic Division of Labor</h3>
<span class="interaction-type">CROSS_FEEDING</span>
<h3>Transcriptomic Responses Associated with Cocultivation</h3>
</div>
<p class="prewrap interaction-description">Cocultivation upregulates C. cellulovorans cellulosomal genes and R. palustris nitrogen fixation genes, indicating complementary functional responses during cellulose-grown hydrogen production.
</p>
<p class="prewrap interaction-description">Cellulosomal and nitrogenase-related transcription changes accompany cocultivation. They are measured responses, not demonstrated metabolite exchange or a selectively established cause of the hydrogen phenotype.</p>



Expand All @@ -806,27 +794,10 @@ <h3>Transcriptomic Division of Labor</h3>
class="term-link" target="_blank" rel="noopener noreferrer">GO:0030245</a>)
</li>

<li>
nitrogen fixation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0009399"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0009399</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Integrated Dark and Photo Fermentation for Hydrogen
<p class="prewrap causal-description">C. cellulovorans cellulosomal induction and R. palustris nitrogenase induction represent the coordinated dark- and photo-fermentative activities that drive enhanced cellulose-fed hydrogen production.
</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -907,6 +878,25 @@ <h2>Associated Datasets</h2>
</div>
</section>

<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 much of the hydrogen enhancement is mediated by nitrogenase activity and pH-dependent product-removal feedback?
</h3>
<p class="prewrap">The ammonium intervention supports nitrogenase involvement. Partner-resolved flux and matched-pH or selective pathway interventions would distinguish the remaining mechanisms. Monoculture carbon substrates differ; the transcriptomic model is inferential.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#VFA Cross-Feeding and pH Stabilization</code>, <code>ecological_interactions#Integrated Dark and Photo Fermentation for Hydrogen</code>, <code>ecological_interactions#Transcriptomic Responses Associated with Cocultivation</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1233,7 +1223,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1247,8 +1237,6 @@ <h4 style="color: var(--text);">Evidence</h4>

processes.push("photosynthesis");

processes.push("nitrogen fixation");


var evidenceCount = 2;

Expand All @@ -1269,22 +1257,20 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("cellulose catabolic process");

processes.push("nitrogen fixation");


var evidenceCount = 1;

nodes.push({
id: intId,
label: "Transcriptomic Division of Labor",
label: "Transcriptomic Responses Associated with Cocultivation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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