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Bound electrosynthetic, algal and gut causal claims (batch 40) #1458

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131 changes: 104 additions & 27 deletions ...communities/Electrosynthetic_Consortia_Shewanella_Clostridium_Acetobacterium_Acetate.html
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Expand Up @@ -610,27 +610,26 @@ <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 Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate</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 (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.</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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>DIET from S. oneidensis to C. aceticum</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair</h3>
</div>
<p class="prewrap interaction-description">In the S. oneidensis-C. aceticum consortium, direct interspecies electron transfer (DIET) mediated by cytochrome c and riboflavin dominates at the biofilm-electrode interface, driving CO2-to-acetate conversion.</p>
<p class="prewrap interaction-description">PARTIAL: In the C. aceticum-S. oneidensis pair, biofilm-associated electron transfer is supported by compartment-removal responses, electrochemical and spectroscopic readouts, and riboflavin add-back. The authors call this DIET, but these assays do not uniquely establish contact-only transfer or selective cytochrome necessity; riboflavin is also a diffusible mediator. The canonical target label Andreesenella acetica preserves the source organism called C. aceticum. Product enhancement does not demonstrate obligatory syntrophy.</p>


<p><strong>Source Taxon:</strong> Shewanella oneidensis MR-1</p>
Expand Down Expand Up @@ -658,8 +657,7 @@ <h3>DIET from S. oneidensis to C. aceticum</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced CO2-to-Acetate Conversion
<p class="prewrap causal-description">Biofilm-localized DIET in the S. oneidensis-C. aceticum consortium contributes electron flow for enhanced CO2-to-acetate electrosynthesis.
</p>
<p class="prewrap causal-description">PARTIAL: Biofilm-associated electron supply and riboflavin-responsive transfer can support the C. aceticum pair&#39;s acetate increase. Compartment removal and add-back support this contribution, but do not isolate the necessity of contact-only DIET or a specific cytochrome. This arrow concerns the CS pair, not a simultaneous three-member culture.</p>
</div>

</div>
Expand All @@ -675,23 +673,35 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

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

<div class="snippet">"DIET via cytochrome c and riboflavin dominates at the biofilm-electrode interface in S. oneidensis-C. aceticum consortia"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"metabolite profiling (H2, formate, riboflavin), biomass distribution and fhs gene copy numbers, and functional prediction"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>H2/formate-mediated IET from S. oneidensis to A. woodii</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair</h3>
</div>
<p class="prewrap interaction-description">In the S. oneidensis-A. woodii consortium, interspecies electron transfer proceeds via H2/formate shuttling in the planktonic phase rather than direct contact, supporting acetate production.</p>
<p class="prewrap interaction-description">PARTIAL: The A. woodii-S. oneidensis pair favors suspension-associated acetate synthesis, consistent with a diffusible hydrogen/formate electron-transfer model. These culture-level profiles and compartment interventions do not trace donor-resolved transfer or establish an exclusive route; hydrogen was detected in both alternative pairs. Daily apparent biofilm/suspension contributions are instantaneous responses to cell removal, not cumulative mass-balanced flux fractions, and may exceed 100% through compensatory responses.</p>


<p><strong>Source Taxon:</strong> Shewanella oneidensis MR-1</p>
Expand Down Expand Up @@ -723,8 +733,7 @@ <h3>H2/formate-mediated IET from S. oneidensis to A. woodii</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced CO2-to-Acetate Conversion
<p class="prewrap causal-description">H2/formate-mediated electron transfer in the S. oneidensis-A. woodii consortium contributes planktonic electron flow for enhanced CO2-to-acetate electrosynthesis.
</p>
<p class="prewrap causal-description">PARTIAL: Diffusible reducing equivalents are a supported explanation for suspension-associated acetate synthesis in the AS pair, including acetate production where A. woodii alone failed at the tested lower cell voltage. This does not establish exclusive hydrogen/formate mediation or identify the molecular donor flux.</p>
</div>

</div>
Expand All @@ -740,27 +749,48 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

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

<div class="snippet">"whereas S. oneidensis-A. woodii consortia prefer H2/formate-mediated IET in the planktonic phase"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"failed to produce acetate"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Enhanced CO2-to-Acetate Conversion</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Co-cultivation of Shewanella oneidensis MR-1 with either electroactive Clostridium aceticum or nonelectroactive Acetobacterium woodii boosts acetate production by linking spatially organized interspecies electron transfer to CO2 reduction.
</p>
<p class="prewrap interaction-description">Two alternative two-member consortia, not one three-member community, increased acetate accumulation relative to their corresponding acetogen monocultures. At 0.88-V applied cell voltage, AS reached 1.16 g/L versus 0.62 g/L for A. woodii alone, and CS reached 1.05 g/L versus 0.56 g/L for C. aceticum alone. The participating taxa are the combined comparison roster; the acetogens were alternatives. Open-circuit cultures used H2/CO2 whereas driven cultures used N2/CO2, so that contrast is not voltage-only. Aggregate production does not prove reciprocal fitness or obligate syntrophy.</p>




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

Shewanella oneidensis MR-1,

Clostridium aceticum (electroactive acetogen),

Acetobacterium woodii (nonelectroactive acetogen)

</p>



Expand Down Expand Up @@ -815,13 +845,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

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

<div class="snippet">"orchestrating electron flow to optimize CO2-to-acetate conversion"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41236292/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41236292</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"representing a 1.87‐fold of A. woodii alone"</div>

</li>

</ul>

</div>
Expand All @@ -831,6 +874,25 @@ <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 electron-transfer routes are necessary within each alternative pair?
</h3>
<p class="prewrap">Keep the two measured alternative pairs separate. Spectroscopy, electrochemistry, metabolite profiles, riboflavin add-back and daily planktonic-cell removal support compartment-associated models but do not isolate contact-only DIET or donor-resolved hydrogen/formate flux. Riboflavin is a diffusible mediator; hydrogen appears in both systems. Instantaneous apparent compartment contributions can exceed 100% and are not cumulative flux partitions. Main Methods describe DNA/16S, fhs copies and normalized gene abundance; do not call these transcript measurements without reviewing the unread supplement. The proposed acetate-formate recycling and future three-member consortium are hypotheses, not new measured causal nodes. Preserve canonical taxonomy and leave non-graph role, voltage and control wording to #1455.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair</code>, <code>ecological_interactions#Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair</code>, <code>ecological_interactions#Enhanced CO2-to-Acetate Conversion</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1007,7 +1069,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1016,11 +1078,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "DIET from S. oneidensis to C. aceticum",
label: "Proposed Biofilm-Associated IET in the S. oneidensis-C. aceticum Pair",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1045,7 +1107,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1056,11 +1118,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "H2/formate-mediated IET from S. oneidensis to A. woodii",
label: "Proposed Planktonic H2/Formate IET in the S. oneidensis-A. woodii Pair",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1085,7 +1147,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1100,7 +1162,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("carbon fixation");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand All @@ -1115,6 +1177,21 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Shewanella oneidensis MR-1",

"Clostridium aceticum (electroactive acetogen)",

"Acetobacterium woodii (nonelectroactive acetogen)"

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

})();


Expand Down
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