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Bound phototrophic carbon, lipid and attachment evidence (batch111) #1870

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78 changes: 56 additions & 22 deletions docs/communities/Synechocystis_Pseudomonas_Acetate_Butanol_Coculture.html
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Expand Up @@ -592,6 +592,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolDiamond"
data-color="#57c7ab"></svg> Cross-feeding
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>

Expand All @@ -601,8 +606,7 @@ <h2>Ecological Interactions</h2>
<h3>Photosynthetic Acetate Supply To Pseudomonas</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The engineered Synechocystis farmer fixes CO2 under illumination and secretes acetate into the CoBG11 medium; the P. taiwanensis_Pem7_ButOH partner was adapted to consume acetate in CoBG11 and grew in coculture with lower acetate accumulation than the matched axenic Synechocystis culture.
</p>
<p class="prewrap interaction-description">The engineered Synechocystis partner supplies photosynthetic organic carbon to P. taiwanensis in the acetate-designed coculture. The heterotroph grows on acetate in separate assays, and coculture acetate levels are lower than in axenic Synechocystis. PARTIAL: these observations support acetate consumption but do not isotope-resolve its flux or exclude other cyanobacterial exudates as carbon sources. CO2 is the photosynthetic substrate, not the exchanged organic molecule.</p>


<p><strong>Source Taxon:</strong> Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_Δacs</p>
Expand Down Expand Up @@ -651,8 +655,7 @@ <h3>Photosynthetic Acetate Supply To Pseudomonas</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Acetate-Coupled 1-Butanol Production
<p class="prewrap causal-description">Photosynthetically derived acetate was the intended extracellular carbon source routed from Synechocystis toward Pseudomonas 1-butanol production.
</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: photosynthetically supplied acetate is a supported candidate carbon route to the observed Pseudomonas 1-butanol output. The experiment does not resolve the fraction of product carbon derived from acetate rather than other cyanobacterial exudates; production detection is not a quantified acetate-to-product flux.</p>
</div>

</div>
Expand Down Expand Up @@ -681,31 +684,46 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42726284/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42726284</a>

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

<div class="snippet">"acetate levels remained lower than in the axenic Synechocystis culture"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42726284/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42726284</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"we cannot conclude that the heterotrophic bacteria used acetate as the only source of carbon"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Acetate-Coupled 1-Butanol Production</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The engineered two-member consortium coupled Synechocystis-derived organic carbon to measurable 1-butanol formation by P. taiwanensis_Pem7_ButOH during the 42-day coculture.
</p>
<p class="prewrap interaction-description">The engineered P. taiwanensis partner produced measurable 1-butanol during the 42-day, periodically replenished coculture. Titers fluctuated and reached a plateau; this does not establish uniformly high productivity. The earlier acetate-adaptation assays improved heterotroph growth without increasing 1-butanol production above pre-adaptation levels. This is a community production endpoint, not a second pairwise exchange. Product-carbon attribution to acetate remains unresolved.</p>


<p><strong>Source Taxon:</strong> Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_Δacs</p>


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

<p><strong>Target Taxon:</strong> Pseudomonas taiwanensis VLB120 Pem7_ButOH</p>
Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_Δacs,

Pseudomonas taiwanensis VLB120 Pem7_ButOH

</p>



Expand Down Expand Up @@ -763,7 +781,20 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"P. taiwanensis_Pem7_ButOH showed high production"</div>
<div class="snippet">"the production was not stable in the systems but it clearly reached a plateau"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42726284/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42726284</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"1-butanol production did not exceed the levels prior to adaptation"</div>

</li>

Expand Down Expand Up @@ -1236,7 +1267,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("acetate metabolic process");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1265,7 +1296,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1280,7 +1311,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("acetate metabolic process");


var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand All @@ -1293,17 +1324,20 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_\u0394acs";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Pseudomonas taiwanensis VLB120 Pem7_ButOH";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_\u0394acs",

"Pseudomonas taiwanensis VLB120 Pem7_ButOH"

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

})();

Expand Down
128 changes: 117 additions & 11 deletions docs/communities/Synthetic_Lichen_Synechococcus_Rhodotorula_Coculture.html
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Expand Up @@ -579,6 +579,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>

Expand All @@ -588,7 +593,7 @@ <h2>Ecological Interactions</h2>
<h3>Photosynthetic Sucrose Provisioning</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Engineered S. elongatus fixes carbon dioxide under illumination and secretes sucrose that supports heterotrophic yeast growth.</p>
<p class="prewrap interaction-description">Sucrose-secreting S. elongatus supplies carbon used by R. glutinis in the synthetic lichen coculture. Yeast growth and lower residual sucrose support feeding. The result is strain-specific: the tested S. cerevisiae pairing did not grow comparably. CO2 is fixed by the phototroph rather than donated as the organic carbon substrate.</p>


<p><strong>Source Taxon:</strong> Synechococcus elongatus PCC 7942 cscB+</p>
Expand Down Expand Up @@ -637,7 +642,7 @@ <h3>Photosynthetic Sucrose Provisioning</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Lipid Production Enhancement
<p class="prewrap causal-description">Cyanobacterial sucrose provisioning supplies the yeast carbon source that is routed into coculture biomass and lipid production.</p>
<p class="prewrap causal-description">Cyanobacterial sucrose supports yeast growth within the consortium that exhibits greater total biomass and fatty-acid yield. The whole-culture comparison does not resolve the partners&#39; separate lipid contributions or a sucrose-to-lipid carbon balance.</p>
</div>

</div>
Expand Down Expand Up @@ -669,7 +674,7 @@ <h4>Evidence</h4>
<h3>Rhodotorula-Enhanced Cyanobacterial Survival</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">R. glutinis improves cyanobacterial growth and survival at low inoculum density by alleviating accumulated reactive oxygen stress.</p>
<p class="prewrap interaction-description">R. glutinis supports cyanobacterial growth while receiving sucrose, consistent with conditional mutualism. In illuminated HEPES-buffered cultures, peroxide measurements and catalase-rescue comparisons support protection against oxidative stress, especially for dilute cyanobacterial inocula. High-density axenic growth remains possible. Yeast enhances growth beyond catalase alone, so peroxide removal is not the sole demonstrated explanation and the additional benefit is unresolved.</p>


<p><strong>Source Taxon:</strong> Rhodotorula glutinis</p>
Expand Down Expand Up @@ -708,7 +713,7 @@ <h3>Rhodotorula-Enhanced Cyanobacterial Survival</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Lipid Production Enhancement
<p class="prewrap causal-description">Yeast relief of low-density cyanobacterial oxidative stress helps stabilize the artificial lichen coculture that produces the increased biomass and lipid yield.</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: protection against oxidative stress could help maintain the phototrophic partner that supports lipid-producing coculture. The ROS/catalase comparisons do not isolate the contribution of that protection to the separately measured whole-culture fatty-acid yield advantage.</p>
</div>

</div>
Expand Down Expand Up @@ -740,7 +745,46 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Accumulated reactive oxygen species was observed to severely inhibit axenic growth of cyanobacteria"</div>
<div class="snippet">"HOOH content was progressively reduced and efficiently minimized"</div>

</li>

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

<a href="https://doi.org/10.1186/s13068-017-0736-x"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1186/s13068-017-0736-x</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"S. elongatus grew better in the cultures with catalase"</div>

</li>

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

<a href="https://doi.org/10.1186/s13068-017-0736-x"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1186/s13068-017-0736-x</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"the axenic growth of S. elongatus was robust"</div>

</li>

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

<a href="https://doi.org/10.1186/s13068-017-0736-x"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1186/s13068-017-0736-x</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"R. glutinis may be providing factors beyond HOOH reduction"</div>

</li>

Expand All @@ -751,9 +795,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Lipid Production Enhancement</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Stable S. elongatus-R. glutinis cocultures increased biomass and overall lipid yield relative to cyanobacterial monocultures.</p>
<p class="prewrap interaction-description">S. elongatus-R. glutinis cultures persisted for more than one month in batch and semi-continuous formats. Batch total fatty-acid yield was 54% higher than in cyanobacterial monoculture, alongside increased total biomass. These are whole-culture endpoints, not an additional exchange or a measurement of yeast-specific lipid output. Semi-continuous total harvest includes withdrawn material and is not equivalent to final biomass alone.</p>



Expand Down Expand Up @@ -811,7 +854,33 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"final biomass and overall lipid yields in the batch co-culture 40 to 60% higher"</div>
<div class="snippet">"The total fatty acids (TFA) in the batch co-culture was 54% higher than in mono-culture"</div>

</li>

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

<a href="https://doi.org/10.1186/s13068-017-0736-x"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1186/s13068-017-0736-x</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"With addition of the 50 mL of culture that was removed both at 10 and 21 days"</div>

</li>

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

<a href="https://doi.org/10.1186/s13068-017-0736-x"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1186/s13068-017-0736-x</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"were sustained over 1 month in both batch and in semi-continuous culture"</div>

</li>

Expand Down Expand Up @@ -859,6 +928,43 @@ <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 lipid-yield benefit is mediated by ROS relief rather than other partner effects?
</h3>
<p class="prewrap">Peroxide measurements and catalase rescue support ROS protection, but the primary growth benefit exceeds catalase alone and the lipid assay measures the mixed culture. Do not infer an identified additional factor, exclusive ROS mediation or yeast-specific lipid yield from these comparisons.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Rhodotorula-Enhanced Cyanobacterial Survival</code>, <code>ecological_interactions#Lipid Production Enhancement</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://doi.org/10.1186/s13068-017-0736-x" rel="noreferrer">doi:10.1186/s13068-017-0736-x</a>

</div>
<p class="snippet small prewrap">R. glutinis may be providing factors beyond HOOH reduction</p>
<p class="muted small prewrap">The source identifies an unresolved contribution beyond peroxide reduction.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1144,7 +1250,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("response to oxidative stress");


var evidenceCount = 2;
var evidenceCount = 5;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1173,7 +1279,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1188,7 +1294,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("lipid biosynthetic process");


var evidenceCount = 1;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down
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