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Bound inferred mechanisms while preserving measured outcomes (batch120) #1938

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69 changes: 65 additions & 4 deletions docs/communities/Thermoleptolyngbya_Chelatococcus_Arsenic_Detoxification_Coculture.html
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Expand Up @@ -598,7 +598,7 @@ <h2>Ecological Interactions</h2>
<h3>Cyanobacterial Organic-Carbon Provisioning</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Under illuminated coculture conditions, XZ-Cy5 secreted organic carbon that supported Chelatococcus sp. XZ-Ab1 heterotrophic growth; 13CO2 NanoSIMS tracing directly detected transfer of cyanobacterium-derived carbon to the heterotroph.</p>
<p class="prewrap interaction-description">Illuminated XZ-Cy5/XZ-Ab1 coculture supports organic-carbon provision from the cyanobacterium to the heterotroph. The abstract reports heterotrophic growth benefit and direct NanoSIMS detection of photoautotroph-derived carbon after 13CO2 labeling. Retain this experimentally supported cross-feeding without assigning an identified secreted molecule or extending the carbon tracer result to nitrogen or oxygen transfer.</p>


<p><strong>Source Taxon:</strong> Thermoleptolyngbya sichuanensis XZ-Cy5</p>
Expand Down Expand Up @@ -664,7 +664,7 @@ <h4>Evidence</h4>
<h3>Chelatococcus Arsenite Detoxification</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Chelatococcus sp. XZ-Ab1 used cyanobacterium-derived carbon and oxygen to oxidize toxic arsenite to less-toxic arsenate, relieving arsenite stress that otherwise damaged XZ-Cy5 chlorophyll content and photosynthetic activity.</p>
<p class="prewrap interaction-description">Chelatococcus sp. XZ-Ab1 oxidizes arsenite to less-toxic arsenate and promotes XZ-Cy5 growth in coculture. Together with the reciprocal heterotrophic benefit from photosynthetic carbon, this supports mutualism under the tested arsenic-stress conditions. The cyanobacterial monoculture did not oxidize arsenite, whereas the heterotroph did so when supplied organic carbon and oxygen. PARTIAL for the exact oxygen-supply route in coculture: genomic interpretation and a supplemented pure-culture comparison are not direct tracing of cyanobacterial oxygen into arsenite oxidation. No nitrogen transfer or thermodynamic product-removal dependence is asserted.</p>


<p><strong>Source Taxon:</strong> Chelatococcus sp. XZ-Ab1</p>
Expand Down Expand Up @@ -695,6 +695,19 @@ <h3>Chelatococcus Arsenite Detoxification</h3>
<h4>Evidence</h4>
<ul class="evidence-list">

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42468699/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42468699</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Chelatococcus sp. XZ-Ab1 promoted growth of &#34;T. sichuanensis&#34; XZ-Cy5"</div>

</li>

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

Expand All @@ -721,6 +734,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42468699/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42468699</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen"</div>

</li>

</ul>

</div>
Expand All @@ -731,7 +757,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand All @@ -746,6 +772,41 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which chemical and oxygen-supply routes account for the measured XZ-Cy5/XZ-Ab1 mutualism?
</h3>
<p class="prewrap">The primary abstract directly supports carbon transfer and reciprocal growth. It separately interprets metabolic complementarity from genomes, including nitrogen provision and oxygen production. These are not equivalent to isotope-resolved oxygen or nitrogen transfer. Full primary methods and route-specific evidence would resolve these details; missing detail does not negate the positive carbon and growth results. The earlier culture-conditions discussion remains open. No new node or arrow is introduced.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Cyanobacterial Organic-Carbon Provisioning</code>, <code>ecological_interactions#Chelatococcus Arsenite Detoxification</code></p>



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

<div class="evidence">
<div class="evidence-head">





<a href="https://pubmed.ncbi.nlm.nih.gov/42468699/" rel="nofollow noreferrer">PMID:42468699</a>


</div>
<p class="snippet small prewrap">Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains</p>

</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -987,7 +1048,7 @@ <h2>Environmental Factors</h2>
processes.push("response to toxic substance");


var evidenceCount = 2;
var evidenceCount = 4;

nodes.push({
id: intId,
Expand Down
91 changes: 66 additions & 25 deletions docs/communities/Thermophilic_ExSitu_Biomethanation_Mixed_Culture.html
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Expand Up @@ -852,21 +852,16 @@ <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 Thermophilic Ex-Situ Biomethanation Mixed Culture</title>
<desc id="network-svg-desc">Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, syntrophy.</desc>
<desc id="network-svg-desc">Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.</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="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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -875,9 +870,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Thermophilic H2/CO2 Biomethanation</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The conditioned archaeal fraction used H2 and CO2 to produce CH4 under a 4:1 H2:CO2 gas feed at 50 C; the final phase favoured hydrogenotrophic Methanobacteria, with Methanosarcina contributing at lower abundance through hydrogenotrophic and acetoclastic metabolism.</p>
<p class="prewrap interaction-description">A conditioned mixed culture converted externally supplied H2/CO2 to methane in a single proof-of-concept CSTR. Output methane content reached 86% by day 69 in the final thermophilic phase; exceeding 90% was proposed, not observed. Cylinder-fed gas conversion is not itself interspecies cross-feeding. Methanobacteria enrichment and contributions by Methanosarcina are source interpretations informed by group-specific qPCR and community profiles, not taxon-resolved flux measurements. The listed phylum, class and genus are overlapping taxonomic summaries rather than independent strain members. Sequential conditioning and washout changes do not independently isolate temperature as the cause of every performance difference.</p>



Expand Down Expand Up @@ -939,7 +933,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"The high H₂: CO₂ throughput at 50"</div>
<div class="snippet">"H₂ and CO₂ gases were supplied from pressurised gas cylinders"</div>

</li>

Expand All @@ -952,7 +946,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"favoured hydrogenotrophic Methanobacteria"</div>
<div class="snippet">"CH₄ levels in the output gas steadily increased with each washout, reaching 86% by day 69"</div>

</li>

Expand All @@ -962,10 +956,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42293522</a>

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

<div class="snippet">"levels in the output gas steadily increased with each washout, reaching 86% by day 69"</div>
<div class="snippet">"favoured hydrogenotrophic Methanobacteria"</div>

</li>

Expand All @@ -975,10 +969,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>VFA Syntrophic Turnover</h3>
<span class="interaction-type">SYNTROPHY</span>
<h3>VFA dynamics and inferred interspecies turnover</h3>
</div>
<p class="prewrap interaction-description">Thermophilic bacterial partners produced and transformed volatile fatty acids while archaeal acetoclastic methanogens consumed acetate for methane production; by day 69, VFA concentrations fell to approximately 3.5 g/L and were dominated by acetate.</p>
<p class="prewrap interaction-description">The measured VFA pool fell from approximately 5 to 3.5 g/L during the final phase and ended with 73% acetate, 16% propionic acid and 10% n-butyric acid. These are pool measurements during washout-managed operation, not direct rates of metabolite exchange. PARTIAL: the authors interpret Firmicutes as VFA producers, Coprothermobacterota as acetate oxidizers and Methanosaeta/Methanothrix as acetoclastic methanogens, with Methanosarcina potentially using both substrates. Group abundance and gene copies do not demonstrate those exact taxa executing each route, metabolic activity per cell, or product-removal-dependent thermodynamic cooperation. Washout and substrate-pool changes remain alternatives to attributing every VFA decrease to consumption.</p>



Expand Down Expand Up @@ -1064,7 +1057,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42293522</a>

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

<div class="snippet">"Overall, in the final phase, the system exhibited a balanced microbial community"</div>
Expand All @@ -1077,7 +1070,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42293522</a>

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

<div class="snippet">"Coprothermobacterota converting acetate"</div>
Expand All @@ -1090,13 +1083,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42293522</a>

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

<div class="snippet">"Methanosaeta converting acetate"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42293522</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"VFA concentrations were measured immediately before washout, capturing peak accumulation prior to dilution or biomass replacement"</div>

</li>

</ul>

</div>
Expand All @@ -1107,7 +1113,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(3)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -1179,6 +1185,41 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which taxon-specific VFA and methane routes were active beyond the bulk chemistry and DNA profiles?
</h3>
<p class="prewrap">The study follows one reactor through sequential temperature, gas and washout changes. Methane production is measured, but its organism-specific allocation and interspecies fluxes are inferred. Direct sludge qPCR/16S can include DNA from killed or inactive cells; bacterial plate recovery is a separate culturable fraction. The original taxonomy-resolution and industrial-stability discussions remain open. No new causal link between the two process nodes is introduced.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Thermophilic H2/CO2 Biomethanation</code>, <code>ecological_interactions#VFA dynamics and inferred interspecies turnover</code></p>



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

<div class="evidence">
<div class="evidence-head">





<a href="https://pubmed.ncbi.nlm.nih.gov/42293522/" rel="nofollow noreferrer">PMID:42293522</a>


</div>
<p class="snippet small prewrap">These approaches reflect the total microbial DNA pool</p>

</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1632,7 +1673,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1683,7 +1724,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1706,11 +1747,11 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("methanogenesis");


var evidenceCount = 4;
var evidenceCount = 5;

nodes.push({
id: intId,
label: "VFA Syntrophic Turnover",
label: "VFA dynamics and inferred interspecies turnover",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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