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Bound endpoint and mechanism claims in four community graphs (batch105) #1828

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78 changes: 70 additions & 8 deletions docs/communities/Space_Habitat_SevenMember_Stress_Tolerance_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -726,16 +726,16 @@ <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 Space Habitat Seven-Member Stress-Tolerance SynCom</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 (competition).</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="symbolTimes"
data-color="#a91919"></svg> Competition
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -744,9 +744,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">After 24 h co-cultivation, culturable B. subtilis CFU were significantly lower in the whole seven-member consortium than in B. subtilis single culture under the tested recovery conditions. The source discusses possible antimicrobial competition but does not resolve which partner, metabolite or mechanism drove this effect.</p>
<p class="prewrap interaction-description">After co-cultivation, culturable B. subtilis CFU were significantly lower in the whole seven-member laboratory consortium than in single culture under the tested recovery conditions. This is decreased cultivability, not definitive loss of viability or demonstrated reciprocal negative effects on a pair of partners. The source discusses possible competition, but does not identify a causal partner or confirmed metabolite activity.</p>



Expand Down Expand Up @@ -781,6 +780,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42577390/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42577390</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability"</div>

</li>

</ul>

</div>
Expand Down Expand Up @@ -826,7 +838,7 @@ <h2>Associated Datasets</h2>
</section>

<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 @@ -841,6 +853,56 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Does the reported colony-recovery decrease establish reciprocal competition or loss of viability?
</h3>
<p class="prewrap">The measured decrease is retained. COMPETITION requires both partners to be negatively affected; this result does not establish that relationship. Candidate genomic functions are not confirmed activity. This metadata review adds no stress-survival procedures or new partner mechanisms.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Whole-consortium reduction of recoverable Bacillus subtilis after co-cultivation</code></p>



<details class="evidence-list">
<summary class="muted small">2 evidence item(s)</summary>

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



<a href="https://pubmed.ncbi.nlm.nih.gov/42577390/" rel="nofollow noreferrer">PMID:42577390</a>


</div>
<p class="snippet small prewrap">reduced CFU recovery corresponds to decreased cultivability rather than definitive loss of viability</p>
<p class="muted small prewrap">The source explicitly limits interpretation of reduced colony recovery.</p>
</div>

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



<a href="https://pubmed.ncbi.nlm.nih.gov/42577390/" rel="nofollow noreferrer">PMID:42577390</a>


</div>
<p class="snippet small prewrap">these findings reflect genomic potential rather than confirmed metabolite activity.</p>
<p class="muted small prewrap">Bounds the source interpretation; no metabolite-mediated causal edge is established.</p>
</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -1184,12 +1246,12 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
78 changes: 43 additions & 35 deletions docs/communities/Sphingobium_Nitrososphaera_Phenanthrene_Carbon_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -592,7 +592,7 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>SynCom phenanthrene removal in lettuce pots</h3>
</div>
<p class="prewrap interaction-description">As a two-member synthetic community, Sphingobium sp. RS2 and Nitrososphaera viennensis EN76 were associated with 90.02% PHE removal from soil and an 81.07% reduction of PHE transfer to lettuce. Pairwise exchange metabolites were not resolved in the accessible abstract.</p>
<p class="prewrap interaction-description">In lettuce-soil pots, SynCom addition was associated with 90.02% PHE removal from soil and an 81.07% reduction of PHE transfer to lettuce. These are pot-level outcomes, not isolated contributions of each inoculant or a traced interspecies exchange in the accessible abstract.</p>



Expand Down Expand Up @@ -633,7 +633,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>

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

<div class="snippet">"The results of the pot experiment indicated that 90.02% of the PHE was effectively removed from the soil and 81.07% of the PHE transferred to the lettuce was reduced by the addition of SynCom."</div>
Expand All @@ -646,35 +646,16 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>SynCom soil carbon restoration</h3>
<h3>SynCom soil carbon endpoints and modeled guild associations</h3>
</div>
<p class="prewrap interaction-description">SynCom addition increased soil organic carbon, microbial carbon, and total carbon, and random-forest/PLS-PM modeling linked those effects to a sustained increase in the absolute abundance of soil carbon-fixing and PHE-degrading microorganisms.</p>
<p class="prewrap interaction-description">SynCom addition significantly increased soil organic carbon, microbial carbon and total carbon content in the pot experiment. PARTIAL: random-forest/PLS-PM analysis links these outcomes to increased absolute abundances of carbon-fixing and PHE-degrading soil microorganisms. Carbon stocks and modeled associations do not themselves quantify carbon-fixation flux, establish exchanged carbon, or isolate each inoculant contribution.</p>






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

carbon dioxide
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16526"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16526</a>)

</p>



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

<li>
carbon fixation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0015977"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0015977</a>)
</li>

</ul>



Expand All @@ -689,7 +670,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>

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

<div class="snippet">"Soil organic carbon, microbial carbon, and total carbon content were also significantly increased."</div>
Expand All @@ -702,7 +683,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41967346/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41967346</a>

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

<div class="snippet">"demonstrated that these effects were primarily driven by a continuous increase in the absolute abundance of soil carbon-fixing microorganisms and PHE-degrading microorganisms after SynCom addition."</div>
Expand All @@ -719,7 +700,7 @@ <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 Down Expand Up @@ -756,6 +737,41 @@ <h3>

</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
What source evidence separates the observed soil carbon increase from carbon-fixation flux and causal contributions of the two inoculants?
</h3>
<p class="prewrap">The accessible abstract supports positive pot endpoints and the authors modeled guild-abundance interpretation. It does not resolve member-specific exchange or direct flux; full methods and model specification were not read. Prior environmental grounding and computational provenance fixes are preserved.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#SynCom phenanthrene removal in lettuce pots</code>, <code>ecological_interactions#SynCom soil carbon endpoints and modeled guild associations</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_VIVO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/41967346/" rel="nofollow noreferrer">PMID:41967346</a>


</div>
<p class="snippet small prewrap">Soil organic carbon, microbial carbon, and total carbon content were also significantly increased.</p>
<p class="muted small prewrap">Supports increased soil organic, microbial, and total carbon after SynCom addition.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->
Expand Down Expand Up @@ -1166,21 +1182,13 @@ <h4 style="color: var(--text);">Evidence</h4>
var intType = "UNKNOWN";
var metabolites = [];


metabolites.push("carbon dioxide");


var processes = [];


processes.push("carbon fixation");


var evidenceCount = 2;

nodes.push({
id: intId,
label: "SynCom soil carbon restoration",
label: "SynCom soil carbon endpoints and modeled guild associations",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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