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Separate transfer, prediction and mediation in four community graphs (batch107) #1842

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139 changes: 123 additions & 16 deletions docs/communities/Suillus_Bacillus_Thiamine_Ectomycorrhizal_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -653,6 +653,11 @@ <h2>Ecological Interactions</h2>
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
</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 @@ -662,7 +667,7 @@ <h2>Ecological Interactions</h2>
<h3>Fungal recruitment of the hyphae-associated bacterium</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Suillus clintonianus secretes ureidosuccinic acid and pregnenolone that recruit Bacillus altitudinis B4 to the fungal mycelial surface, establishing the association.</p>
<p class="prewrap interaction-description">Suillus clintonianus exudates attract Bacillus altitudinis B4 and support attachment to fungal hyphae. Ureidosuccinic acid promoted chemotaxis, whereas pregnenolone primarily enhanced swimming and swarming. Their separate effects support recruitment without showing that both compounds are equivalent chemoattractants or that no other exudate contributes.</p>


<p><strong>Source Taxon:</strong> Suillus clintonianus</p>
Expand Down Expand Up @@ -694,8 +699,7 @@ <h3>Fungal recruitment of the hyphae-associated bacterium</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Ureidosuccinic acid stimulation of bacterial thiamine production
<p class="prewrap causal-description">Recruitment of B. altitudinis B4 to the S. clintonianus mycelial surface precedes ureidosuccinic-acid stimulation of the recruited bacterium&#39;s thiamine biosynthesis.
</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: recruitment establishes the close fungal-bacterial association in which fungal exudates can stimulate bacterial thiamine production. The authors propose this sequence, but recruitment was not isolated as a necessary mediator of the cue response; ureidosuccinic acid also acted in the separate bacterial assay.</p>
</div>

</div>
Expand All @@ -718,16 +722,28 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41454778/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41454778</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"However, pregnenolone could only improve the bacterial motility, including swimming and swarming of B. altitudinis B4"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Ureidosuccinic acid stimulation of bacterial thiamine production</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Ureidosuccinic acid secreted by S. clintonianus stimulates B. altitudinis B4 to increase biomass and upregulate thiamine biosynthesis genes, enhancing thiamine production.</p>
<p class="prewrap interaction-description">Ureidosuccinic acid associated with S. clintonianus exudates increased B. altitudinis B4 growth, extracellular thiamine and expression of selected thiamine-metabolism genes in the tested assays. This is a measured metabolite response, not demonstrated uptake of ureidosuccinate as a carbon or nitrogen nutrient. The proposed precursor explanation and the benefit received by the bacterial partner remain unresolved.</p>


<p><strong>Source Taxon:</strong> Suillus clintonianus</p>
Expand Down Expand Up @@ -766,8 +782,7 @@ <h3>Ureidosuccinic acid stimulation of bacterial thiamine production</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Thiamine provisioning fulfilling the fungal requirement
<p class="prewrap causal-description">Ureidosuccinic acid-induced biomass increase and thiamine-gene upregulation in B. altitudinis B4 enhance the thiamine pool supplied to the thiamine-limited fungus.
</p>
<p class="prewrap causal-description">Ureidosuccinic acid increased extracellular thiamine in the bacterial assay, supporting a greater vitamin supply available to the fungal recipient. Separate coculture and tracer observations support fungal acquisition of bacterial thiamine; they do not quantify what fraction of endogenous transfer is caused by this one exudate.</p>
</div>

</div>
Expand All @@ -790,6 +805,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41454778/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41454778</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"However, it remains unclear what benefits the bacteria gain in this consortium."</div>

</li>

</ul>

</div>
Expand All @@ -799,7 +827,7 @@ <h4>Evidence</h4>
<h3>Thiamine provisioning fulfilling the fungal requirement</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Bacillus altitudinis B4 supplies thiamine that Suillus clintonianus absorbs, promoting fungal growth; the fungus cannot effectively obtain or synthesize thiamine on its own.</p>
<p class="prewrap interaction-description">B. altitudinis B4 supplies thiamine that S. clintonianus acquires under thiamine-deficient conditions. Bacterial supernatant rescued fungal growth, and labeled thiamine derived from bacterial metabolites was detected in fungal hyphae, supporting actual bacterial-to-fungal vitamin transfer. Genomic evidence and vitamin-omission phenotypes support fungal thiamine auxotrophy; the biosynthetic annotation refers to the bacterial donor.</p>


<p><strong>Source Taxon:</strong> Bacillus altitudinis B4</p>
Expand Down Expand Up @@ -838,8 +866,7 @@ <h3>Thiamine provisioning fulfilling the fungal requirement</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Enhanced ectomycorrhizal colonization of the pine host
<p class="prewrap causal-description">Bacterially produced thiamine is absorbed by S. clintonianus to promote fungal growth, increasing ectomycorrhizal colonization of P. massoniana.
</p>
<p class="prewrap causal-description">HYPOTHESIZED/PARTIAL: bacterial thiamine supports fungal growth and is proposed to contribute to the higher ectomycorrhizal colonization observed with B4 in the pot experiment. The vitamin-mediated route is supported across the assays but is not isolated as the exclusive mediator of the in-plant phenotype.</p>
</div>

</div>
Expand All @@ -862,6 +889,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41454778/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41454778</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites from B. altitudinis B4"</div>

</li>

</ul>

</div>
Expand All @@ -871,7 +911,7 @@ <h4>Evidence</h4>
<h3>Enhanced ectomycorrhizal colonization of the pine host</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The bacterial thiamine supply promotes fungal growth and increases the ectomycorrhizal colonization rate of Suillus clintonianus in association with the host pine Pinus massoniana, completing a vitamin-mediated tripartite symbiosis.</p>
<p class="prewrap interaction-description">The combined S. clintonianus-B4 treatment increased fungal relative biomass and ectomycorrhizal colonization compared with the fungus-only treatment. Pine dry weight, root activity and phosphorus content also increased, supporting a beneficial ectomycorrhizal association rather than colonization alone. B4 alone did not significantly improve seedling performance. The authors interpret this as support for fungal-host mutualism; the pot comparison does not isolate thiamine as the sole mediator or measure bidirectional host-fungal nutrient flux.</p>


<p><strong>Source Taxon:</strong> Suillus clintonianus</p>
Expand Down Expand Up @@ -915,6 +955,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41454778/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41454778</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"the dry weight, root activity, and phosphorus content of P. massoniana were significantly greater in the combined treatment compared to the S. clintonianus-only treatment"</div>

</li>

</ul>

</div>
Expand All @@ -924,6 +977,60 @@ <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 parts of recruitment and pine improvement are specifically mediated by the identified fungal cues and bacterial thiamine?
</h3>
<p class="prewrap">Direct thiamine transfer and positive fungal/plant outcomes are retained. The source leaves bacterial benefit and cue mechanism unresolved, and the pot treatment does not isolate thiamine as the only driver. Retain the proposed sequence with these limits, without turning cue exposure into demonstrated nutrient consumption or universal reciprocity.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Fungal recruitment of the hyphae-associated bacterium</code>, <code>ecological_interactions#Ureidosuccinic acid stimulation of bacterial thiamine production</code>, <code>ecological_interactions#Thiamine provisioning fulfilling the fungal requirement</code>, <code>ecological_interactions#Enhanced ectomycorrhizal colonization of the pine host</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/41454778/" rel="nofollow noreferrer">PMID:41454778</a>


</div>
<p class="snippet small prewrap">However, it remains unclear what benefits the bacteria gain in this consortium.</p>
<p class="muted small prewrap">The source explicitly leaves bacterial benefit unresolved; it does not establish reciprocal nutrient exchange.</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/41454778/" rel="nofollow noreferrer">PMID:41454778</a>


</div>
<p class="snippet small prewrap">13C12-thiamine was detected within the S. clintonianus hyphae following their cultivation with metabolites from B. altitudinis B4</p>
<p class="muted small prewrap">The reported isotope observation directly supports transfer, beyond bulk supernatant depletion.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1424,7 +1531,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1453,7 +1560,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1466,7 +1573,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("thiamine biosynthetic process");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1508,7 +1615,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("thiamine biosynthetic process");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1546,7 +1653,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("biological process involved in interspecies interaction between organisms");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
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