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Bound wheat treatment outcomes and inferred mechanisms (batch122) #1953

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105 changes: 74 additions & 31 deletions docs/communities/Wheat_CrownRot_TB_CrossKingdom_SynCom.html
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Expand Up @@ -595,21 +595,16 @@ <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 Wheat Crown-Rot TB Cross-Kingdom SynCom</title>
<desc id="network-svg-desc">Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for competition, colonization facilitation.</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="symbolTimes"
data-color="#a91919"></svg> Competition
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -618,9 +613,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Fusarium pseudograminearum WCR suppression by TB</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Soil drenching with the T. harzianum T19 / B. rugosus PM16 TB SynCom suppressed Fusarium-pseudograminearum-driven wheat crown rot in the controlled pot experiment, alongside improved wheat biomass, chlorophyll content, and yield-related traits.</p>
<p class="prewrap interaction-description">The two-member T19/PM16 TB inoculum suppressed Fusarium pseudograminearum crown rot in controlled wheat pots, with reported biocontrol efficacy of 70.97% and improved biomass, chlorophyll and yield-related traits. The listed fungus is the challenge organism, not a TB member. These positive whole-inoculum outcomes do not establish bilateral competition, reciprocal microbial benefit or a unique immune mechanism. The plant experiment has no single-member treatment that isolates each member contribution.</p>



Expand Down Expand Up @@ -670,16 +664,28 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41821943/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41821943</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"with a biocontrol efficacy of 70.97%"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>TB-associated rhizosphere remodeling</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">TB SynCom inoculation remodeled the resident wheat rhizosphere community, including enrichment of beneficial taxa and reduction of pathogen-associated fungi, during the 45-day Fusarium challenge assay.</p>
<p class="prewrap interaction-description">TB treatment changed rhizosphere DNA-based community profiles, including relative enrichment of Mortierella and reduced pathogen-associated fungi. Relative sequence abundance does not establish absolute viable abundance or strain-resolved persistence of T19/PM16. Genus annotations and correlation networks do not establish beneficial function, nutrient exchange or microbial necessity. Network robustness was assessed by simulated node removal, not biological removal experiments. Remodeling is not isolated as the cause of the positive disease-control outcome.</p>



Expand All @@ -688,17 +694,6 @@ <h3>TB-associated rhizosphere remodeling</h3>



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

<li>
regulation of defense response
(<a href="http://amigo.geneontology.org/amigo/term/GO:0031347"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0031347</a>)
</li>

</ul>




Expand All @@ -719,6 +714,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/41821943/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41821943</a>

- SUPPORT (OTHER)
</div>

<div class="snippet">"Hub-targeted simulations showed a similar trend"</div>

</li>

</ul>

</div>
Expand Down Expand Up @@ -795,6 +803,45 @@ <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>
Which TB-dependent mechanisms explain protection beyond correlated community and soil-metabolite changes?
</h3>
<p class="prewrap">T19 plate inhibition and PM16 growth-promoting screens support separate traits; compatibility is not reciprocal fitness or proof of synergy in the host. Soil metabolites were measured, not directly collected root exudates. The paper explicitly limits daidzein origin and recruitment claims; quorum sensing and volatile effects remain working hypotheses. Structural-equation paths and simulated network attacks are not selective biological perturbations. Do not transfer exogenous-metabolite validation from the distinct six-strain SMC study.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Fusarium pseudograminearum WCR suppression by TB</code>, <code>ecological_interactions#TB-associated rhizosphere remodeling</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/41821943/" rel="nofollow noreferrer">PMID:41821943</a>


</div>
<p class="snippet small prewrap">these QS- and volatile-mediated effects are proposed as working hypotheses and were not directly tested in the present study.</p>

</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1068,7 +1115,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1077,7 +1124,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("defense response to fungus");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down Expand Up @@ -1111,16 +1158,12 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("regulation of defense response");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
73 changes: 67 additions & 6 deletions docs/communities/Wheat_DT_Rhizosphere_SynCom.html
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Expand Up @@ -1085,8 +1085,7 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>Wheat DT-SynCom powdery mildew resistance</h3>
</div>
<p class="prewrap interaction-description">Barley seedlings root-inoculated with the wheat-origin DT-SynCom showed lower Blumeria graminis f. sp. hordei DAF fluorescence intensity than mock-treated controls after pathogen challenge, consistent with SynCom-induced systemic resistance under the assay conditions.
</p>
<p class="prewrap interaction-description">The wheat-origin, 16-member DT-SynCom reduced barley leaf powdery-mildew DAF fluorescence by 43.3% relative to mock treatment after Blumeria graminis f. sp. hordei challenge. All three inoculants protected plants; their pairwise differences were not significant. This supports ISR-like protection but does not assign necessity to JA, ethylene or SA signaling. PEG-tolerant isolate selection is not a test of whole-plant drought protection.</p>



Expand Down Expand Up @@ -1138,8 +1137,7 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>Wheat DT-SynCom selective rhizosphere functional shifts</h3>
</div>
<p class="prewrap interaction-description">The wheat-origin DT-SynCom produced selective metatranscriptomic changes in the barley rhizosphere, including downregulation of PF02868, PF01614, and the KEGG stress-induced DnaJ-like molecular chaperone term K05516, rather than a broad shift in rhizosphere functional profiles.
</p>
<p class="prewrap interaction-description">Before pathogen challenge, the wheat DT-SynCom treatment produced selective changes in measured barley-rhizosphere RNA features, including downregulation of PF02868, PF01614 and K05516. Overall functional profiles and bacterial community structure showed no significant treatment shift. These are metatranscriptomic observations, not PICRUSt predictions. Similarity-based contig annotations do not attribute transcripts to individual inoculant strains, and no perturbation establishes these changes as necessary mediators of the later disease-protection outcome.</p>



Expand Down Expand Up @@ -1183,6 +1181,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42453107/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42453107</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"The metatranscriptomic contigs were assigned based on sequence similarity (not reference SynCom genomes)"</div>

</li>

</ul>

</div>
Expand Down Expand Up @@ -1229,7 +1240,7 @@ <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 @@ -1245,6 +1256,56 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which pre-infection responses mediate wheat DT-SynCom disease protection in barley?
</h3>
<p class="prewrap">Molecular samples preceded the pathogen assay, so these profiles cannot be described as post-infection responses. No significant pairwise difference establishes a superior inoculant. The authors could not assign ISR to specific hormone pathways. OTU matches at 99% identity suggest persistence of related taxa, not unique viable-strain identification. Preserve the prior selective-versus-broad correction and the dated BioProject-visibility discussion.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Wheat DT-SynCom powdery mildew resistance</code>, <code>ecological_interactions#Wheat DT-SynCom selective rhizosphere functional shifts</code></p>



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

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





<a href="https://pubmed.ncbi.nlm.nih.gov/42453107/" rel="nofollow noreferrer">PMID:42453107</a>


</div>
<p class="snippet small prewrap">Although our data did not allow direct assignment of ISR to specific JA-, ET-, or SA-dependent pathways</p>

</div>

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





<a href="https://pubmed.ncbi.nlm.nih.gov/42453107/" rel="nofollow noreferrer">PMID:42453107</a>


</div>
<p class="snippet small prewrap">Although strain-level identity cannot be confirmed by 16S rRNA gene-based identification alone</p>

</div>

</details>


</div>

</section>
Expand Down Expand Up @@ -1732,7 +1793,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand Down
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