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Bound nursery, bioleaching and FOS graph evidence (batch 39) #1451

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230 changes: 174 additions & 56 deletions docs/communities/Eucalyptus_Nursery_FiveStrain_Inoculant_SynCom.html
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Original file line number Diff line number Diff line change
Expand Up @@ -691,21 +691,16 @@ <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 Eucalyptus Nursery Five-Strain Bacterial Inoculant Consortium</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 (mutualism, colonization facilitation).</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="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="symbolPlus"
data-color="#edab12"></svg> Colonization facilitation
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -714,40 +709,37 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Complementary Nitrogen-Phosphate Trait Pool</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">The five-strain consortium was built from Eucalyptus root and rhizosphere isolates selected in previous work for phosphate solubilization, indolic-compound production, nifH presence, nitrogen cycling traits and rhizosphere colonization traits. That trait pool is the engineered community starting point for the nursery-scale root-endophyte and seedling-performance responses.
</p>
<p class="prewrap interaction-description">The five bacterial inoculant members were selected using prior phosphate-solubilization screens, with nifH detected and indolic compounds produced by some candidates. These prior traits do not demonstrate nitrogen fixation in the nursery, specific indole-3-acetic acid exchange or persistence of each inoculant. The participants name the inoculant, not every member of the native root microbiome.</p>




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

Bacillus subtilis,

<p><strong>Metabolites:</strong>
Paraburkholderia caribensis,

phosphate
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18367"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18367</a>),
Methylobacterium tardum,

Paenibacillus sp. (putative novel species),

indole-3-acetic acid
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=16411"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:16411</a>)
Mesorhizobium sp. (putative novel species)

</p>



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

phosphate
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=18367"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:18367</a>)

</p>

<li>
nitrogen fixation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0009399"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0009399</a>)
</li>

</ul>



Expand All @@ -769,35 +761,51 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42050290/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42050290</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"direct nitrogen fixation was not measured in this study"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Root Endophytic Community Restructuring</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">The five-strain inoculant changed 13-week Eucalyptus root endophytic community structure by Bray-Curtis nMDS and two-way PERMANOVA without a significant shift in richness or Shannon diversity. The source did not resolve this into a pairwise displacement or niche-partitioning mechanism, so this is curated as a measured community-level graph node.
</p>
<p class="prewrap interaction-description">At 13 weeks, inoculation changed root community structure by PERMANOVA without significantly changing richness or Shannon diversity. No genus or phylum showed robust differential abundance after ANCOM-BC-2 sensitivity analysis; reported Mesorhizobium enrichment and Ralstonia reduction are exploratory, not proof of inoculant persistence or disease suppression. Endpoint profiles of 30 A/B-category seedlings do not resolve strain-specific colonization through time. Participants identify inoculant plus host context, not an exhaustive root community.</p>




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

Bacillus subtilis,

Paraburkholderia caribensis,

Methylobacterium tardum,

Paenibacillus sp. (putative novel species),

Mesorhizobium sp. (putative novel species),

Eucalyptus (three clones)

</p>


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

<li>
symbiotic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044403"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044403</a>)
</li>

</ul>



Expand All @@ -819,21 +827,48 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42050290/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42050290</a>

- SUPPORT (COMPUTATIONAL)
</div>

<div class="snippet">"No taxa were identified as robustly differentially abundant after ANCOM-BC-2 sensitivity analysis"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Genotype-Dependent Improvement of Seedling Quality and Survival</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Two of three Eucalyptus genotypes showed improved seedling quality after inoculation, and one showed mortality fall from 21.8% to 6.7%. The benefit is therefore conditional on host genotype rather than a uniform property of the consortium.
</p>
<p class="prewrap interaction-description">The nursery trial compared five-strain inoculation with a water control across three Eucalyptus genotypes. At 13 weeks, quality improvements were genotype-dependent: the reported nonviable/dead category fell from 21.8% to 6.7% for genotype Y, and genotype Z had improved quality. The operational dead category also included severe stem curvature greater than 45 degrees, so this is not exclusively literal mortality. Morphological responses were not uniformly positive across genotypes and traits. Host outcomes do not establish reciprocal bacterial fitness or a resolved microbial mediator.</p>




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

Bacillus subtilis,

Paraburkholderia caribensis,

Methylobacterium tardum,

Paenibacillus sp. (putative novel species),

Mesorhizobium sp. (putative novel species),

Eucalyptus (three clones)

</p>




Expand Down Expand Up @@ -869,6 +904,19 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/42050290/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42050290</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"Seedlings exhibiting severe stem curvature (defined as a deviation greater than 45° from the vertical axis) or found dead during the evaluation period were counted as dead"</div>

</li>

</ul>

</div>
Expand All @@ -878,6 +926,25 @@ <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 inoculant functions mediate the genotype-dependent nursery response?
</h3>
<p class="prewrap">Prior trait screens do not establish nursery nitrogen fixation or specific IAA flux. Root compositional change does not demonstrate persistence of each inoculant; differential taxon trends were not robust after sensitivity analysis. Host quality is genotype-dependent and the dead category includes severe stem curvature. Preserve both workflow-arrow removals from 2026-10-02: none of these observations resolves a mediator linking traits, root composition and host outcome. The control received water; the trial does not isolate PBS-carrier effects. Canonical five-member inoculant and Eucalyptus host labels are preserved, including AMBIGUOUS Paenibacillus grounding. Non-graph fields are preserved, not certified.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Complementary Nitrogen-Phosphate Trait Pool</code>, <code>ecological_interactions#Root Endophytic Community Restructuring</code>, <code>ecological_interactions#Genotype-Dependent Improvement of Seedling Quality and Survival</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1220,22 +1287,16 @@ <h4 style="color: var(--text);">Evidence</h4>

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


metabolites.push("phosphate");

metabolites.push("indole-3-acetic acid");


var processes = [];


processes.push("nitrogen fixation");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1250,20 +1311,35 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bacillus subtilis",

"Paraburkholderia caribensis",

"Methylobacterium tardum",

"Paenibacillus sp. (putative novel species)",

"Mesorhizobium sp. (putative novel species)"

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

})();

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

var processes = [];


processes.push("symbiotic process");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1278,11 +1354,32 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bacillus subtilis",

"Paraburkholderia caribensis",

"Methylobacterium tardum",

"Paenibacillus sp. (putative novel species)",

"Mesorhizobium sp. (putative novel species)",

"Eucalyptus (three clones)"

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

})();

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

var processes = [];
Expand All @@ -1291,7 +1388,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("growth");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand All @@ -1306,6 +1403,27 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Bacillus subtilis",

"Paraburkholderia caribensis",

"Methylobacterium tardum",

"Paenibacillus sp. (putative novel species)",

"Mesorhizobium sp. (putative novel species)",

"Eucalyptus (three clones)"

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

})();


Expand Down
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