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Bound coculture and living-host causal claims (batch63) #1560

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21 changes: 18 additions & 3 deletions docs/communities/Leptolyngbya_Pseudomonas_Mangrove_Coculture.html
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Expand Up @@ -586,7 +586,7 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>Pseudomonas-Associated Leptolyngbya Growth Promotion</h3>
</div>
<p class="prewrap interaction-description">P. monteilii-containing co-cultures reached a larger biomass peak earlier than axenic L. lignicola cultures and P. monteilii produced several growth-promoting compounds, including indole-3-acetic acid, indole-3-butyric acid, vitamin B12, and siderophores.</p>
<p class="prewrap interaction-description">The primary abstract reports a coculture biomass maximum of 298.19 mg/L on day 6 versus 198.08 mg/L on day 9 for axenic Leptolyngbya lignicola, with greater pigment and biochemical accumulation. These are maxima on different days, not a matched-time comparison. Pseudomonas monteilii produced IAA, IBA, vitamin B12 and siderophores, but metabolite production does not establish transfer or selective mediation of growth. Full Methods were unavailable, so the biomass measurement cannot be assumed to resolve each partner separately.</p>


<p><strong>Source Taxon:</strong> Pseudomonas monteilii</p>
Expand Down Expand Up @@ -667,7 +667,7 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>Pseudomonas Physical Association With Leptolyngbya</h3>
</div>
<p class="prewrap interaction-description">Scanning electron microscopy and supporting morphology and biochemical analyses showed P. monteilii in close physical association with L. lignicola during co-culture.</p>
<p class="prewrap interaction-description">Morphological, biochemical and scanning electron microscopic analyses in the primary abstract support close physical association between Leptolyngbya lignicola and Pseudomonas monteilii. Association is not a selective test that contact is required for growth promotion, nor proof of metabolite transfer or reciprocal benefit. No physical-association-to-growth arrow is inferred.</p>


<p><strong>Source Taxon:</strong> Pseudomonas monteilii</p>
Expand Down Expand Up @@ -710,7 +710,7 @@ <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 @@ -745,6 +745,21 @@ <h3>
</details>


</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which partner contributes to the biomass measurement, and which processes mediate the reported growth response?
</h3>
<p class="prewrap">Retain both observations and zero arrows. The complete primary abstract and subscription-preview boundary were read, not the full paper, original images or supplements. Compare day6 coculture and day9 axenic maxima, not matched-time measurements. Metabolite production and physical association do not establish transfer, contact necessity or reciprocal benefit. Earlier #1154/#1155 fixes remain intact. The existing exact-growth-conditions discussion remains open; #1559 tracks separate metadata/source limits. No new mechanistic structure or paid research submission.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Pseudomonas-Associated Leptolyngbya Growth Promotion</code>, <code>ecological_interactions#Pseudomonas Physical Association With Leptolyngbya</code></p>




</div>

</section>
Expand Down
145 changes: 87 additions & 58 deletions docs/communities/Lotus_LjSC3.html
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Expand Up @@ -895,21 +895,16 @@ <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 Lotus Lj-SC3 Synthetic Community</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, 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="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 @@ -918,12 +913,17 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Cognate-host preference of commensal SynComs</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Taxonomically paired Lotus japonicus- and Arabidopsis thaliana-derived synthetic communities display host preference only in the multi-species community context, where strains have to compete for root colonization of their cognate host, rather than in mono-associations.</p>
<p class="prewrap interaction-description">In living-host FlowPots, mixed LjAt-SC3 commensal communities preferentially colonized roots of their cognate Lotus or Arabidopsis host. The SC3 mono-association experiment did not reproduce this preference. This supports community-context dependence, not facilitation by a particular strain or reciprocal benefit. The sole listed canonical participant is the Lotus host: the current bacterial roster is not a verified SC3 membership list, and Arabidopsis is missing. Broader SC1 exudate and SC2 experiments are not silently relabeled SC3.</p>




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

Lotus japonicus

</p>



Expand All @@ -942,16 +942,6 @@ <h3>Cognate-host preference of commensal SynComs</h3>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Host preference increases invasion of standing root communities
<p class="prewrap causal-description">Host preference in the competition assay predicts which SynCom can invade an already established cognate-host root community.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -963,10 +953,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/34312531/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34312531</a>

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

<div class="snippet">"detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations"</div>
<div class="snippet">"commensal SynComs preferentially colonized roots of their cognate host"</div>

</li>

Expand All @@ -977,13 +967,18 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Resident-community priority effect</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Root-associated SynComs established before a second inoculation resist later-arriving communities, so root and rhizosphere assembly depend on inoculation order and resident occupancy of the host-associated niche.</p>
<p class="prewrap interaction-description">SC3 experiment L established communities for four weeks, then challenged them with the complementary host-derived SynCom and harvested two weeks later. Early arrivals retained higher relative proportions in roots and rhizosphere than late arrivals. Arrival order affects assembly, but does not demonstrate absolute exclusion, final equilibrium, selective resource preemption or host-feedback mediation. Secondary inoculation did not significantly increase total bacterial load. The listed Lotus host is only the securely grounded canonical subset, not the microbial roster.</p>




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

Lotus japonicus

</p>




Expand All @@ -1001,16 +996,6 @@ <h3>Resident-community priority effect</h3>



<div class="interaction-flow">
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Host preference increases invasion of standing root communities
<p class="prewrap causal-description">The sequential-inoculation priority effect creates the standing-community context in which cognate-host preference modulates invasion success.</p>
</div>

</div>



<h4>Evidence</h4>
Expand All @@ -1022,10 +1007,10 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/34312531/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34312531</a>

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

<div class="snippet">"established communities are resilient to invasion by latecomers"</div>
<div class="snippet">"early-arriving SynComs invariably reached higher proportions"</div>

</li>

Expand All @@ -1035,13 +1020,18 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Host preference increases invasion of standing root communities</h3>
<span class="interaction-type">COMPETITION</span>
<h3>Cognate-Root Invasion Advantage Associated With Host Preference</h3>
</div>
<p class="prewrap interaction-description">In sequential inoculation experiments, Lotus- and Arabidopsis-derived commensal SynComs invade standing root communities more successfully on their cognate host, showing that host preference gives commensals a competitive advantage during invasion.</p>
<p class="prewrap interaction-description">In SC3 experiment L, host-derived SynComs invaded resident communities more successfully in cognate roots than in the other host; that differential invasion advantage was absent in rhizosphere samples. Strain-level host-preference and invasiveness indices were strongly correlated in roots, not the rhizosphere. This is an association, not selective manipulation of host preference establishing it as the causal mediator. Early-arrival advantages persisted, and later equilibrium was not established. The listed Lotus host does not imply complete microbial or comparator-host coverage.</p>




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

Lotus japonicus

</p>



Expand Down Expand Up @@ -1071,36 +1061,42 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/34312531/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34312531</a>

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

<div class="snippet">"host preference of commensal bacteria confers a competitive advantage in their cognate host"</div>
<div class="snippet">"correlation between host preference and invasiveness"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/34312531/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:34312531</a>
</div>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities"</div>
</section>

</li>
<!-- Associated Datasets -->

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

</div>
<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which host and microbial processes mediate SC3 preference and invasion, and which strains belong to SC3?
</h3>
<p class="prewrap">Retain living-host preference, priority effects and differential root invasion; remove correlation and standing-community-context arrows. Niche preemption, host feedback and unfilled niches are hypotheses. Relative abundance is not absolute exclusion; lack of a significant total-load increase is not proof of invariant abundance. SC1 millifluidic exudates, SC2 experiments, SC3 competition/invasion and mono-associations must remain distinct. Full primary main body and captions read, not original figure pixels, raw data or separate supplements. Public Europe PMC supplemental download timed out after90s with an incomplete archive; no supplement contents certified. Only the canonical Lotus host is confidently grounded for these nodes; the three listed nodule isolates and family-associated bacterium IDs are not validated as the16 SC3 members. Omitted entries expose connectivity warnings rather than being silently certified. #1559 tracks roster/metadata repair, alongside existing #497/#1082.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Cognate-host preference of commensal SynComs</code>, <code>ecological_interactions#Resident-community priority effect</code>, <code>ecological_interactions#Cognate-Root Invasion Advantage Associated With Host Preference</code></p>

</section>

<!-- Associated Datasets -->


</div>

</section>

<!-- Environmental Factors -->


Expand Down Expand Up @@ -1563,7 +1559,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1587,11 +1583,22 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Lotus japonicus"

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

})();

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

var processes = [];
Expand All @@ -1615,11 +1622,22 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Lotus japonicus"

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

})();

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

var processes = [];
Expand All @@ -1628,11 +1646,11 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("interspecies interaction between organisms");


var evidenceCount = 2;
var evidenceCount = 1;

nodes.push({
id: intId,
label: "Host preference increases invasion of standing root communities",
label: "Cognate-Root Invasion Advantage Associated With Host Preference",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1643,6 +1661,17 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Lotus japonicus"

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

})();


Expand Down
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