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Bound core enrichment, conditional rescue and substrate mediation (batch74) #1625

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115 changes: 59 additions & 56 deletions docs/communities/Model_Cyanobacterial_Consortia_Core_Microbiome.html
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Expand Up @@ -561,45 +561,30 @@ <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 Model Cyanobacterial Consortia Core Microbiome</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 (cross-feeding, 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="symbolDiamond"
data-color="#57c7ab"></svg> Cross-feeding
</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>


<div class="interaction-card">
<div class="interaction-header">
<h3>Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>Putative Plasmid Functions in the Cyanobacterial Core Microbiome</h3>
</div>
<p class="prewrap interaction-description">Core noncyanobacterial species are significantly enriched in plasmids, and plasmid-encoded functions are suggested to mediate symbiotic interactions with the cyanobacterial hosts.</p>

<p class="prewrap interaction-description">PARTIAL - Core microbiome MAGs are enriched in putative plasmid contigs carrying transport, carbohydrate-metabolism and signaling functions. Cobinning assigns plasmids to MAGs and 98% of predicted plasmids were not circularized. Their contribution to phototroph-heterotroph establishment or maintenance is HYPOTHESIZED from genomic content, not demonstrated plasmid transfer, curing, reciprocal fitness or metabolite flux.</p>

<p><strong>Source Taxon:</strong> core noncyanobacterial heterotrophs</p>



<p><strong>Target Taxon:</strong> model cyanobacterial hosts</p>




Expand Down Expand Up @@ -628,7 +613,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>

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

<div class="snippet">"core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions"</div>
Expand All @@ -642,9 +627,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Core Micronutrient and Anoxygenic Photosynthesis Functions</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">The 25-species core microbiome is statistically enriched for micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis functions, indicating shared community-level metabolic contributions across consortia.</p>
<p class="prewrap interaction-description">Core microbiome MAGs are statistically enriched in micronutrient biosynthesis, membrane transport and anoxygenic photosynthesis potential; 20 of 25 core MAGs encode anoxygenic photosystem components. These are genomic capabilities. Cross-feeding of costly cofactors or cyanobacterial products is HYPOTHESIZED, not measured expression, transferred metabolites or partner-specific growth benefit.</p>



Expand Down Expand Up @@ -702,10 +686,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Host- and Inoculum-Independent Core Recruitment</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>Reproducible Core Recruitment Across Hosts and Inocula</h3>
</div>
<p class="prewrap interaction-description">Despite varying cyanobacterial host species and freshwater inoculum sources, the 108 consortia converged on the same noncyanobacterial core, indicating reproducible cyanobacterium-driven recruitment.</p>
<p class="prewrap interaction-description">Among 108 retained consortia, 25 species met an operational core definition: occurrence with at least four host strains and at least two source environments under replicated criteria. Individual core species occurred in 18.5%-68.5% of samples, not universally. Communities stabilized and showed broad convergence, while both host strain and inoculum significantly affected composition. Host-driven facilitation is PARTIAL because cyanobacteria-free controls were absent, leaving medium and laboratory selection unresolved.</p>



Expand All @@ -727,25 +710,23 @@ <h3>Host- and Inoculum-Independent Core Recruitment</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Core Micronutrient and Anoxygenic Photosynthesis Functions
<p class="prewrap causal-description">Reproducible 25-species core recruitment made it possible to statistically validate shared micronutrient-biosynthesis, metabolite- transport, and anoxygenic-photosynthesis functions in the core microbiome.</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis
<p class="prewrap causal-description">The recruited core species were significantly enriched in plasmids whose encoded functions suggested plasmid-mediated cyanobacteria-heterotroph symbiotic roles.</p>
</div>
<h4>Evidence</h4>
<ul class="evidence-list">

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

<a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>

- SUPPORT (IN_VITRO)
</div>

<h4>Evidence</h4>
<ul class="evidence-list">
<div class="snippet">"despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa"</div>

</li>

<li class="evidence-item">
<div>
Expand All @@ -756,7 +737,20 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa"</div>
<div class="snippet">"Individual core species were present in 18.5%–68.5% of all samples"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/40626910/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:40626910</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"The absence of cyanobacteria-free controls limited our ability to disentangle effects solely attributable to media or laboratory conditions."</div>

</li>

Expand All @@ -769,6 +763,25 @@ <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 selective mechanisms explain the measured community responses?
</h3>
<p class="prewrap">The primary source establishes replicated enrichment, but host/source variation persists and the authors report no cyanobacteria-free controls. Bioinformatic removal of predicted plasmid contigs is an analytical comparison, not a biological plasmid intervention. Quantify selective host, plasmid and metabolite-exchange contributions before adding mechanistic arrows; statistical analysis enabled by recruitment is not a downstream ecological cause.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Putative Plasmid Functions in the Cyanobacterial Core Microbiome</code>, <code>ecological_interactions#Core Micronutrient and Anoxygenic Photosynthesis Functions</code>, <code>ecological_interactions#Reproducible Core Recruitment Across Hosts and Inocula</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1059,7 +1072,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1072,7 +1085,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Plasmid-Mediated Cyanobacteria-Heterotroph Symbiosis",
label: "Putative Plasmid Functions in the Cyanobacterial Core Microbiome",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1081,23 +1094,13 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "core noncyanobacterial heterotrophs";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}



var tgtKey = "model cyanobacterial hosts";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}

})();

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

var processes = [];
Expand Down Expand Up @@ -1129,7 +1132,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1138,11 +1141,11 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("interspecies interaction between organisms");


var evidenceCount = 1;
var evidenceCount = 3;

nodes.push({
id: intId,
label: "Host- and Inoculum-Independent Core Recruitment",
label: "Reproducible Core Recruitment Across Hosts and Inocula",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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