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Bound wetland and host-helper causal claims (batch87) #1723

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197 changes: 145 additions & 52 deletions docs/communities/Prairie_Pothole_Wetland_Sulfur_Carbon_Virus_Community.html
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Expand Up @@ -689,22 +689,12 @@ <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 Prairie Pothole Wetland Sulfur-Carbon Virus-Host 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 (cross-feeding, niche partitioning).</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="symbolSquare2"
data-color="#1212ed"></svg> Niche partitioning
</div>
<div class="legend-item">
<svg class="legend-symbol" width="14" height="14" viewBox="-9 -9 18 18"
aria-hidden="true" data-symbol="symbolTriangle2"
Expand All @@ -717,14 +707,17 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Diverse Sulfate-Reduction Guild</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Candidate sulfate reducers encode sulfate-reduction marker genes and span multiple bacterial phyla, supporting high sulfate reduction and carbon mineralization in Prairie Pothole wetland sediments.</p>
<p class="prewrap interaction-description">Candidate sulfate-reducer marker genes and MAGs support diverse genomic potential. PARTIAL: predicted donor use and reaction direction are not measured fluxes or experimentally confirmed sulfate reduction for each genome.</p>



<p><strong>Source Taxon:</strong> Prairie Pothole candidate sulfate reducers</p>

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

Prairie Pothole candidate sulfate reducers

</p>



Expand Down Expand Up @@ -770,7 +763,7 @@ <h3>Diverse Sulfate-Reduction Guild</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Niche Differentiation In Heterogeneous Wetland Sediment
<p class="prewrap causal-description">Sulfate-reducer metabolic versatility is one component of the diversity inferred to sustain high carbon and sulfur cycling rates in the heterogeneous sediment matrix.</p>
<p class="prewrap causal-description">HYPOTHESIZED: metabolic versatility may allow sulfate-reducing guilds to occupy different sediment niches and contribute to high cycling rates; substrate partitioning and its effect on ecosystem rates were not experimentally isolated.</p>
</div>

</div>
Expand Down Expand Up @@ -813,16 +806,17 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Alcohol-Linked Methanogenesis Potential</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Methanogen marker genes and reconstructed methanogen genomes suggest that multiple methanogenesis pathways operate in these sediments, with ethanol and 2-propanol hypothesized as important substrates.</p>
<p class="prewrap interaction-description">HYPOTHESIZED: methanogen markers, putative alcohol dehydrogenases and porewater alcohols suggest alcohol-fueled methanogenesis. These findings do not identify an interspecies producer-to-consumer transfer route or quantify its contribution.</p>


<p><strong>Source Taxon:</strong> Prairie Pothole wetland sediment microbial community</p>


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

<p><strong>Target Taxon:</strong> Prairie Pothole methanogens</p>
Prairie Pothole methanogens

</p>



Expand Down Expand Up @@ -894,17 +888,22 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Viral Control Of Sulfate Reducers And Methanogens</h3>
<span class="interaction-type">PREDATION</span>
<h3>Predicted Viral Links to Sulfate Reducers and Methanogens</h3>
</div>
<p class="prewrap interaction-description">Novel viral populations were predicted to infect dominant sulfate-reducing and methanogenic hosts, suggesting top-down viral control over sulfur and carbon cycling guilds.</p>
<p class="prewrap interaction-description">Metagenomic analyses predict virus-host links. HYPOTHESIZED: infection could affect these guilds, but host predictions can be false positives and do not establish current lysis or its effect on sulfur and carbon cycling.</p>




<p><strong>Source Taxon:</strong> Prairie Pothole wetland sediment viruses</p>
<p><strong>Participating Taxa:</strong>

Prairie Pothole candidate sulfate reducers,

Prairie Pothole methanogens,

<p><strong>Target Taxon:</strong> Prairie Pothole wetland sediment microbial community</p>
Prairie Pothole wetland sediment viruses

</p>



Expand All @@ -928,7 +927,7 @@ <h3>Viral Control Of Sulfate Reducers And Methanogens</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Niche Differentiation In Heterogeneous Wetland Sediment
<p class="prewrap causal-description">Predicted infection of dominant sulfate reducers and methanogens adds a viral control to the processes inferred to modulate wetland carbon and sulfur cycling.</p>
<p class="prewrap causal-description">HYPOTHESIZED: host lysis may open niche space and release substrates, potentially changing diversity and cycling. Host suppression and substrate release could have opposing effects, so this existing direction has no established net sign.</p>
</div>

</div>
Expand Down Expand Up @@ -971,13 +970,24 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Niche Differentiation In Heterogeneous Wetland Sediment</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The source study concludes that microbial diversity, metabolic versatility, dynamic environmental conditions, viral infection, and sediment niche differentiation together modulate carbon and sulfur cycling.</p>
<p class="prewrap interaction-description">HYPOTHESIZED: diversity, metabolic versatility, local geochemistry and viral activity may jointly explain heterogeneous niches and high cycling rates. The study does not resolve their causal contributions.</p>




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

Prairie Pothole wetland sediment microbial community,

Prairie Pothole candidate sulfate reducers,

Prairie Pothole methanogens,

Prairie Pothole wetland sediment viruses

</p>



<p><strong>Metabolites:</strong>
Expand Down Expand Up @@ -1088,6 +1098,60 @@ <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 predicted activities and viral effects control measured ecosystem rates?
</h3>
<p class="prewrap">Retain the genomic findings and both proposed directions. Candidate genomes do not guarantee sulfate-reduction direction; alcohol use and viral host links remain inferred. Viral suppression versus release of labile substrates could lower or raise cycling rates. Exact activities, lysis and net effects need experiments; no new arrows were added.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Diverse Sulfate-Reduction Guild</code>, <code>ecological_interactions#Alcohol-Linked Methanogenesis Potential</code>, <code>ecological_interactions#Predicted Viral Links to Sulfate Reducers and Methanogens</code>, <code>ecological_interactions#Niche Differentiation In Heterogeneous Wetland Sediment</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">COMPUTATIONAL</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/30086797/" rel="nofollow noreferrer">PMID:30086797</a>


</div>
<p class="snippet small prewrap">these alcohols may drive a significant fraction of methanogenesis</p>
<p class="muted small prewrap">Supports the alcohol-linked methanogenesis hypothesis in this ecosystem.</p>
</div>

<div class="evidence">
<div class="evidence-head">
<span class="badge small">COMPUTATIONAL</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/30086797/" rel="nofollow noreferrer">PMID:30086797</a>


</div>
<p class="snippet small prewrap">viral populations were predicted to target dominant sulfate reducers and methanogens</p>
<p class="muted small prewrap">Supports virus-host targeting of key sulfur- and methane-cycling guilds.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1408,7 +1472,7 @@ <h2>Environmental Factors</h2>

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


Expand Down Expand Up @@ -1440,18 +1504,24 @@ <h2>Environmental Factors</h2>
});


var srcKey = "Prairie Pothole candidate sulfate reducers";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

"Prairie Pothole candidate sulfate reducers"

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

})();

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


Expand Down Expand Up @@ -1481,23 +1551,24 @@ <h2>Environmental Factors</h2>
});


var srcKey = "Prairie Pothole wetland sediment microbial community";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Prairie Pothole methanogens";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Prairie Pothole methanogens"

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

})();

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

var processes = [];
Expand All @@ -1510,7 +1581,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Viral Control Of Sulfate Reducers And Methanogens",
label: "Predicted Viral Links to Sulfate Reducers and Methanogens",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1519,23 +1590,28 @@ <h2>Environmental Factors</h2>
});


var srcKey = "Prairie Pothole wetland sediment viruses";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Prairie Pothole wetland sediment microbial community";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Prairie Pothole candidate sulfate reducers",

"Prairie Pothole methanogens",

"Prairie Pothole wetland sediment viruses"

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

})();

(function() {
var intId = "interaction:3";
var intType = "NICHE_PARTITIONING";
var intType = "UNKNOWN";
var metabolites = [];


Expand Down Expand Up @@ -1567,6 +1643,23 @@ <h2>Environmental Factors</h2>



var participantKeys = [

"Prairie Pothole wetland sediment microbial community",

"Prairie Pothole candidate sulfate reducers",

"Prairie Pothole methanogens",

"Prairie Pothole wetland sediment viruses"

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

})();


Expand Down
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