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Bound mat carbon models, conditional floc assembly and Naica physiology (batch76) #1636

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114 changes: 60 additions & 54 deletions docs/communities/Mushroom_Spring_Hot_Spring_Phototrophic_Mat_Community.html
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Original file line number Diff line number Diff line change
Expand Up @@ -691,28 +691,26 @@ <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 Mushroom Spring Hot-Spring Phototrophic Mat 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 (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="symbolSquare2"
data-color="#1212ed"></svg> Niche partitioning
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Diel Phototrophic Carbon Fixation</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Putative Diel Phototrophic Carbon Fixation</h3>
</div>
<p class="prewrap interaction-description">Roseiflexus and Chloroflexus populations show diel expression of bacteriochlorophyll, reaction-center, and 3-hydroxypropionate carbon dioxide fixation genes, indicating time-resolved phototrophic carbon metabolism in the mat.
</p>
<p class="prewrap interaction-description">Metatranscriptomics measured diel expression in Roseiflexus and Chloroflexus populations: bacteriochlorophyll and reaction-center transcripts were more abundant at night, whereas key 3-hydroxypropionate carbon-fixation genes were expressed during the day. PARTIAL - The authors infer daytime photomixotrophic carbon fixation from these RNA patterns; direct fixation flux or resource partitioning between the genera is not established by the available abstract.</p>



Expand Down Expand Up @@ -767,7 +765,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/23575369/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:23575369</a>

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

<div class="snippet">"expressed key genes involved in the 3-hydroxypropionate (3-OHP) carbon dioxide fixation bi-cycle during the day"</div>
Expand All @@ -793,11 +791,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Phototroph Storage Polymer Cycling</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Putative Diel Phototroph Storage Polymer Cycling</h3>
</div>
<p class="prewrap interaction-description">Filamentous anoxygenic phototrophs shift between synthesis and use of storage polymers across the diel cycle, coupling light availability to community carbon and energy flow.
</p>
<p class="prewrap interaction-description">PARTIAL - Diel expression of storage-polymer synthesis and degradation genes supports the authors proposed model: nighttime polyhydroxyalkanoate and wax-ester synthesis with glycogen fermentation, followed by daytime use of stored carbon and electron reserves. Polymer turnover and flux through this model are inferred from transcripts in the available abstract, not directly measured here.</p>



Expand Down Expand Up @@ -837,9 +833,8 @@ <h3>Phototroph Storage Polymer Cycling</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Diel Phototrophic Carbon Fixation
<p class="prewrap causal-description">Daytime degradation of polyhydroxyalkanoates and wax esters supplies carbon and electron reserves that support filamentous-anoxygenic- phototroph photomixotrophy through the 3-OHP bi-cycle.
</p>
<span class="flow-arrow">→</span> Putative Diel Phototrophic Carbon Fixation
<p class="prewrap causal-description">HYPOTHESIZED - The source model proposes that daytime polyhydroxyalkanoate and wax-ester degradation supplies carbon and electron reserves that support photomixotrophic carbon fixation through the 3-OHP bi-cycle. This metabolic link targets putative carbon fixation, not a demonstrated effect of polymer degradation on gene expression.</p>
</div>

</div>
Expand All @@ -855,7 +850,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/23575369/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:23575369</a>

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

<div class="snippet">"storage polymers, including glycogen, polyhydroxyalkanoates and wax esters"</div>
Expand All @@ -868,7 +863,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/23575369/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:23575369</a>

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

<div class="snippet">"in daytime, polyhydroxyalkanoates and wax esters are degraded"</div>
Expand All @@ -881,18 +876,20 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Upper-Mat and Undermat Nitrogen Fixation Partitioning</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
<h3>Upper-Mat and Undermat Nitrogen Fixation Potential</h3>
</div>
<p class="prewrap interaction-description">Nitrogen fixation potential is spatially partitioned between Synechococcus spp. in the upper phototrophic layer and Thermodesulfovibrio sp. in the undermat, while nitrate and nitrite metabolism appears limited.
</p>
<p class="prewrap interaction-description">PARTIAL - The undermat study contrasts previously demonstrated Synechococcus nitrogen fixation with putative Thermodesulfovibrio diazotrophy supported by nifHDK and accessory genes. Thermodesulfovibrio nitrogen fixation was not demonstrated in this study. This is a comparison of spatially associated capacities, not nitrogen transfer between these taxa or exclusive layer occupancy. Limited nitrate/nitrite gene recovery in abundant-member partial genomes does not establish pathway absence.</p>




<p><strong>Source Taxon:</strong> Mushroom Spring Synechococcus spp.</p>
<p><strong>Participating Taxa:</strong>

Mushroom Spring Synechococcus spp.,

Mushroom Spring Thermodesulfovibrio sp.

<p><strong>Target Taxon:</strong> Mushroom Spring Thermodesulfovibrio sp.</p>
</p>



Expand Down Expand Up @@ -922,7 +919,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/28634470/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28634470</a>

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

<div class="snippet">"Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat"</div>
Expand All @@ -935,7 +932,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/28634470/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:28634470</a>

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

<div class="snippet">"nitrate/nitrite metabolism was limited"</div>
Expand All @@ -949,10 +946,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Stratified Chlorophototrophic Community Structure</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">The Mushroom Spring mat is a stratified, highly uneven phototrophic community in which upper-layer cyanobacteria coexist with abundant filamentous anoxygenic phototrophs and an undermat assemblage resolved by amplicon and metagenomic sequencing.
</p>
<p class="prewrap interaction-description">Amplicon and metagenomic sequencing resolve a diverse but extremely uneven Mushroom Spring undermat and a stratified phototrophic mat. Upper-layer members also occur in the undermat: the layers differ in relative abundance, not exclusive occupancy. This positive community-structure result does not establish nitrogen transfer or show that stratification causes nitrogen fixation.</p>



Expand Down Expand Up @@ -986,17 +981,6 @@ <h3>Stratified Chlorophototrophic Community Structure</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Upper-Mat and Undermat Nitrogen Fixation Partitioning
<p class="prewrap causal-description">Vertical separation of the upper phototrophic layer and orange undermat places nitrogen-fixation potential in Synechococcus spp. above the Thermodesulfovibrio sp. undermat population.
</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -1090,6 +1074,25 @@ <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 observations distinguish activity and causal mediation from inferred potential?
</h3>
<p class="prewrap">Preserve measured RNA and community structure. The 2013 carbon-flow model is explicit in the accessible abstract; full-text XML failed and publisher access was restricted, so do not claim a complete Methods audit. The 2017 main body supports inferred Thermodesulfovibrio diazotrophy, with maturation genes relevant beyond nifHDK alone. Incomplete genomes limit absence claims. Distinct sampling campaigns and overlapping layers do not establish spatially directed nitrogen exchange or a stratification-to-fixation causal link.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Putative Diel Phototrophic Carbon Fixation</code>, <code>ecological_interactions#Putative Diel Phototroph Storage Polymer Cycling</code>, <code>ecological_interactions#Upper-Mat and Undermat Nitrogen Fixation Potential</code>, <code>ecological_interactions#Stratified Chlorophototrophic Community Structure</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1296,7 +1299,7 @@ <h2>Environmental Factors</h2>

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


Expand All @@ -1315,7 +1318,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Diel Phototrophic Carbon Fixation",
label: "Putative Diel Phototrophic Carbon Fixation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down Expand Up @@ -1343,7 +1346,7 @@ <h2>Environmental Factors</h2>

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

var processes = [];
Expand All @@ -1358,7 +1361,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Phototroph Storage Polymer Cycling",
label: "Putative Diel Phototroph Storage Polymer Cycling",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down Expand Up @@ -1386,7 +1389,7 @@ <h2>Environmental Factors</h2>

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

var processes = [];
Expand All @@ -1399,7 +1402,7 @@ <h2>Environmental Factors</h2>

nodes.push({
id: intId,
label: "Upper-Mat and Undermat Nitrogen Fixation Partitioning",
label: "Upper-Mat and Undermat Nitrogen Fixation Potential",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1408,23 +1411,26 @@ <h2>Environmental Factors</h2>
});


var srcKey = "Mushroom Spring Synechococcus spp.";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Mushroom Spring Thermodesulfovibrio sp.";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Mushroom Spring Synechococcus spp.",

"Mushroom Spring Thermodesulfovibrio sp."

];
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 = [];

var processes = [];
Expand Down
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