Skip to content

Bound soil and mucin community causal claims (batch65) #1570

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
realmarcin wants to merge 1 commit into from
Closed

Bound soil and mucin community causal claims (batch65) #1570

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
163 changes: 98 additions & 65 deletions docs/communities/MSC1_Dominant_Core.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -799,21 +799,16 @@ <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 MSC-1 Dominant Core</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 (syntrophy, 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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
</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>
Expand All @@ -822,13 +817,33 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Chitin-Selected MSC-1 Stabilization</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Serial enrichment on chitin/soil-extract agar selected MSC-1 as a stable, naturally interacting arid-grassland soil consortium whose dominant members persisted through extended passaging and two storage-revival cycles.
</p>
<p class="prewrap interaction-description">Chitin-selected MSC-1 retained a broadly similar composition across prolonged passaging and storage-revival cycles, with residual drift rather than invariant membership. The selected consortium had 31 detected bacterial OTUs in Table 1 and Results, with its top 13 accounting for over 98% of reads; other source passages say approximately 35. The nine canonical participants represent an incomplete roster, not a defined nine-strain mixture. HYPOTHESIZED - repeated co-enrichment could reflect metabolic codependencies, but persistence and selection on chitin/soil-extract agar do not demonstrate obligate dependence, niche partitioning or measured chitin turnover.</p>




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

Rhodococcus sp.,

Streptomyces sp.,

Dyadobacter sp.,

Taibaiella sp.,

Bosea sp.,

Sphingopyxis sp.,

Ensifer sp.,

Variovorax sp.,

Mycobacterium sp.

</p>



Expand All @@ -842,17 +857,6 @@ <h3>Chitin-Selected MSC-1 Stabilization</h3>



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

<li>
chitin catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006032"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006032</a>)
</li>

</ul>




Expand All @@ -879,7 +883,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32983014/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32983014</a>

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

<div class="snippet">"Because these species were co-enriched together over a 22-week period and through two rounds of freezing and revival, we hypothesized that there existed metabolic co-dependencies within MSC-1."</div>
Expand All @@ -893,10 +897,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>NAG Positive Co-Cultures</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Pairwise MSC-1 isolate assays in M9 plus N-acetylglucosamine detected statistically significant positive interactions, including Streptomyces-Rhodococcus, Streptomyces-Variovorax, Rhizobium-Rhodococcus, and Ensifer-Rhodococcus co-cultures.
</p>
<p class="prewrap interaction-description">Pairwise isolates in M9 with 10 mM soluble N-acetylglucosamine (NAG) showed higher early-exponential optical density than the expected average of the two corresponding monocultures (p &lt; 0.01 for reported positive comparisons). Named examples include Streptomyces-Rhodococcus, Streptomyces-Variovorax, Rhizobium-Rhodococcus and Ensifer-Rhodococcus. The difference was not significant in late exponential phase. Total OD does not resolve each partner biomass, reciprocal benefit or obligate syntrophy, and these NAG assays do not measure chitin-polymer degradation. The four canonical participants are a partial set of the named positive pairs; the source Rhizobium isolate is not canonically resolved here, and V4 does not distinguish which Ensifer OTU matches the isolate.</p>



Expand Down Expand Up @@ -925,17 +927,6 @@ <h3>NAG Positive Co-Cultures</h3>



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

<li>
glucosamine catabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006046"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006046</a>)
</li>

</ul>




Expand Down Expand Up @@ -976,28 +967,23 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Soil Co-Abundance Central Hubs</h3>
<span class="interaction-type">NICHE_PARTITIONING</span>
</div>
<p class="prewrap interaction-description">Soil incubations across chitin, temperature, salt, and herbicide perturbations produced a Pearson co-abundance network whose high-centrality MSC-1 taxa included Rhodococcus, Mycobacterium, and Rhizobiales members.
</p>
<p class="prewrap interaction-description">A Pearson network pooled normalized relative 16S abundances across soil-incubation conditions, replicate samples and time points. Rhodococcus, Mycobacterium and Rhizobiales-associated OTUs had high betweenness centrality. Rhizobiales is an order, not a genus or a verified isolate identity. The two explicit canonical participants identify the named Rhodococcus and Mycobacterium subset, not every hub. Positive and negative co-abundance associations can reflect common environmental or temporal responses; they do not establish pairwise facilitation, competition, niche partitioning or keystone necessity. Soil chitin and liquid NAG assays are distinct contexts, and their partly matching correlation signs do not establish a shared mechanism.</p>




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

Rhodococcus sp.,

Mycobacterium sp.

</p>


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

<li>
biological process involved in interspecies interaction between organisms
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044419</a>)
</li>

</ul>



Expand All @@ -1012,7 +998,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32983014/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32983014</a>

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

<div class="snippet">"Rhodococcus had several positive and negative correlations with other genera of MSC-1, including Streptomyces, Variovorax, and Delftia (negative) and Rhizobiales (positive)."</div>
Expand All @@ -1025,7 +1011,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/32983014/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:32983014</a>

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

<div class="snippet">"species of the Rhodococcus, Mycobacterium and Rhizobiales genera occupied positions of high centrality in the network"</div>
Expand All @@ -1041,6 +1027,25 @@ <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 MSC-1 dependencies explain persistence and conditional coculture growth?
</h3>
<p class="prewrap">Retain three observations and zero arrows, preserving the earlier workflow-edge deletion. Early total OD on supplied soluble NAG is not partner-resolved benefit or late-phase improvement. Soil-network centrality from pooled relative abundance is not causal interaction or keystone necessity. Canonical participants are explicitly incomplete, and the source Table 1 maps the Rhizobium isolate to Rhizomicrobium OTU68; no new taxon equivalence is asserted. Storage drift, 31-versus-35 OTUs, Sect_C_4-versus-C2 naming, herbicide dose and inconsistent positive/negative Methods inequalities need separate reconciliation under #1569. Whole fresh primary body and main text table read; figure pixels, separate supplements and raw data not audited.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Chitin-Selected MSC-1 Stabilization</code>, <code>ecological_interactions#NAG Positive Co-Cultures</code>, <code>ecological_interactions#Soil Co-Abundance Central Hubs</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1314,7 +1319,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1323,10 +1328,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("chitin catabolic process");


var evidenceCount = 2;

nodes.push({
Expand All @@ -1342,11 +1343,38 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Rhodococcus sp.",

"Streptomyces sp.",

"Dyadobacter sp.",

"Taibaiella sp.",

"Bosea sp.",

"Sphingopyxis sp.",

"Ensifer sp.",

"Variovorax sp.",

"Mycobacterium sp."

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

})();

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


Expand All @@ -1355,10 +1383,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("glucosamine catabolic process");


var evidenceCount = 2;

nodes.push({
Expand Down Expand Up @@ -1395,15 +1419,11 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("biological process involved in interspecies interaction between organisms");


var evidenceCount = 2;

nodes.push({
Expand All @@ -1419,6 +1439,19 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Rhodococcus sp.",

"Mycobacterium sp."

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

})();


Expand Down
Loading