Skip to content

Bound KB1 and KBase model causal graphs (batch56) #1529

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 KB1 and KBase model causal graphs (batch56) #1529

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
160 changes: 97 additions & 63 deletions docs/communities/KB1_Chlorinated_Ethene_Dechlorinating_Consortium.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -611,21 +611,16 @@ <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 KB-1 Chlorinated Ethene Dechlorinating Consortium</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, syntrophy).</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="symbolTriangle"
data-color="#7f30cf"></svg> Syntrophy
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -634,14 +629,21 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Reductive Dechlorination to Ethene</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Dehalococcoides-related organisms in KB-1 use chlorinated ethenes as electron acceptors under anaerobic conditions, driving sequential reductive dechlorination of PCE and TCE to ethene in laboratory microcosms and field groundwater.</p>
<p class="prewrap interaction-description">KB-1 bioaugmentation produced ethene in laboratory microcosms and the Kelly Air Force Base field test. Field ethene accounted for chlorinated-ethene mass loss and KB-1-associated Dehalococcoides spread downgradient. These are consortium outcomes, not assignment of every PCE/TCE reaction to Dehalococcoides. Separate vitamin-free KB-1 enrichment experiments also sustained TCE-to-ethene conversion. The canonical taxa are a community subset, not a proven three-member inoculant or reciprocal syntrophy.</p>


<p><strong>Source Taxon:</strong> Dehalococcoides spp. in KB-1</p>


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

Dehalococcoides spp. in KB-1,

Acetobacterium spp. in KB-1,

Sporomusa spp. in KB-1

</p>



Expand Down Expand Up @@ -696,23 +698,39 @@ <h4>Evidence</h4>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/31441646/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31441646</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Acetobacterium supports complete TCE dechlorination by Dehalococcoides"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Acetogen Cobamide Support</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Acetobacterium and Sporomusa provide a supporting acetogenic guild in KB-1. Acetobacterium can synthesize the cobalamin lower ligand DMB, supporting Dehalococcoides dechlorination in vitamin-free medium and highlighting a cofactor-mediated syntrophic dependency.</p>
<p class="prewrap interaction-description">Vitamin-free KB-1 transfers sustained TCE dechlorination with increased Acetobacterium abundance and cobalamin, supported by a DMB-biosynthesis operon. These positive community experiments support Acetobacterium-associated cofactor provision. PARTIAL - donor-resolved transfer, exclusive mediation and the return benefit remain unresolved. The canonical Acetobacterium woodii label is not verified as the source population Acetobacterium sp. KB-1; its grounding remains #1526. Acid inhibition is distinct from cofactor shortage: DMB did not rescue stalled low-pH dechlorination, whereas pH adjustment did.</p>



<p><strong>Source Taxon:</strong> Acetobacterium spp. in KB-1</p>

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

Dehalococcoides spp. in KB-1,

<p><strong>Target Taxon:</strong> Dehalococcoides spp. in KB-1</p>
Acetobacterium spp. in KB-1

</p>



Expand Down Expand Up @@ -744,7 +762,7 @@ <h3>Acetogen Cobamide Support</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Reductive Dechlorination to Ethene
<p class="prewrap causal-description">Acetogen-derived cobalamin support supplies the cofactor context required for complete Dehalococcoides reductive dechlorination in KB-1 without exogenous vitamins.</p>
<p class="prewrap causal-description">PARTIAL - Acetobacterium-associated cofactor availability can support Dehalococcoides dechlorination in the vitamin-free KB-1 laboratory cultures. Community transfers, cofactor measurements and biosynthetic genes support this route, but do not isolate its exclusive contribution or establish its mediation of the separate field bioaugmentation result.</p>
</div>

</div>
Expand All @@ -763,7 +781,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"the lower ligand of cobalamin, and Sporomusa are dominant acetogens"</div>
<div class="snippet">"Acetobacterium supports complete TCE dechlorination by Dehalococcoides"</div>

</li>

Expand All @@ -787,16 +805,17 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Sporomusa DMB-Guided Cobalamin Support</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Sporomusa is a dominant acetogen in vitamin-free KB-1 cultures. A Sporomusa sp. strain KB-1 isolate was also tested as a Dehalococcoides partner population; its phenolic cobamides did not by themselves satisfy Dehalococcoides corrinoid requirements, but DMB amendment guided cobalamin biosynthesis in Sporomusa sp. cocultures and supported Dehalococcoides reductive dechlorination activity and growth.</p>
<p class="prewrap interaction-description">Controlled cocultures tested a Sporomusa sp. KB-1 isolate with Dehalococcoides strains BAV1, GT and FL2. DMB amendment changed donor cobamide chemistry and restored partner dechlorination and growth; without DMB, the phenolic cofactors did not support those requirements. FL2 still produced both VC and ethene. The explicit canonical participant is the KB-1-derived donor only: these external recipient strains are not established as the record&#39;s KB-1 Dehalococcoides population. This positive conditional partner-support result is not demonstrated mediation of the field endpoint.</p>



<p><strong>Source Taxon:</strong> Sporomusa spp. in KB-1</p>

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

Sporomusa spp. in KB-1

<p><strong>Target Taxon:</strong> Dehalococcoides spp. in KB-1</p>
</p>



Expand All @@ -823,26 +842,10 @@ <h3>Sporomusa DMB-Guided Cobalamin Support</h3>
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006766</a>)
</li>

<li>
cobalamin transport
(<a href="http://amigo.geneontology.org/amigo/term/GO:0015889"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0015889</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Reductive Dechlorination to Ethene
<p class="prewrap causal-description">DMB-guided cobalamin support can supply the corrinoid cofactor context required for Dehalococcoides reductive dechlorination.</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -896,6 +899,25 @@ <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 same-system cofactor routes mediate KB-1 dechlorination?
</h3>
<p class="prewrap">Keep the positive field outcome, vitamin-free community support and controlled donor chemistry/partner phenotypes distinct. Remove the Sporomusa-to-KB-1-outcome arrow because external recipient strains were not identified as the KB-1 population. The Acetobacterium route remains PARTIAL for exact transfer and field mediation. Canonical taxonomy and non-graph blocks are preserved, not recertified; #1526 tracks Acetobacterium identity. Full 2013/2019 primary main texts read; 2019 selected tables/figures inspected, 2002 field abstract only. No separate supplements/raw-data audit or new graph structure.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Reductive Dechlorination to Ethene</code>, <code>ecological_interactions#Acetogen Cobamide Support</code>, <code>ecological_interactions#Sporomusa DMB-Guided Cobalamin Support</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1155,7 +1177,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1168,7 +1190,7 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];

var evidenceCount = 2;
var evidenceCount = 3;

nodes.push({
id: intId,
Expand All @@ -1181,18 +1203,28 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Dehalococcoides spp. in KB-1";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

"Dehalococcoides spp. in KB-1",

"Acetobacterium spp. in KB-1",

"Sporomusa spp. in KB-1"

];
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 All @@ -1218,23 +1250,26 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Acetobacterium spp. in KB-1";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Dehalococcoides spp. in KB-1";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Dehalococcoides spp. in KB-1",

"Acetobacterium spp. in KB-1"

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

})();

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


Expand All @@ -1248,8 +1283,6 @@ <h4 style="color: var(--text);">Evidence</h4>

processes.push("vitamin metabolic process");

processes.push("cobalamin transport");


var evidenceCount = 3;

Expand All @@ -1264,17 +1297,18 @@ <h4 style="color: var(--text);">Evidence</h4>
});


var srcKey = "Sporomusa spp. in KB-1";
if (taxonNodeIds[srcKey]) {
links.push({ source: taxonNodeIds[srcKey], target: intId });
}


var participantKeys = [

var tgtKey = "Dehalococcoides spp. in KB-1";
if (taxonNodeIds[tgtKey]) {
links.push({ source: intId, target: taxonNodeIds[tgtKey] });
}
"Sporomusa spp. in KB-1"

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

})();

Expand Down
Loading