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realmarcin merged 1 commit into from
Oct 6, 2026
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Review GenX, compost and wheat-straw causal graphs (batch 23) #1350

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34 changes: 24 additions & 10 deletions docs/communities/Community_G_GenX_Biodegradation_Consortium.html
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Expand Up @@ -729,27 +729,26 @@ <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 Community G GenX Biodegradation 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 (competition).</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="symbolTimes"
data-color="#a91919"></svg> Competition
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>


<div class="interaction-card">
<div class="interaction-header">
<h3>Community G GenX-Driven Taxonomic Restructuring</h3>
<span class="interaction-type">COMPETITION</span>
<h3>Community G Relative Taxonomic Restructuring During GenX Exposure</h3>
</div>
<p class="prewrap interaction-description">During active GenX biodegradation, Salmonella enterica, Pseudomonas tolaasii, Stenotrophomonas sp. LM091, and Stenotrophomonas sp. MYb57 expanded while initially abundant Stenotrophomonas cyclobalanopsidis and Pseudomonas arcuscaelestis declined or disappeared.</p>
<p class="prewrap interaction-description">Community G 16S profiles showed relative enrichment of Salmonella enterica, Pseudomonas tolaasii and two Stenotrophomonas strains, with relative declines of initially abundant taxa, during GenX exposure. The six named participants are an observed subset, not the complete consortium. Bulk GenX loss and fluoride release support community activity; relative profiles, genomic homology and docking do not establish absolute viable expansion or extinction, member-specific degradation, complete carbon mineralization or reciprocal competitive harm.</p>



Expand Down Expand Up @@ -798,7 +797,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42422733/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42422733</a>

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

<div class="snippet">"This restructuring reflects adaptive enrichment of efficient GenX-degrading specialists."</div>
Expand Down Expand Up @@ -850,7 +849,7 @@ <h2>Associated Datasets</h2>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(1)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -900,6 +899,21 @@ <h3>
</details>


</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which Community G members causally contribute to GenX transformation?
</h3>
<p class="prewrap">Absolute viable abundance, partner perturbations, enzyme assays and carbon/fluorine mass balance would distinguish compositional change from degrader activity and competitive effects. Homology and docking predict potential, not catalytic flux. Community G was followed in sterile soil; GENIA indigenous-microbiome comparisons do not establish Community G ecological safety. The partial roster remains unresolved; the previously removed dangling outcome arrow is not restored.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Community G Relative Taxonomic Restructuring During GenX Exposure</code></p>




</div>

</section>
Expand Down Expand Up @@ -1251,7 +1265,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -1264,7 +1278,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Community G GenX-Driven Taxonomic Restructuring",
label: "Community G Relative Taxonomic Restructuring During GenX Exposure",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
58 changes: 37 additions & 21 deletions docs/communities/Composting_SynCom_Lignocellulose_Degradation_Humus.html
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Expand Up @@ -558,27 +558,26 @@ <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 Five-member bacterial-fungal composting SynCom for lignocellulose degradation</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 (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="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>SynCom-driven restructuring and enrichment of native degraders</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>Native Microbiome Response To SynCom Inoculation</h3>
</div>
<p class="prewrap interaction-description">SynCom inoculation restructures the indigenous composting microbiome, enriching key lignocellulose-degrading functional genera (Thermobifida, Actinomadura) that carry an enriched carbohydrate-active enzyme repertoire in the SynCom-treated compost.</p>
<p class="prewrap interaction-description">The available abstract reports a native compost microbiome response to five-member bacterial-fungal SynCom inoculation, including enrichment of Thermobifida and Actinomadura. These are enriched native genera, not the five inoculant identities. The community abundance response does not by itself demonstrate establishment or identify which genera carry every enriched functional gene.</p>



Expand Down Expand Up @@ -616,8 +615,8 @@ <h3>SynCom-driven restructuring and enrichment of native degraders</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Carbohydrate-active enzyme repertoire expansion
<p class="prewrap causal-description">Enrichment of native Thermobifida and Actinomadura is linked to a larger cellulase, hemicellulase, and lignin-modifying auxiliary-activity enzyme repertoire in SynCom-treated compost.</p>
<span class="flow-arrow">→</span> Metagenomic CAZyme Repertoire Enrichment
<p class="prewrap causal-description">HYPOTHESIZED - a compositional shift toward native degraders could contribute to the enriched CAZyme gene repertoire. The abstract links community and functional profiles, but does not establish gene ownership or selective mediation by Thermobifida and Actinomadura.</p>
</div>

</div>
Expand Down Expand Up @@ -646,10 +645,9 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Carbohydrate-active enzyme repertoire expansion</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
<h3>Metagenomic CAZyme Repertoire Enrichment</h3>
</div>
<p class="prewrap interaction-description">SynCom-treated compost showed greater abundance of cellulases (GH5 and GH12), hemicellulases (CE1 and CE3), and lignin-modifying auxiliary-activity enzymes (AA1 and AA6), linking the Thermobifida/Actinomadura-rich native microbiome to faster polymer deconstruction.</p>
<p class="prewrap interaction-description">Metagenomic analysis associates SynCom-treated compost with enriched CAZyme families GH5, GH12, CE1, CE3, AA1 and AA6. This is community gene-repertoire potential, not a direct measurement of enzyme expression or catalytic activity. The available abstract does not resolve each gene to the two named native genera.</p>



Expand Down Expand Up @@ -688,7 +686,7 @@ <h3>Carbohydrate-active enzyme repertoire expansion</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Enriched lignocellulose degradation and humus accumulation
<p class="prewrap causal-description">The expanded cellulase, hemicellulase, and lignin-modifying enzyme repertoire enables higher lignin, cellulose, and hemicellulose degradation in SynCom-treated compost.</p>
<p class="prewrap causal-description">HYPOTHESIZED - the enriched gene repertoire could support polymer hydrolysis and supply humification precursors, contributing to the measured degradation and humus outcomes. Metagenomic, metabolomic and correlation analyses support this model, not a selective enzyme or precursor perturbation establishing mediation.</p>
</div>

</div>
Expand All @@ -704,7 +702,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41297400/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41297400</a>

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

<div class="snippet">"crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6)"</div>
Expand All @@ -718,9 +716,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Enriched lignocellulose degradation and humus accumulation</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">The SynCom-treated compost showed higher overall degradation of lignin, cellulose, and hemicellulose, plus a higher humus content, consistent with the SynCom-enriched CAZyme and lignin-modifying enzyme repertoire.</p>
<p class="prewrap interaction-description">The available abstract reports that SynCom-treated compost had greater lignin, cellulose and hemicellulose degradation and higher humus content than the control, together with earlier maturation. These are positive treatment-level outcomes. Their association with community genes and humification precursors does not establish which organisms or enzymes mediate the improvement.</p>



Expand Down Expand Up @@ -778,7 +775,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/41297400/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:41297400</a>

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

<div class="snippet">"crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6)"</div>
Expand All @@ -794,6 +791,25 @@ <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 inoculant and native functions mediate improved degradation and humification?
</h3>
<p class="prewrap">The complete abstract supports treatment-level benefits, native-community enrichment, metagenomic potential and associated metabolites. The full body and exact five-member inoculant roster were unavailable. Gene ownership, enzyme activity and selective mediator perturbations are needed before assigning the two native genera a complete causal pathway or claiming establishment. Retain both arrows as hypotheses rather than directly demonstrated mediation.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Native Microbiome Response To SynCom Inoculation</code>, <code>ecological_interactions#Metagenomic CAZyme Repertoire Enrichment</code>, <code>ecological_interactions#Enriched lignocellulose degradation and humus accumulation</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -940,7 +956,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -957,7 +973,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "SynCom-driven restructuring and enrichment of native degraders",
label: "Native Microbiome Response To SynCom Inoculation",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -972,7 +988,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand All @@ -989,7 +1005,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Carbohydrate-active enzyme repertoire expansion",
label: "Metagenomic CAZyme Repertoire Enrichment",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1004,7 +1020,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down
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