Skip to content

Bound CL95 biocontrol and S11 nitrogen-removal causal claims (batch48) #1489

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 CL95 biocontrol and S11 nitrogen-removal causal claims (batch48) #1489

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
46 changes: 14 additions & 32 deletions docs/communities/Ginseng_CL95_Rusty_Root_Rot_Biocontrol_SynCom.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -769,21 +769,16 @@ <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 Ginseng CL95 Rusty Root Rot Biocontrol SynCom</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 (mutualism, 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="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
</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>
Expand All @@ -792,9 +787,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>CL95 Ilyonectria robusta suppression</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">CL95 suppressed Ilyonectria robusta in mycelial-growth and wounded-ginseng assays and was the strongest field-performing biocontrol consortium, with 66.67% control efficacy against ginseng rusty root rot.</p>
<p class="prewrap interaction-description">CL95 inhibited Ilyonectria robusta in plate and wounded-ginseng-root assays and had the highest reported field rusty-root-rot control efficacy among the tested treatments, 66.67%. Plate colony-growth inhibition was 73%; that endpoint is distinct from disease control. These experiments support whole-consortium antagonistic capacity and field disease suppression, not a selectively established resource-competition mechanism or a causal attribution to any one member. Fungal qPCR measures DNA abundance, not necessarily viable pathogen numbers. Plant growth improved under the same field treatment, but suppression was not selectively manipulated to establish it as the mediator of growth.</p>



Expand Down Expand Up @@ -832,16 +826,6 @@ <h3>CL95 Ilyonectria robusta suppression</h3>



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

<div class="flow-item">
<span class="flow-arrow">→</span> CL95 plant growth promotion
<p class="prewrap causal-description">Rusty-root-rot suppression in the field accompanied enhanced ginseng root length, fresh root weight, root diameter, and chlorophyll content under CL95 and five other high-performing consortia.</p>
</div>

</div>



<h4>Evidence</h4>
Expand Down Expand Up @@ -880,9 +864,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>CL95 plant growth promotion</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Field-tested CL95 belonged to the subset of six consortia that both suppressed rusty root rot and promoted ginseng growth, and its plate assays showed nitrogen fixation, phosphate solubilization, and potassium-release zones.</p>
<p class="prewrap interaction-description">CL95 was among six selected field treatments that reduced disease and increased ginseng growth. Separate plate screens reported nitrogen-fixation, phosphate-solubilization and potassium-release zone phenotypes; Table S5 lists CL95 zones of 13.00, 15.50 and 19.00 mm, respectively. Those screens are functional proxies, not measurements of nutrient flux into the plant or proof that any one plate phenotype mediates the field response. Improved host growth and higher consortium performance do not by themselves establish reciprocal fitness benefits for the host and all five bacterial strains.</p>



Expand Down Expand Up @@ -962,9 +945,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>CL95 colonization and rhizosphere enzyme response</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Antibiotic-labeled CL95 strains colonized ginseng tissues and rhizosphere soil more efficiently than single strains and the CL95 field treatment increased phosphatase, sucrase, catalase, and urease activities during the ginseng root expansion period.</p>
<p class="prewrap interaction-description">Antibiotic-selection colony counts support recovery of labeled bacteria from ginseng tissues and rhizosphere soil after CL95 treatment over the 63-day experiment, with higher recovery than single-strain treatments. The Methods name labeled NJ13, NT35 and FG14 strains mixed with unlabeled partners; these counts do not independently track all five CL95 members or show that every member benefits. Tissue-specific time courses motivate the authors&#39; proposed upward-migration trajectory but do not directly track individual cells moving between tissues. Separately, CL95 treatment increased measured rhizosphere phosphatase, sucrase, catalase and urease activities during root expansion. These soil activities do not identify their producing organism or establish a colonization-to-enzyme-to-growth causal chain, reciprocal mutualism or a specific biofilm mechanism.</p>



Expand Down Expand Up @@ -993,9 +975,9 @@ <h3>CL95 colonization and rhizosphere enzyme response</h3>
<ul>

<li>
symbiotic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044403"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0044403</a>)
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 Down Expand Up @@ -1051,7 +1033,7 @@ <h3>
<span class="role-badge">OPEN</span>
Which CL95 member strains and secreted metabolites directly suppress Ilyonectria robusta or drive the measured ginseng growth-promotion and rhizosphere enzyme phenotypes?
</h3>
<p class="prewrap">Tian et al. 2026 connected CL95 to strong pathogen suppression, plant growth promotion, tissue/rhizosphere colonization, and soil-enzyme responses, but did not assign the community phenotypes to a specific member or molecule.</p>
<p class="prewrap">Tian et al. 2026 connected CL95 to strong pathogen suppression, plant growth promotion, tissue/rhizosphere colonization, and soil-enzyme responses, but did not assign the community phenotypes to a specific member or molecule. Plate antagonism does not isolate resource competition, and improved host growth does not measure reciprocal bacterial fitness. Selective-CFU recovery, plate nutrient-screen zones, soil enzyme activities, defense-gene expression and amplicon correlations were measured in distinct assays; they do not selectively establish a colonization, nutrient-flux, induced-systemic-resistance or microbiome-recruitment mediation chain. In particular, defense transcription is positive host-response evidence, not a pathway-blockade test of necessity. The suppression-to-growth arrow is removed because it encodes joint treatment outcomes rather than isolated mediation. Resolve strain-specific marker readout, relevant perturbations and the abstract/main-text soil-enzyme percentage discrepancy before assigning exact member effects or new causal branches.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#CL95 Ilyonectria robusta suppression</code>, <code>ecological_interactions#CL95 plant growth promotion</code>, <code>ecological_interactions#CL95 colonization and rhizosphere enzyme response</code></p>

Expand Down Expand Up @@ -1343,7 +1325,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1392,7 +1374,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down Expand Up @@ -1441,13 +1423,13 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


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


var evidenceCount = 2;
Expand Down
51 changes: 21 additions & 30 deletions docs/communities/Glutamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -561,16 +561,16 @@ <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 Glutamicibacter S11 Aquaculture Nitrogen Removal SynCom</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 (mutualism).</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="symbolSquare"
data-color="#9f2ebb"></svg> Mutualism
aria-hidden="true" data-symbol="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>
Expand All @@ -579,9 +579,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Synergistic S11 ammonium and nitrite removal</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The two-strain S11 consortium removed ammonium and nitrite nitrogen more efficiently than the corresponding single-strain cultures under the reported pH and C/N ranges.</p>
<p class="prewrap interaction-description">The two-strain S11 consortium removed ammonium and nitrite more efficiently than the corresponding single-strain cultures. The primary abstract reports 95% ammonium-N and 97% nitrite-N removal within 24 h at initial concentrations of 30 mg/L each, pH 6-9 and C/N at least 15, described as a 15%-25% improvement over monocultures. This positive whole-consortium removal phenotype does not by itself establish reciprocal microbial fitness, exchanged intermediates or a formal interaction mechanism. The authors characterize the isolates as heterotrophic nitrification-aerobic denitrification strains, but the accessible abstract does not partition consortium removal among oxidation, denitrification, assimilation and other sinks or provide a nitrogen mass balance. Sponge-immobilized recirculation and industrial trials are separate assay contexts, not steps in a demonstrated causal chain; reported industrial residual nitrite fractions are not removal percentages.</p>



Expand Down Expand Up @@ -610,23 +609,6 @@ <h3>Synergistic S11 ammonium and nitrite removal</h3>



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

<li>
ammonia oxidation
(<a href="http://amigo.geneontology.org/amigo/term/GO:0019329"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0019329</a>)
</li>

<li>
denitrification
(<a href="http://amigo.geneontology.org/amigo/term/GO:0019333"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0019333</a>)
</li>

</ul>




Expand Down Expand Up @@ -670,7 +652,7 @@ <h4>Evidence</h4>
<!-- Associated Datasets -->

<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 All @@ -685,6 +667,21 @@ <h3>



</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which nitrogen routes and partner effects explain S11 removal performance?
</h3>
<p class="prewrap">The accessible primary abstract identifies both strains as HNAD organisms and reports a positive consortium removal contrast, but does not resolve partner-specific viable growth, isotope flux, nitrogen mass balance, exchanged intermediates or pathway perturbations. Retain that positive HNAD characterization without assigning resolved graph-level ammonia-oxidation or denitrification flux. Full Methods and controls are unavailable for this review. Separate batch, sponge and industrial endpoints and do not equate residual concentration percentages with removal. Resolve these gaps before adding a reciprocal-benefit, route-specific or cross-feeding edge.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Synergistic S11 ammonium and nitrite removal</code></p>




</div>

</section>
Expand Down Expand Up @@ -971,7 +968,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -982,12 +979,6 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("ammonia oxidation");

processes.push("denitrification");


var evidenceCount = 2;

nodes.push({
Expand Down
25 changes: 25 additions & 0 deletions ...ecords/Ginseng_CL95_Rusty_Root_Rot_Biocontrol_SynCom/2026-10-06T133304Z-codex-ad2e45.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
history_version: 1
target:
kind: record
path: kb/communities/Ginseng_CL95_Rusty_Root_Rot_Biocontrol_SynCom.yaml
slug: Ginseng_CL95_Rusty_Root_Rot_Biocontrol_SynCom
session:
id: 2026-10-06T133304Z-codex-ad2e45
timestamp: '2026-10-06T13:33:04Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1487
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Bound CL95 antagonism, host growth and marker recovery; remove unproven ecological
labels and the suppression-to-growth correlation arrow.
details: Source-based self-adversarial graph repair. reports/causal_graph_review/decisions/20261006-ginseng-s11-batch48.yaml
25 changes: 25 additions & 0 deletions ...tamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom/2026-10-06T133304Z-codex-93714d.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
history_version: 1
target:
kind: record
path: kb/communities/Glutamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom.yaml
slug: Glutamicibacter_S11_Aquaculture_Nitrogen_Removal_SynCom
session:
id: 2026-10-06T133304Z-codex-93714d
timestamp: '2026-10-06T13:33:04Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1488
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Retain S11 nitrogen-removal performance without unmeasured mutualism or resolved
consortium flux routes.
details: Source-based self-adversarial graph repair. reports/causal_graph_review/decisions/20261006-ginseng-s11-batch48.yaml
Loading