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Bound SC2 MFC and Mars panel causal claims to measured assays (batch68) #1587

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106 changes: 54 additions & 52 deletions docs/communities/Maize_SC2_RootRot_Biocontrol_SynCom.html
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Expand Up @@ -648,21 +648,16 @@ <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 Maize SC2 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 @@ -671,9 +666,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Pythium torulosum suppression by SC2</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">SC2 inhibited the oomycete pathogen Pythium torulosum in PDA dual-culture assays at a level comparable to C7 and, in maize growth-chamber assays, protected B73 seedlings from P. torulosum while improving plant height and root biomass more than either a pathogen-only challenge or the parent C7 community.</p>
<p class="prewrap interaction-description">The three-member SC2 inhibited Pythium torulosum radial growth on PDA after seven days, comparably to C7. In a separate growth-chamber experiment, SC2-treated B73 seedlings challenged with Pythium had improved height and fresh root biomass at 14 days. These positive antagonist and protection phenotypes do not isolate nutrient competition, secreted antimicrobials or host immune activation. The three canonical bacterial terms identify the curated SC2 roster; Pythium is an external challenge organism, not an inoculum member. Exact strain-number and ZK-alias mapping is preserved, not independently recertified.</p>



Expand All @@ -694,25 +688,14 @@ <h3>Pythium torulosum suppression by SC2</h3>



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

<li>
defense response
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006952"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006952</a>)
</li>

</ul>



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

<div class="flow-item">
<span class="flow-arrow">→</span> Maize growth promotion under Pythium challenge
<p class="prewrap causal-description">Reduced pathogen pressure in the SC2 plus P. torulosum treatment was accompanied by higher maize plant height and fresh root biomass than the C7 plus P. torulosum treatment.</p>
<p class="prewrap causal-description">HYPOTHESIZED - pathogen inhibition could reduce injury and thereby contribute to improved maize growth under challenge. Plate inhibition and plant height/root-mass outcomes support this interpretation, but inhibition was not selectively separated from direct growth promotion in the pot experiment; pathogen load and immune mediation were not established.</p>
</div>

</div>
Expand Down Expand Up @@ -755,9 +738,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Maize growth promotion under Pythium challenge</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Maize seeds soaked with SC2 before growth in P. torulosum-infested potting mix developed greater 14-day plant height and fresh root biomass than C7- or pathogen-only treatments, linking the reduced community to a plant-beneficial outcome under oomycete stress.</p>
<p class="prewrap interaction-description">SC2 seed treatment improved B73 maize height and fresh root biomass after 14 days in Pythium-infested potting mix relative to the challenged comparison treatments, with SC1 and SC2 outperforming C7 in the reported experiment. These are treatment-level plant benefits, not reciprocal bacterial benefit, field yield or proof of IAA-mediated protection. Zea mays is an external host, not a fourth bacterial inoculum member. The candidate IAA mechanism derives from a separate culture assay, not a measured plant hormone pool or traced bacterial-to-host delivery.</p>



Expand Down Expand Up @@ -823,13 +805,22 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>SC2 auxin and siderophore output</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>SC2 Salkowski and CAS assay outputs</h3>
</div>
<p class="prewrap interaction-description">As a whole consortium, SC2 accumulated about 45 ug/mL indole-3-acetic acid by day 2 and about 65 ug/mL by day 7, the highest measured IAA output among the assayed C7-derived communities; SC2 also produced a significant 0.50 cm CAS-agar siderophore halo at day 7.</p>
<p class="prewrap interaction-description">SC2 culture supernatants gave Salkowski estimates of approximately 45 ug/mL at day 2 and 65 ug/mL at day 7 against a pure-IAA calibration, highest among the tested C7-derived communities. CAS agar activity was reported as a 0.50 cm halo at day 7 (p=0.015 versus control). Retain the authors auxin and siderophore interpretation at assay scope: these colorimetric and halo measurements do not resolve molecular identities, biosynthetic pathways, member-specific contributions, plant delivery or reciprocal mutualism. They were not selective mediator perturbations of the plant or pathogen assays.</p>




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

Enterobacter cloacae S4,

Stenotrophomonas maltophilia S1,

Chryseobacterium indologenes S5

</p>



Expand All @@ -847,17 +838,6 @@ <h3>SC2 auxin and siderophore output</h3>



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

<li>
indole-3-acetic acid biosynthetic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0009684"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0009684</a>)
</li>

</ul>




Expand Down Expand Up @@ -901,7 +881,7 @@ <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 @@ -911,7 +891,22 @@ <h3>
</h3>
<p class="prewrap">Kaki et al. 2026 showed that the S4/S1/S5 subcommunity inhibited Pythium in plate assays, protected maize in growth-chamber assays, and produced high IAA plus significant siderophore activity, but the specific antimicrobials, responsible members, and causal links among siderophores, auxin, root growth, and oomycete suppression remain unresolved.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Pythium torulosum suppression by SC2</code>, <code>ecological_interactions#SC2 auxin and siderophore output</code></p>
<p class="muted small">Attaches to: <code>ecological_interactions#Pythium torulosum suppression by SC2</code>, <code>ecological_interactions#SC2 Salkowski and CAS assay outputs</code></p>




</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
Which SC2 processes mediate pathogen protection and maize growth?
</h3>
<p class="prewrap">Preserve positive inhibition, plant benefit and biochemical assays. Qualify the existing suppression-to-growth arrow and retain the earlier open metabolite question. Competition, immune activation, reciprocal benefit and IAA/siderophore necessity were not established. External pathogen and host participants remain as in #888; #887 incidental metal and #889 removed design pseudo-node remain unchanged. #1582 is the graph repair; #1586 and #1580 track non-graph mapping/metadata. No new structure.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Pythium torulosum suppression by SC2</code>, <code>ecological_interactions#Maize growth promotion under Pythium challenge</code>, <code>ecological_interactions#SC2 Salkowski and CAS assay outputs</code></p>



Expand Down Expand Up @@ -1200,15 +1195,11 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];


processes.push("defense response");


var evidenceCount = 2;

nodes.push({
Expand Down Expand Up @@ -1245,7 +1236,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1294,7 +1285,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1305,15 +1296,11 @@ <h4 style="color: var(--text);">Evidence</h4>

var processes = [];


processes.push("indole-3-acetic acid biosynthetic process");


var evidenceCount = 2;

nodes.push({
id: intId,
label: "SC2 auxin and siderophore output",
label: "SC2 Salkowski and CAS assay outputs",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1324,6 +1311,21 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Enterobacter cloacae S4",

"Stenotrophomonas maltophilia S1",

"Chryseobacterium indologenes S5"

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

})();


Expand Down
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