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Preserve plant outcomes and mixture assay contrasts (batch121) #1946

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125 changes: 87 additions & 38 deletions docs/communities/Tomato_Oxylipin_SynCom3.html
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Original file line number Diff line number Diff line change
Expand Up @@ -600,27 +600,26 @@ <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 Tomato Oxylipin-Protective SynCom3</title>
<desc id="network-svg-desc">Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for mutualism.</desc>
<desc id="network-svg-desc">Bipartite graph where circles represent taxa and non-circular symbols represent interactions. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.</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>


<div class="interaction-card">
<div class="interaction-header">
<h3>Simplified Community Synergistic Protection</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>SynCom3-associated biofilm and host defense</h3>
</div>
<p class="prewrap interaction-description">The three-species tomato rhizosphere community combines one phytopathogen-inducible Asticcacaulis member that triggers plant defense responses with two stably colonizing Arachidicoccus and Phenylobacterium members that promote biofilm formation.</p>
<p class="prewrap interaction-description">The three-genus tomato-root inoculum combines pathogen-inducible Asticcacaulis with stably colonizing Arachidicoccus and Phenylobacterium. The abstract attributes host-defense triggering to the inducible member and biofilm promotion to the stable colonizers, with protection similar to the 38-member precursor. These positive complementary phenotypes do not measure reciprocal bacterial fitness or metabolite exchange. Exact strain identities and selective biofilm mediation are not resolved by the inspected abstract.</p>



Expand All @@ -646,8 +645,8 @@ <h3>Simplified Community Synergistic Protection</h3>
<strong>Downstream Effects:</strong>

<div class="flow-item">
<span class="flow-arrow">→</span> Oxylipin-Mediated Disease Resistance
<p class="prewrap causal-description">The synergistic three-species community intensifies oxylipin pathway activation in phytopathogen-infected tomato leaves.</p>
<span class="flow-arrow">→</span> SynCom3-induced leaf oxylipin responses
<p class="prewrap causal-description">SynCom3 treatment intensified oxylipin responses in infected tomato leaves. PARTIAL for biofilm formation as the mediator: the abstract links complementary community functions to protection but does not isolate biofilm formation as the unique cause of leaf pathway activation.</p>
</div>

</div>
Expand All @@ -663,23 +662,35 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

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

<div class="snippet">"the phytopathogen-inducible species triggering plant defense responses and the stably-colonizing species promoting biofilm formation"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"The simplified community exhibited similar protective effects as the 38-species community"</div>

</li>

</ul>

</div>

<div class="interaction-card">
<div class="interaction-header">
<h3>Oxylipin-Mediated Disease Resistance</h3>
<span class="interaction-type">MUTUALISM</span>
<h3>SynCom3-induced leaf oxylipin responses</h3>
</div>
<p class="prewrap interaction-description">Inducible and stable colonizers synergize to trigger host defense and biofilm-mediated protection.</p>
<p class="prewrap interaction-description">The simplified community intensified oxylipin-pathway activation in Botrytis-infected tomato leaves. This is a host response to the bacterial treatment, not microbial mutualism or evidence that the bacteria themselves synthesize the listed divinyl ethers. The downstream biosynthesis perturbation provides stronger mechanistic evidence than association alone.</p>



Expand Down Expand Up @@ -711,7 +722,7 @@ <h3>Oxylipin-Mediated Disease Resistance</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Divinyl Ether-Dependent Botrytis Protection
<p class="prewrap causal-description">Intensified oxylipin-pathway activation feeds production of antimicrobial divinyl ethers required for community-induced protection against Botrytis cinerea.</p>
<p class="prewrap causal-description">The host oxylipin branch supplies divinyl ethers implicated in protection: inhibiting their biosynthesis abolished the community-induced resistance, while SlLOX5/SlDES1 overexpression with higher divinyl-ether levels increased resistance. Retain this pathway-level perturbation evidence without claiming separate necessity of each compound or bacterial-to-plant transfer.</p>
</div>

</div>
Expand All @@ -727,20 +738,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Through the analysis of the rhizosphere bacterial community, we established a synthetic community harboring 8 phytopathogen-inducible and 30 stably-colonizing bacteria species."</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

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

<div class="snippet">"the activation of oxylipin pathways in the phytopathogen-infected leaves was significantly intensified by the simplified community"</div>
Expand All @@ -754,9 +752,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Divinyl Ether-Dependent Botrytis Protection</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The community-induced tomato defense requires biosynthesis of the antimicrobial divinyl ethers colneleic acid and colnelenic acid; when this branch is blocked, the SynCom no longer protects against Botrytis.</p>
<p class="prewrap interaction-description">Inhibiting divinyl-ether biosynthesis abolished SynCom-induced tomato resistance to Botrytis cinerea. Conversely, SlLOX5/SlDES1-overexpressing plants with higher divinyl-ether levels had stronger resistance than wild type. Preserve this positive pathway-level evidence for colneleic/colnelenic-acid-associated defense. The abstract does not specify the inhibition method or establish that each named compound is independently indispensable, sufficient alone, or transferred from bacteria.</p>



Expand Down Expand Up @@ -790,13 +787,26 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

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

<div class="snippet">"the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully abolished the community-induced plant disease resistance"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:37549573</a>

- SUPPORT (IN_VIVO)
</div>

<div class="snippet">"transgenic plants overexpressing SlLOX5 and SlDES1, with higher levels of divinyl ethers, displayed stronger resistance against B. cinerea compared to wild-type plants"</div>

</li>

</ul>

</div>
Expand All @@ -806,6 +816,45 @@ <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 microbial contributions and individual divinyl ethers mediate SynCom3 protection?
</h3>
<p class="prewrap">The abstract supports complementary functions, host oxylipin activation and a real biosynthesis perturbation, not merely correlation. Detailed primary methods would resolve the inhibition target, individual-compound necessity and biofilm mediation. Reciprocal bacterial benefit and cross-feeding are not established. Preserve both existing directions and positive protection without inventing a new mechanism.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#SynCom3-associated biofilm and host defense</code>, <code>ecological_interactions#SynCom3-induced leaf oxylipin responses</code>, <code>ecological_interactions#Divinyl Ether-Dependent Botrytis Protection</code></p>



<details class="evidence-list">
<summary class="muted small">1 evidence item(s)</summary>

<div class="evidence">
<div class="evidence-head">





<a href="https://pubmed.ncbi.nlm.nih.gov/37549573/" rel="nofollow noreferrer">PMID:37549573</a>


</div>
<p class="snippet small prewrap">the inhibited biosynthesis of antimicrobial divinyl ethers, including colneleic and colnelenic acid, fully abolished the community-induced plant disease resistance</p>

</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -951,7 +1000,7 @@ <h2>Environmental Factors</h2>

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

var processes = [];
Expand All @@ -960,11 +1009,11 @@ <h2>Environmental Factors</h2>
processes.push("biofilm formation");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
label: "Simplified Community Synergistic Protection",
label: "SynCom3-associated biofilm and host defense",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -979,7 +1028,7 @@ <h2>Environmental Factors</h2>

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


Expand All @@ -992,11 +1041,11 @@ <h2>Environmental Factors</h2>

var processes = [];

var evidenceCount = 2;
var evidenceCount = 1;

nodes.push({
id: intId,
label: "Oxylipin-Mediated Disease Resistance",
label: "SynCom3-induced leaf oxylipin responses",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand All @@ -1011,7 +1060,7 @@ <h2>Environmental Factors</h2>

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


Expand All @@ -1022,7 +1071,7 @@ <h2>Environmental Factors</h2>

var processes = [];

var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
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