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Separate ecological observations from genomic candidates (batch95) #1765

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89 changes: 53 additions & 36 deletions docs/communities/Rice_P_Uptake_Intercropping_SynCom4.html
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Original file line number Diff line number Diff line change
Expand Up @@ -642,16 +642,16 @@ <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 Rice Phosphorus Uptake Intercropping SynCom4</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 @@ -660,9 +660,8 @@ <h2>Ecological Interactions</h2>
<div class="interaction-card">
<div class="interaction-header">
<h3>Soil Available Phosphorus Activation</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">Intercropping-derived SynCom members directly activate the plant-accessible soil phosphorus pool, increasing the phosphate available for rice roots in pot experiments.</p>
<p class="prewrap interaction-description">SynCom inoculation increased available soil phosphorus in the rice pot experiment, alongside lower rhizosphere pH and changes in phosphorus fractions. This is a measured inoculation response; contributions of particular strains or acids are not separately resolved.</p>



Expand All @@ -686,7 +685,7 @@ <h3>Soil Available Phosphorus Activation</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Phosphorus Acquisition Promotion
<p class="prewrap causal-description">SynCom-driven phosphate activation contributes to the belowground phosphorus-acquisition program that also changes root morphology and up-regulates rice Pi transporter genes.</p>
<p class="prewrap causal-description">PARTIAL: greater soil phosphorus availability is a proposed contributor to improved rice phosphorus acquisition. The comparisons do not isolate this contribution from root architectural and transport-associated responses.</p>
</div>

</div>
Expand Down Expand Up @@ -716,9 +715,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Phosphorus Acquisition Promotion</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">SynCom members increase soil available phosphorus and support root-to-shoot phosphorus transport.</p>
<p class="prewrap interaction-description">SynCom-treated rice showed altered root architecture, phosphorus allocation and expression of phosphate-transporter genes. PARTIAL: these observations support the proposed acquisition/translocation pathway, but expression and endpoint concentrations do not independently establish transporter-mediated flux or necessity.</p>



Expand Down Expand Up @@ -753,7 +751,7 @@ <h3>Phosphorus Acquisition Promotion</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Rice Biomass and Phosphorus Uptake Increase
<p class="prewrap causal-description">Better available-phosphorus access, larger root absorptive surface, and higher root-to-shoot Pi transporter expression drive the measured increases in potted rice biomass and phosphorus uptake.</p>
<p class="prewrap causal-description">PARTIAL: improved phosphorus access, root architecture and transport-associated responses are proposed contributors to the positive pot biomass/phosphorus outcome. Their separate contributions and necessity for that outcome remain unresolved.</p>
</div>

</div>
Expand All @@ -769,20 +767,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/39684532/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39684532</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass and P uptake of potted rice plants."</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/39684532/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39684532</a>

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

<div class="snippet">"promotion of root-to-shoot P translocation through up-regulation of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6)"</div>
Expand All @@ -796,9 +781,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Rice Biomass and Phosphorus Uptake Increase</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The synthetic community significantly enhances rice biomass and phosphorus uptake in the pot assays, tying the soil-phosphorus and root-translocation effects to the plant-growth endpoint.</p>
<p class="prewrap interaction-description">The four-strain SynCom significantly increased rice dry biomass and phosphorus uptake in the pot comparison. This positive inoculation outcome is distinct from the field rice/soybean intercropping comparison, where rice yield and phosphorus uptake decreased. Benefit to rice is not evidence of reciprocal bacterial fitness.</p>



Expand All @@ -807,10 +791,6 @@ <h3>Rice Biomass and Phosphorus Uptake Increase</h3>

<p><strong>Metabolites:</strong>

phosphorus
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=28659"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:28659</a>),

phosphate ion
(<a href="https://www.ebi.ac.uk/chebi/searchId.do?chebiId=35780"
class="term-link" target="_blank" rel="noopener noreferrer">CHEBI:35780</a>)
Expand All @@ -832,7 +812,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/39684532/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:39684532</a>

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

<div class="snippet">"A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass and P uptake of potted rice plants."</div>
Expand All @@ -848,6 +828,45 @@ <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 pathways mediate the positive pot response?
</h3>
<p class="prewrap">The complete primary main text distinguishes negative field intercropping effects on rice from positive SynCom pot effects. Soil-P fractions, root traits, root IAA and transporter expression support proposed pathways but do not establish each mediator as necessary. Preserve both existing directions as PARTIAL. MUTUALISM requires reciprocal benefit, not a plant response alone. Non-graph CROSS_FEEDER labels and aliased evidence are unchanged pending issue1764.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Soil Available Phosphorus Activation</code>, <code>ecological_interactions#Phosphorus Acquisition Promotion</code>, <code>ecological_interactions#Rice Biomass and Phosphorus Uptake Increase</code></p>



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

<div class="evidence">
<div class="evidence-head">
<span class="badge small">IN_VIVO</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/39684532/" rel="nofollow noreferrer">PMID:39684532</a>


</div>
<p class="snippet small prewrap">the yield and P uptake of intercropped rice were lower than those of rice grown in monoculture</p>
<p class="muted small prewrap">The field comparison must not be conflated with SynCom inoculation of potted rice.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1057,7 +1076,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand Down Expand Up @@ -1085,7 +1104,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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


Expand All @@ -1098,7 +1117,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("phosphate ion transport");


var evidenceCount = 2;
var evidenceCount = 1;

nodes.push({
id: intId,
Expand All @@ -1117,12 +1136,10 @@ <h4 style="color: var(--text);">Evidence</h4>

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


metabolites.push("phosphorus");

metabolites.push("phosphate ion");


Expand Down
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