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Bound field selection, yeast rescue and hydrolysis causal claims (batch79) #1659

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134 changes: 63 additions & 71 deletions docs/communities/Oak_Ridge_FRC_Uranium_Nitrate_Groundwater_Community.html
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59 changes: 51 additions & 8 deletions docs/communities/Ogataea_Met10_Str3_Sulfur_CrossFeeding_Coculture.html
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Original file line number Diff line number Diff line change
Expand Up @@ -596,6 +596,11 @@ <h2>Ecological Interactions</h2>
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="symbolTriangle2"
data-color="#929caa"></svg> Other
</div>
</div>
</div>

Expand All @@ -605,7 +610,7 @@ <h2>Ecological Interactions</h2>
<h3>MET10-STR3 Sulfur Auxotrophy Cross-Feeding</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The FY34 met10Δ and FY31 str3Δ O. polymorpha auxotrophs were co-cultured as a sulfur-assimilation cross-feeding pair whose deleted metabolic nodes complemented one another in Delft minimal medium.</p>
<p class="prewrap interaction-description">The met10Delta-str3Delta O. polymorpha pair showed reproducible growth complementation in Delft minimal medium on glucose and methanol. The reported glucose maximum OD600 range 27.3-28.5 spans this pair and str3Delta-leu2Delta, with no significant advantage over FY00 (26.8); methanol growth remained below FY00. FY34 met10Delta-mCherry and FY31 str3Delta-EGFP were the labeled derivatives used for population tracking, not identities established for every screening assay. Cooperative rescue is observed; specific sulfur exchange remains inferred.</p>



Expand Down Expand Up @@ -664,7 +669,7 @@ <h4>Evidence</h4>
<h3>Asymmetric Homocysteine Dependency</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Supplementation assays indicated that the met10Δ mutant could recover growth with L-cysteine, cystathionine, or homocysteine, whereas str3Δ only showed substantial recovery with homocysteine.</p>
<p class="prewrap interaction-description">HYPOTHESIZED - The model proposes homocysteine supply from met10Delta to str3Delta and multiple organic sulfur intermediates in the reverse direction. Single-strain supplementation at 20 mg/L restored met10Delta growth with L-cysteine, cystathionine or homocysteine, but not sodium sulfide; str3Delta recovered substantially only with homocysteine among the tested compounds. These are demonstrated nutrient-rescue profiles, not measured interstrain transfer, secretion, exchange rates or an exhaustive nutrient requirement. The paper calls for isotope labeling or targeted metabolomics to identify coculture exchange.</p>


<p><strong>Source Taxon:</strong> Ogataea polymorpha FY34 met10Δ-mCherry</p>
Expand All @@ -690,7 +695,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42318495/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42318495</a>

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

<div class="snippet">"met10Δ can utilize multiple sulfur-containing intermediates, whereas str3Δ relies exclusively on homocysteine."</div>
Expand All @@ -717,9 +722,8 @@ <h4>Evidence</h4>
<div class="interaction-card">
<div class="interaction-header">
<h3>Initial Ratio-Dependent Met10 Enrichment</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">The inoculated met10Δ:str3Δ ratio controlled community establishment and final biomass, while surviving cocultures shifted toward a met10Δ-biased composition.</p>
<p class="prewrap interaction-description">Controlled initial met10Delta:str3Delta ratios at total OD600 0.4 changed growth and composition on glucose. Ratios 1:10, 1:5 and 1:1 achieved higher final biomass, with met10Delta fractions increasing; 5:1 and 10:1 maintained met10Delta dominance but grew weakly. Endpoint composition was generally met10Delta-biased at 168 h, not evidence that every culture increased its met10Delta fraction, grew robustly or converged to one identical ratio. Longer-term continuous and product-producing stability was not established.</p>



Expand Down Expand Up @@ -752,7 +756,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"the initial inoculation ratio critically determines community establishment and final biomass"</div>
<div class="snippet">"Communities with initially higher frequencies of str3Δ (1:10, 1:5, and 1:1 groups) achieved higher final OD600 values."</div>

</li>

Expand All @@ -765,7 +769,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"all co-cultures converging toward met10Δ enrichment over time"</div>
<div class="snippet">"In contrast, groups initially dominated by met10Δ (5:1 and 10:1) showed weak growth throughout."</div>

</li>

Expand All @@ -778,6 +782,45 @@ <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 metabolites are actually exchanged, and how do they mediate the tested initial-ratio effect on growth?
</h3>
<p class="prewrap">The full paper explicitly infers directional exchange from single-strain supplement profiles and proposes tracers/metabolomics. Figure schematics are not transfer measurements. Growth restoration and ratio effects remain supported; distinct input/outcome and proposed exchange-to-rescue topology remain a research task. Prior dangling phenotype arrows remain absent. One-record Edison dry run is not an inspected provider report or paid authorization.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#MET10-STR3 Sulfur Auxotrophy Cross-Feeding</code>, <code>ecological_interactions#Asymmetric Homocysteine Dependency</code>, <code>ecological_interactions#Initial Ratio-Dependent Met10 Enrichment</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">OTHER</span>
<span class="badge small">SUPPORT</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/42318495/" rel="nofollow noreferrer">PMID:42318495</a>


</div>
<p class="snippet small prewrap">The isotopic labeling or targeted metabolomics would help to directly identify the specific metabolites exchanged in co-culture</p>
<p class="muted small prewrap">Explicitly identifies the unresolved exchange measurement.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1309,7 +1352,7 @@ <h4 style="color: var(--text);">Evidence</h4>

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

var processes = [];
Expand Down
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