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Bound fucoidan, GENIA and Transwell graphs; correct review counter interpretation (batch 42) #1470

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109 changes: 103 additions & 6 deletions docs/communities/Fucoidan_Seven_Degrader_Combinatorial_SynCom.html
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Expand Up @@ -1033,11 +1033,29 @@ <h2>Ecological Interactions</h2>
<div class="interaction-header">
<h3>Complementary fucoidan monomer degradation</h3>
</div>
<p class="prewrap interaction-description">The SynCom&#39;s community-level degradation emerges from combining fucose specialists, rare-sugar specialists, and generalists whose enzyme repertoires unlock distinct fractions of the sulfated F. vesiculosus fucoidan substrate.</p>
<p class="prewrap interaction-description">Across the seven-degrader panel, V4/V25 preferentially degrade fucose, F12/F40/F94 rare sugars, and V69/F56 act as generalists. Genomic predictions were compared with experimental LC-MS monomer depletion. Monomer degradation combines cleavage of fucoidan-bound sugars and uptake, not measured CO2 mineralization. Cell-free residual-fucoidan and purified-enzyme assays support complementary substrate accessibility without requiring contact or small-molecule cross-feeding. Six of nine tested soluble enzymes had detectable activity; this does not establish each enzyme as necessary in every community. Participants identify the panel, not seven obligatory partners in every assay. G88 and the algal substrate producer are not members.</p>




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

Algibacter sp. AS12,

Algibacter lectus AS40,

Mariniflexile sp. AS56,

Zobellia laminariae AS94,

Luteolibacter sp. AS25,

Roseibacillus persicicus AS69,

Lentimonas sp. CC4

</p>




Expand Down Expand Up @@ -1066,7 +1084,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/42649294/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:42649294</a>

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

<div class="snippet">"V69 and F56 function as generalists, whereas V4, V25 and G88 are fucose-specialists and F12, F40 and F94 are rare-sugar specialists."</div>
Expand Down Expand Up @@ -1094,10 +1112,28 @@ <h4>Evidence</h4>
<div class="interaction-header">
<h3>Seven-degrader synergistic function landscape</h3>
</div>
<p class="prewrap interaction-description">The complete non-empty panel of seven fucoidan degraders produced a smooth community-function landscape in which synergism remained common even among combinations approaching nearly complete degradation.</p>
<p class="prewrap interaction-description">All 127 nonempty combinations of the seven listed degraders were assayed, not a single invariant seven-member community. The reported maximum 97.1% monomer degradation occurred in the five-member F40/F56/V69/F94/V4 subset. Functional synergism, reported for 80% of interactions relative to the resource-partitioning null, is distinct from reciprocal fitness benefit; pairwise outcomes include commensalism, amensalism and competition. The mutualistic V69/G88 pair lies outside this panel. Initial OD600 was 0.01 per strain, so total inoculum varied with richness. These endpoint assays do not isolate a richness-only effect or establish ocean carbon-sequestration rates. The model is fitted prediction, not independent enzyme-necessity evidence.</p>




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

Algibacter sp. AS12,

Algibacter lectus AS40,

Mariniflexile sp. AS56,

Zobellia laminariae AS94,

Luteolibacter sp. AS25,

Roseibacillus persicicus AS69,

Lentimonas sp. CC4

</p>



Expand Down Expand Up @@ -1224,7 +1260,7 @@ <h2>Associated Datasets</h2>
</section>

<section id="discussions">
<h2>Knowledge gaps &amp; discussions <span class="muted">(2)</span></h2>
<h2>Knowledge gaps &amp; discussions <span class="muted">(3)</span></h2>

<div class="discussion">
<h3>
Expand Down Expand Up @@ -1279,10 +1315,10 @@ <h3>
<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
<span class="role-badge">RESOLVED</span>
Does the article&#39;s prose label for Lentimonas sp. CC4 resolve to V4 or V43?
</h3>
<p class="prewrap">Supplementary Table 2 maps LCC_4 to Lentimonas sp. CC4, Verruco4, and V4, and the full-combinatorial Methods use V4. One article paragraph refers to the previously characterized CC4 degrader as strain V43, so this record follows the spreadsheet and Methods convention for the member code.</p>
<p class="prewrap">Publisher HTML inspected on 2026-10-06 shows V4 immediately followed by a superscript link to reference 3, not strain V43. The selected-text cache flattened this citation into V43. Table 2 selected rows and combinatorial Methods consistently use V4 for Lentimonas sp. CC4. Preserve the historical question and original cache, but do not treat the rendering artifact as a biological alias. The decision ledger retains the source HTML hash and exact DOM fragment.</p>

<p class="muted small">Attaches to: <code>taxonomy#Lentimonas sp. CC4</code></p>

Expand Down Expand Up @@ -1324,6 +1360,21 @@ <h3>
</details>


</div>

<div class="discussion">
<h3>
<span class="role-badge">KNOWLEDGE_GAP</span>
<span class="role-badge">OPEN</span>
How should complementary substrate accessibility connect to panel-level degradation without overstating partner benefit?
</h3>
<p class="prewrap">Full public primary main body and Methods read. Cell-free residual substrate and six active purified enzymes support complementary accessibility; no universal contact requirement, small-molecule exchange or reciprocal benefit follows. Depletion combines cleavage and uptake, not CO2 mineralization. Preserve the five-member maximum, G88 exclusion, variable total inoculum and experimental/model distinction. The Results describe fitting one-, two- and three-member communities while Methods more generally reference the 127-community data; code and raw data were not audited, so no independent train/test verification is claimed. New structure is pending #1465 after the one-community Edison dry run; specific credit authorization requested, no job or spend. Two corrected existing nodes and zero arrows are not a completed causal expansion. Figure images and original supplements were not inspected.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Complementary fucoidan monomer degradation</code>, <code>ecological_interactions#Seven-degrader synergistic function landscape</code></p>




</div>

</section>
Expand Down Expand Up @@ -1668,6 +1719,29 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Algibacter sp. AS12",

"Algibacter lectus AS40",

"Mariniflexile sp. AS56",

"Zobellia laminariae AS94",

"Luteolibacter sp. AS25",

"Roseibacillus persicicus AS69",

"Lentimonas sp. CC4"

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

})();

(function() {
Expand Down Expand Up @@ -1696,6 +1770,29 @@ <h4 style="color: var(--text);">Evidence</h4>



var participantKeys = [

"Algibacter sp. AS12",

"Algibacter lectus AS40",

"Mariniflexile sp. AS56",

"Zobellia laminariae AS94",

"Luteolibacter sp. AS25",

"Roseibacillus persicicus AS69",

"Lentimonas sp. CC4"

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

})();


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