Skip to content

Bound nitrogen mediation and separate gallium bioleaching evidence (batch73) #1619

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
realmarcin wants to merge 1 commit into from
Closed

Bound nitrogen mediation and separate gallium bioleaching evidence (batch73) #1619

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
43 changes: 26 additions & 17 deletions docs/communities/Microcoleus_Massilia_Cyanosphere_Urea_Mutualism.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -602,7 +602,7 @@ <h2>Ecological Interactions</h2>
<h3>Carbon-for-Nitrogen Resource Trading</h3>
<span class="interaction-type">MUTUALISM</span>
</div>
<p class="prewrap interaction-description">M. vaginatus and Massilia sp. METH4 form a resource-trading mutualism under carbon- and nitrogen-limited conditions, with cyanobacterial photosynthate supporting the heterotroph and heterotrophic nitrogen acquisition supporting cyanobacterial growth.</p>
<p class="prewrap interaction-description">M. vaginatus PCC 9802 and Massilia sp. METH4 participate in selective carbon-for-nitrogen mutualism: coculture growth under organic-carbon and fixed-nitrogen limitation is consistent with photosynthate supporting the heterotroph and diazotrophic nitrogen acquisition supporting the cyanobacterium. The shared growth phenotype does not by itself identify the transferred organic-carbon compound or quantify partner-specific fluxes.</p>


<p><strong>Source Taxon:</strong> Microcoleus vaginatus PCC 9802</p>
Expand Down Expand Up @@ -669,7 +669,7 @@ <h4>Evidence</h4>
<h3>Urea-Mediated Nitrogen Transfer</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">In the M. vaginatus PCC 9802-Massilia sp. METH4 coculture, Massilia upregulates urea-biosynthesis functions while M. vaginatus upregulates urea uptake and urea carboxylase/allophanate hydrolase functions, supporting urea as the nitrogen-transfer vehicle.</p>
<p class="prewrap interaction-description">PARTIAL - Urea is a strongly supported likely nitrogen-transfer vehicle in the exact PCC 9802/METH4 pair. Coculture increases extracellular urea release; METH4 upregulates urea-cycle genes and PCC 9802 upregulates uptake and urea carboxylase/allophanate hydrolase genes. PCC 9802 can grow on supplied urea down to 5 micromolar, but not 2 micromolar in the tested assay. These convergent results support cross-feeding without directly tracing the origin and assimilation of each urea molecule or proving urea is the exclusive nitrogen carrier. Release rates use total coculture biomass, because a heterotrophic origin of extracellular urea is inferred rather than absolutely resolved.</p>


<p><strong>Source Taxon:</strong> Massilia sp. METH4</p>
Expand Down Expand Up @@ -714,8 +714,7 @@ <h3>Urea-Mediated Nitrogen Transfer</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Carbon-for-Nitrogen Resource Trading
<p class="prewrap causal-description">Massilia urea release supplies the low-concentration nitrogen vehicle that completes the M. vaginatus carbon-for-nitrogen exchange with its heterotrophic partner.
</p>
<p class="prewrap causal-description">PARTIAL - Coculture-associated urea release and cyanobacterial low-concentration urea utilization provide a plausible, experimentally supported route for the nitrogen side of carbon-for-nitrogen trading. Coordinated expression supports Massilia-to-Microcoleus transfer, but exclusive donor attribution and the fraction of growth sustained by this route are not directly resolved.</p>
</div>

</div>
Expand All @@ -731,7 +730,7 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1093/ismejo/wrae246"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1093/ismejo/wrae246</a>

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

<div class="snippet">"M. vaginatus and Massilia sp. METH4 in co-culture on N and C free media"</div>
Expand All @@ -744,7 +743,7 @@ <h4>Evidence</h4>
<a href="https://doi.org/10.1093/ismejo/wrae246"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1093/ismejo/wrae246</a>

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

<div class="snippet">"these results are consistent with the notion that urea is likely the vehicle for interspecies N transfer"</div>
Expand All @@ -760,7 +759,7 @@ <h4>Evidence</h4>
<h3>GABA and Glutamate Spatial Signaling</h3>
<span class="interaction-type">COLONIZATION_FACILITATION</span>
</div>
<p class="prewrap interaction-description">Nitrogen-starved M. vaginatus and carbon-limited Massilia sp. METH4 produce GABA and glutamate signals that modulate M. vaginatus motility and bundle formation, optimizing close spatial organization for the mutualism.</p>
<p class="prewrap interaction-description">GABA and glutamate released by C-limited Massilia sp. METH4 and N-starved M. vaginatus influence cyanobacterial motility and bundling. Addition experiments establish N-dependent chemokinetic and chemophobic responses, not measured Massilia migration; PCC 9802 did not show true chemotaxis to glutamate. Natural-bundle assays additionally measure gliding reversals, a response poorly retained in the long-cultured PCC 9802 strain. Low GABA can stabilize bundles, whereas high GABA can destabilize natural bundles, so increasing signal is not uniformly beneficial. The proposed benefit to carbon-for-nitrogen exchange is spatial retention near heterotrophic partners, not a directly measured flux increase.</p>


<p><strong>Source Taxon:</strong> Massilia sp. METH4</p>
Expand Down Expand Up @@ -788,12 +787,6 @@ <h3>GABA and Glutamate Spatial Signaling</h3>
<p><strong>Biological Processes:</strong></p>
<ul>

<li>
chemotaxis
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006935"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006935</a>)
</li>

<li>
biological process involved in interspecies interaction between organisms
(<a href="http://amigo.geneontology.org/amigo/term/GO:0044419"
Expand All @@ -809,8 +802,7 @@ <h3>GABA and Glutamate Spatial Signaling</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Carbon-for-Nitrogen Resource Trading
<p class="prewrap causal-description">GABA and glutamate signaling spatially organizes Massilia near nitrogen-starved M. vaginatus, concentrating diazotrophic cyanosphere partners where they can optimize carbon-for-nitrogen exchange.
</p>
<p class="prewrap causal-description">PARTIAL - GABA/glutamate responses keep nitrogen-limited Microcoleus trichomes bundled near cyanosphere partners, providing spatial proximity expected to facilitate nutrient exchange. Signal-addition and cyanosphere-cleansing experiments support bundle organization, but the increase in carbon-for-nitrogen flux or fitness attributable to this organization was not directly quantified. The responding motile organism is Microcoleus, not demonstrated recruitment of motile Massilia.</p>
</div>

</div>
Expand Down Expand Up @@ -938,6 +930,25 @@ <h2>Associated Datasets</h2>
</div>
</section>

<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>
How much nutrient exchange is mediated specifically by heterotrophic urea and GABA/Glu-dependent spatial retention?
</h3>
<p class="prewrap">Retain demonstrated mutualistic growth, urea pool/release changes, supplied-urea growth and signal-induced motility. The wrae246 Results explicitly does not absolutely resolve the urea donor in coculture; total biomass normalizes release. No selective transfer tracing or uc/ah enzyme-affinity characterization establishes an exclusive carrier. The wrad029 experiments distinguish PCC 9802 from natural bundles, chemokinesis/chemophobia from true glutamate chemotaxis, and concentration-dependent stabilization from high-GABA destabilization. Improved nutrient-flux efficiency is the mechanistic interpretation, not an independently quantified endpoint. No new self-loop is inferred from the proposed feedback model.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Urea-Mediated Nitrogen Transfer</code>, <code>ecological_interactions#GABA and Glutamate Spatial Signaling</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1303,8 +1314,6 @@ <h4 style="color: var(--text);">Evidence</h4>
var processes = [];


processes.push("chemotaxis");

processes.push("biological process involved in interspecies interaction between organisms");


Expand Down
Loading