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Qualify thermophilic syntrophy mechanisms and assay contrasts (batch114) #1892

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61 changes: 49 additions & 12 deletions docs/communities/Thermacetogenium_Methanothermobacter_Acetate_Oxidation_Coculture.html
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Expand Up @@ -621,7 +621,7 @@ <h2>Ecological Interactions</h2>
<h3>Syntrophic Acetate Oxidation by Thermacetogenium</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">T. phaeum oxidizes acetate in coculture through the reversible CO dehydrogenase/ acetyl-CoA pathway, producing reduced carriers that require removal by the methanogenic partner for favorable syntrophic growth.</p>
<p class="prewrap interaction-description">T. phaeum PB oxidizes acetate in the studied syntrophic coculture with M. thermautotrophicus TM. Enzyme activities and substrate-switch experiments support reversible use of the CO dehydrogenase/acetyl-CoA (Wood-Ljungdahl) pathway. Removal of reduced products supports acetate oxidation; this does not assert obligate partnership on other substrates, since T. phaeum also grows acetogenically in pure culture. Hydrogen and formate are extracellular electron-carrier candidates, not a claim that intracellular cofactors are passed between cells. The detailed formate-linked energy-conservation mechanism remains a model.</p>


<p><strong>Source Taxon:</strong> Thermacetogenium phaeum PB</p>
Expand Down Expand Up @@ -674,8 +674,7 @@ <h3>Syntrophic Acetate Oxidation by Thermacetogenium</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Hydrogenotrophic Methanogenesis by Methanothermobacter
<p class="prewrap causal-description">T. phaeum acetate oxidation produces low-concentration reduced carriers that M. thermautotrophicus consumes during hydrogenotrophic methanogenesis.
</p>
<p class="prewrap causal-description">Acetate oxidation by T. phaeum supplies reduced products for the methanogenic partner, coupling acetate conversion to methane formation. Hydrogen consumption is supported by the TM/PB coculture experiments; PARTIAL for the partition of electron flow between hydrogen and formate and the specific formate-producing energy-conservation model. This is not direct acetate utilization by the methanogen.</p>
</div>

</div>
Expand Down Expand Up @@ -717,7 +716,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31849917/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31849917</a>

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

<div class="snippet">"yielding formate as reduced product"</div>
Expand All @@ -733,7 +732,7 @@ <h4>Evidence</h4>
<h3>Hydrogenotrophic Methanogenesis by Methanothermobacter</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">M. thermautotrophicus TM consumes low-concentration hydrogen and carbon dioxide during syntrophic growth and expresses methanogenesis machinery adapted to coculture conditions.</p>
<p class="prewrap interaction-description">M. thermautotrophicus TM consumes hydrogen during acetate-fed coculture with T. phaeum PB, supporting product removal and methane formation. The 2002 TM/PB experiment maintained 20 to 80 Pa hydrogen and detected mcr/MRI rather than mrt/MRII expression in coculture; other assayed methanogenesis genes were expressed in both culture modes. This is not a universal activation of all methanogenesis genes or evidence of obligate dependence on PB. TM can also use formate; the hydrogenotrophic designation does not exclude formate-supported electron transfer. The separate DeltaH/butyrate coculture is not the PB/TM system.</p>


<p><strong>Source Taxon:</strong> Methanothermobacter thermautotrophicus TM</p>
Expand Down Expand Up @@ -815,7 +814,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"catalyzing the final step of methanogenesis"</div>
<div class="snippet">"only the mcr gene"</div>

</li>

Expand All @@ -825,10 +824,10 @@ <h4>Evidence</h4>

<div class="interaction-card">
<div class="interaction-header">
<h3>Formate Transfer to the Methanogenic Partner</h3>
<h3>Formate-Linked Syntrophic Electron Transfer</h3>
<span class="interaction-type">CROSS_FEEDING</span>
</div>
<p class="prewrap interaction-description">Proteomic and enzyme evidence supports a reversed electron transport mechanism in T. phaeum that produces formate for transfer to the methanogenic partner.</p>
<p class="prewrap interaction-description">PARTIAL: formate involvement in T. phaeum PB to M. thermautotrophicus TM electron transfer is supported by the partner-comparison literature discussed in the 2019 study, not dismissed as a genomic conjecture. The 2019 proteome and enzyme assays support a quinone-linked formate dehydrogenase and methyl-THF oxidation machinery. HYPOTHESIZED: their coupling through reverse electron transport, an ATP-supported proton gradient and ATP-independent acetate activation. Proton-gradient coupling and physiological acetate reduction were not demonstrated there. Neither the exact in vivo formate flux nor its fraction of total transferred electrons is established by these enzyme assays.</p>


<p><strong>Source Taxon:</strong> Thermacetogenium phaeum PB</p>
Expand Down Expand Up @@ -871,8 +870,7 @@ <h3>Formate Transfer to the Methanogenic Partner</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Hydrogenotrophic Methanogenesis by Methanothermobacter
<p class="prewrap causal-description">Formate and reducing equivalents generated by T. phaeum are transferred to the methanogenic partner that completes syntrophic acetate oxidation.
</p>
<p class="prewrap causal-description">PARTIAL: formate produced by T. phaeum can supply reducing equivalents to the formate-utilizing TM partner for methanogenesis, while removal helps maintain favorable acetate oxidation. HYPOTHESIZED for the specific proton-coupled production mechanism; this arrow does not establish its in vivo flux or convert formate utilization into hydrogen-only metabolism.</p>
</div>

</div>
Expand All @@ -888,7 +886,7 @@ <h4>Evidence</h4>
<a href="https://pubmed.ncbi.nlm.nih.gov/31849917/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:31849917</a>

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

<div class="snippet">"transferred to the methanogenic partner"</div>
Expand Down Expand Up @@ -952,6 +950,45 @@ <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 electron transfer uses formate, and which proton-coupled steps operate during PB/TM acetate oxidation?
</h3>
<p class="prewrap">The formate-transfer interpretation is supported, but enzyme/proteome results do not establish the complete energy budget or in vivo electron partition. The 2019 study explicitly leaves proton coupling and physiological acetate reduction unresolved. Preserve these distinctions when interpreting the two incoming methanogenesis arrows. Non-graph assay-condition followup remains issue #1890.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Syntrophic Acetate Oxidation by Thermacetogenium</code>, <code>ecological_interactions#Hydrogenotrophic Methanogenesis by Methanothermobacter</code>, <code>ecological_interactions#Formate-Linked Syntrophic Electron Transfer</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_VITRO</span>
<span class="badge small">PARTIAL</span>



<a href="https://pubmed.ncbi.nlm.nih.gov/31849917/" rel="nofollow noreferrer">PMID:31849917</a>


</div>
<p class="snippet small prewrap">transferred to the methanogenic partner</p>
<p class="muted small prewrap">Authors interpret formate as a transferred product; the quoted conclusion does not itself measure interspecies flux or validate all proposed coupling steps.</p>
</div>

</details>


</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1602,7 +1639,7 @@ <h4 style="color: var(--text);">Evidence</h4>

nodes.push({
id: intId,
label: "Formate Transfer to the Methanogenic Partner",
label: "Formate-Linked Syntrophic Electron Transfer",
type: "interaction",
interactionType: intType,
metabolites: metabolites,
Expand Down
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