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Bound DVM substrate and methane pathway claims (batch57) #1531

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74 changes: 51 additions & 23 deletions docs/communities/DVM_Triculture.html
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Expand Up @@ -628,8 +628,7 @@ <h2>Ecological Interactions</h2>
<h3>Lactate Oxidation and H2/Acetate Production</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Desulfovibrio vulgaris oxidizes lactate to acetate, CO2, and H2. In the absence of sulfate, this oxidation occurs syntrophically with both methanogens maintaining low H2 partial pressure. The stoichiometric degradation of lactate produces intermediates (H2 and acetate) that both methanogens can utilize. When sulfate is present, D. vulgaris shifts metabolism to use sulfate as the electron acceptor, altering the balance of H2 and acetate production and creating competitive dynamics with the methanogens.
</p>
<p class="prewrap interaction-description">In the constructed 2019 DVM cultures, D. vulgaris fermented lactate to acetate and hydrogen under no-added-sulfate conditions. M. maripaludis uses hydrogen, whereas M. barkeri can use hydrogen and acetate; acetate is not a substrate for both methanogens. The tri-culture and Dv-Mm pair showed full lactate conversion, but residual acetate remained in the tri-culture and Dv-Mb pair. Sulfate availability shifts the balance toward donor respiration. The experimental Dv was a laboratory Hildenborough variant with two syntrophy-enabling polymorphisms, not an unqualified wild-type strain.</p>


<p><strong>Source Taxon:</strong> Desulfovibrio vulgaris</p>
Expand Down Expand Up @@ -680,7 +679,7 @@ <h3>Lactate Oxidation and H2/Acetate Production</h3>
</li>

<li>
lactate oxidation
lactate metabolic process
(<a href="http://amigo.geneontology.org/amigo/term/GO:0006089"
class="term-link" target="_blank" rel="noopener noreferrer">GO:0006089</a>)
</li>
Expand All @@ -694,12 +693,12 @@ <h3>Lactate Oxidation and H2/Acetate Production</h3>

<div class="flow-item">
<span class="flow-arrow">→</span> Hydrogenotrophic Methanogenesis by M. maripaludis
<p class="prewrap causal-description">H2 produced by D. vulgaris is consumed by M. maripaludis for methanogenesis</p>
<p class="prewrap causal-description">PARTIAL - lactate fermentation supplies hydrogen that can support M. maripaludis methanogenesis and product removal. The functional pair and tri-culture support this physiological route, but partner-resolved flux and the fraction supplied by fermentation were not isolated; initial headspace also contained hydrogen and carbon dioxide.</p>
</div>

<div class="flow-item">
<span class="flow-arrow">→</span> Dual-pathway Methanogenesis by M. barkeri
<p class="prewrap causal-description">Both H2 and acetate produced by D. vulgaris are consumed by M. barkeri</p>
<p class="prewrap causal-description">PARTIAL - lactate fermentation supplies acetate and hydrogen that can support M. barkeri methane production. Monoculture hydrogen perturbations and Dv-Mb mass balances support hydrogen co-utilization, but do not resolve pathway shares in the tri-culture or establish complete acetate consumption.</p>
</div>

</div>
Expand All @@ -712,13 +711,13 @@ <h4>Evidence</h4>
<li class="evidence-item">
<div>

<a href="https://pubmed.ncbi.nlm.nih.gov/16345708/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:16345708</a>
<a href="https://doi.org/10.1098/rsif.2019.0129"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1098/rsif.2019.0129</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"vulgaris was grown in the absence of added sulfate in coculture with Methanosarcina barkeri (type strain), which uses both H(2)-CO(2) and acetate for methanogenesis, lactate was stoichiometrically degraded to CH(4) and presumably to CO(2)"</div>
<div class="snippet">"chemically defined media with lactate (30 mM), as the sole organic carbon source"</div>

</li>

Expand All @@ -731,7 +730,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate"</div>
<div class="snippet">"was not able to consume all of the acetate fermented"</div>

</li>

Expand All @@ -744,8 +743,7 @@ <h4>Evidence</h4>
<h3>Hydrogenotrophic Methanogenesis by M. maripaludis</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Methanococcus maripaludis consumes H2 and CO2 produced by D. vulgaris to produce methane via hydrogenotrophic methanogenesis. This H2 removal maintains low H2 partial pressure, making lactate oxidation thermodynamically favorable for D. vulgaris. However, increasing sulfate availability reduces the effectiveness of this syntrophy as D. vulgaris can use sulfate instead of relying on H2 transfer, creating competition for available H2.
</p>
<p class="prewrap interaction-description">M. maripaludis is the hydrogenotrophic partner in the lactate-fed Dv-Mm pair and DVM tri-culture. Hydrogen consumption provides the product-removal basis of syntrophy. The pair remained stable at 7.5 mM sulfate but methane production diminished at 15 mM sulfate across transfers. These measured outcomes support the route, not a traced partition of donor-derived hydrogen or carbon dioxide; culture headspace already contained both gases. PARTIAL - the exact contribution of resource competition to the sulfate response is inferred.</p>


<p><strong>Source Taxon:</strong> Methanococcus maripaludis</p>
Expand Down Expand Up @@ -801,7 +799,7 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate"</div>
<div class="snippet">"displayed stable coexistence at half-sulfate treatments"</div>

</li>

Expand All @@ -814,8 +812,7 @@ <h4>Evidence</h4>
<h3>Dual-pathway Methanogenesis by M. barkeri</h3>
<span class="interaction-type">SYNTROPHY</span>
</div>
<p class="prewrap interaction-description">Methanosarcina barkeri can utilize both H2-CO2 and acetate produced by D. vulgaris for methanogenesis. This dual metabolic capability is particularly important in the absence of sulfate, where M. barkeri contributes significantly to methane production. However, under sulfate treatments, M. barkeri&#39;s contribution is diminished even when acetate is available, likely due to competitive interactions with D. vulgaris for H2 and potentially other resources. This demonstrates differential sensitivity of acetotrophic versus hydrogenotrophic methanogenesis to sulfate-mediated perturbations.
</p>
<p class="prewrap interaction-description">M. barkeri contributed to the higher methane output of the no-added-sulfate DVM tri-culture, while substantial acetate remained. Separate monocultures supplied with 30 mM acetate produced more methane with higher hydrogen pressure, including about 60 mM versus 20 mM methane with 80% versus no added headspace hydrogen. Mass balances in no-added-sulfate Dv-Mb pairs require hydrogen utilization in addition to acetate use. PARTIAL - parallel hydrogenotrophic/acetotrophic routes versus coupled hydrogen oxidation and acetate reduction, and their shares in the tri-culture, are not resolved. This is not evidence for complete acetate use or an obligate hydrogen requirement under every condition.</p>


<p><strong>Source Taxon:</strong> Methanosarcina barkeri</p>
Expand Down Expand Up @@ -877,20 +874,20 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood"</div>
<div class="snippet">"increasing H2 pressure in the headspace"</div>

</li>

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

<a href="https://pubmed.ncbi.nlm.nih.gov/16345708/"
class="pmid-link" target="_blank" rel="noopener noreferrer">PMID:16345708</a>
<a href="https://doi.org/10.1098/rsif.2019.0129"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1098/rsif.2019.0129</a>

- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"vulgaris was grown in the absence of added sulfate in coculture with Methanosarcina barkeri (type strain), which uses both H(2)-CO(2) and acetate for methanogenesis, lactate was stoichiometrically degraded to CH(4) and presumably to CO(2)"</div>
<div class="snippet">"the methane production in the system cannot be explained solely by acetotrophic methanogenesis"</div>

</li>

Expand All @@ -903,8 +900,7 @@ <h4>Evidence</h4>
<h3>Sulfate-mediated Competition</h3>
<span class="interaction-type">COMPETITION</span>
</div>
<p class="prewrap interaction-description">Increasing sulfate availability shifts community dynamics by enabling D. vulgaris to use sulfate as an electron acceptor rather than relying solely on syntrophic H2 transfer. This creates competitive situations where D. vulgaris can use both H2 and lactate, potentially outcompeting the methanogens. The differential impact on the two methanogens reveals that acetotrophic (M. barkeri) and hydrogenotrophic (M. maripaludis) pathways respond differently to sulfate gradients, providing insights into how geochemical conditions regulate methanogenic community structure.
</p>
<p class="prewrap interaction-description">With 30 mM lactate, sulfate was added at 0, 7.5 or 15 mM across three 21-day culturing periods. Methane production and methanogen gene abundance declined with sulfate, with M. barkeri more sensitive than M. maripaludis; acetate remained available. Dv-Mb methane production was already impaired at 7.5 mM, while the Dv-Mm pair showed a diminishing trend at 15 mM. PARTIAL - sulfate-enabled donor respiration and competition for hydrogen provide the source-supported explanation, strengthened by Mb monoculture hydrogen perturbations and pair mass balances. These assays do not selectively isolate that mechanism in the tri-culture or establish acetate competition, lactate use by the methanogens, or an irreversible loss of every methanogen.</p>


<p><strong>Source Taxon:</strong> Desulfovibrio vulgaris</p>
Expand Down Expand Up @@ -964,7 +960,20 @@ <h4>Evidence</h4>
- SUPPORT (IN_VITRO)
</div>

<div class="snippet">"With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate"</div>
<div class="snippet">"resulted in a loss of methane production already in half-sulfate treatments"</div>

</li>

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

<a href="https://doi.org/10.1098/rsif.2019.0129"
class="pmid-link" target="_blank" rel="noopener noreferrer">doi:10.1098/rsif.2019.0129</a>

- PARTIAL (IN_VITRO)
</div>

<div class="snippet">"competition with Dv and Mm for this compound"</div>

</li>

Expand All @@ -977,6 +986,25 @@ <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>
What fractions of DVM methane flux follow each pathway, and how much of the sulfate effect is mediated by hydrogen competition?
</h3>
<p class="prewrap">Preserve positive lactate conversion, increased tri-culture methane output, sulfate responses and the separate Mb monoculture hydrogen perturbation. Pair mass balance does not uniquely distinguish biochemical routes or quantify tri-culture flux. Initial headspace hydrogen/carbon dioxide prevents an exclusive donor-origin claim. The 1981 cached abstract concerns different pair experiments and medium conditions, not the 2019 tri-culture. Full 2019 primary main text, Methods, Tables1-2 and main captions read; no original images, external supplements or raw-data audit. All four nodes and two existing arrows retained, with exact-system uncertainty exposed. Canonical taxa and non-graph metadata are preserved, not recertified; #1364 remains open. No new causal structure or Edison spend.</p>

<p class="muted small">Attaches to: <code>ecological_interactions#Lactate Oxidation and H2/Acetate Production</code>, <code>ecological_interactions#Hydrogenotrophic Methanogenesis by M. maripaludis</code>, <code>ecological_interactions#Dual-pathway Methanogenesis by M. barkeri</code>, <code>ecological_interactions#Sulfate-mediated Competition</code></p>




</div>

</section>

<!-- Environmental Factors -->

Expand Down Expand Up @@ -1332,7 +1360,7 @@ <h4 style="color: var(--text);">Evidence</h4>

processes.push("lactate catabolic process");

processes.push("lactate oxidation");
processes.push("lactate metabolic process");


var evidenceCount = 2;
Expand Down Expand Up @@ -1468,7 +1496,7 @@ <h4 style="color: var(--text);">Evidence</h4>
processes.push("dissimilatory sulfate reduction");


var evidenceCount = 1;
var evidenceCount = 2;

nodes.push({
id: intId,
Expand Down
25 changes: 25 additions & 0 deletions history/records/DVM_Triculture/2026-10-06T185257Z-codex-5706a2.yaml
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@@ -0,0 +1,25 @@
history_version: 1
target:
kind: record
path: kb/communities/DVM_Triculture.yaml
slug: DVM_Triculture
session:
id: 2026-10-06T185257Z-codex-5706a2
timestamp: '2026-10-06T18:52:57Z'
actors:
- type: ai_agent
name: codex
model: unspecified
agent_tool: codex
links:
issues:
- https://github.com/CultureBotAI/CommunityMech/issues/1530
events:
- type: EDIT
outcome: changed
sections:
- interactions
- discussions
summary: Bound DVM substrate provision, methane pathway partition and sulfate competition
by exact assay.
details: Source-based self-adversarial review. reports/causal_graph_review/decisions/20261006-dvm-batch57.yaml
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