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DVM Tri-culture

Community ID CommunityMech:000021
Ecological State STABLE
Environment laboratory bioreactor — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

A three-member synthetic consortium consisting of Desulfovibrio vulgaris (Dv), Methanococcus maripaludis (Mm), and Methanosarcina barkeri (Mb) that converts lactate to methane under varying sulfate conditions. D. vulgaris oxidizes lactate to acetate, CO2, and H2. Both methanogens (Mm and Mb) can consume the H2 produced by Dv, with Mm being a hydrogenotrophic methanogen and Mb capable of using both H2-CO2 and acetate for methanogenesis. The community demonstrates differential responses to geochemical gradients, particularly sulfate availability. In the absence of sulfate, all three species co-exist and methane production increases by almost 100% compared to Dv-Mm co-cultures. However, increasing sulfate levels shift community dynamics as Dv preferentially uses sulfate as an electron acceptor, creating competitive situations for both methanogens. This system provides insights into how geochemical gradients (particularly sulfate) regulate microbial interactions and methane production in anaerobic environments.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Desulfovibrio vulgaris — ontology label: Nitratidesulfovibrio vulgaris NCBITaxon:881 · TaxonMech · TraitMech
PRIMARY_DEGRADER SYNTROPHIC_PARTNER
N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate"
Methanococcus maripaludis NCBITaxon:39152 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate"
Methanosarcina barkeri NCBITaxon:2208 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER
N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "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"

Ecological Interactions

The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.

Ecological interaction network for DVM Tri-culture Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for syntrophy, competition.
Taxon
Syntrophy
Competition

Lactate Oxidation and H2/Acetate Production

SYNTROPHY

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.

Source Taxon: Desulfovibrio vulgaris

Participating Taxa: Desulfovibrio vulgaris, Methanococcus maripaludis, Methanosarcina barkeri

Metabolites: lactate (CHEBI:24996 · MediaIngredientMech · CMMMech), acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Hydrogenotrophic Methanogenesis by M. maripaludis

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.

→ Dual-pathway Methanogenesis by M. barkeri

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.

Evidence

Hydrogenotrophic Methanogenesis by M. maripaludis

SYNTROPHY

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.

Source Taxon: Methanococcus maripaludis

Target Taxon: Desulfovibrio vulgaris

Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

Dual-pathway Methanogenesis by M. barkeri

SYNTROPHY

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.

Source Taxon: Methanosarcina barkeri

Target Taxon: Desulfovibrio vulgaris

Metabolites: dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech), acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

Sulfate-mediated Competition

COMPETITION

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.

Source Taxon: Desulfovibrio vulgaris

Participating Taxa: Desulfovibrio vulgaris, Methanococcus maripaludis, Methanosarcina barkeri

Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN What fractions of DVM methane flux follow each pathway, and how much of the sulfate effect is mediated by hydrogen competition?

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.

Attaches to: ecological_interactions#Lactate Oxidation and H2/Acetate Production, ecological_interactions#Hydrogenotrophic Methanogenesis by M. maripaludis, ecological_interactions#Dual-pathway Methanogenesis by M. barkeri, ecological_interactions#Sulfate-mediated Competition

Environmental Factors

Factor Value Unit
Anaerobic Conditions Strict anaerobic N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "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"
Sulfate Gradient Variable (0 to increasing concentrations) N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "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"
Hydrogen Partial Pressure Must be maintained at low levels for syntrophy N/A
  • PMID:16345708 - SUPPORT (IN_VITRO)
    "The results suggest that H(2) produced by the Desulfovibrio species during growth with lactate inhibited acetate degradation by M"
Lactate Availability Primary carbon and energy source N/A
  • PMID:16345708 - SUPPORT (IN_VITRO)
    "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)"
Community Productivity Response 100% increase in no-sulfate conditions N/A
  • doi:10.1098/rsif.2019.0129 - SUPPORT (IN_VITRO)
    "We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate"

Growth Media

defined anaerobic medium (lactate 30 mM as sole organic carbon source)

Temperature 37 °C
Atmosphere ANAEROBIC

Preparation notes: Chemically defined anaerobic medium (basal salt, trace metal and vitamin stocks) reduced with Na2S; lactate (30 mM) sole organic carbon source; cultures incubated at 37 C in triplicate and sub-cultured every three weeks (5% v/v dilution).

Evidence

doi:10.1098/rsif.2019.0129

"A defined anaerobic medium, adapted from previous studies"

doi:10.1098/rsif.2019.0129

"The cultivations were performed in triplicate, with each set incubated at 37°C for three weeks. The dilution level for sub-culturing was 5% (v/v)"

doi:10.1098/rsif.2019.0129

"chemically defined media with lactate (30 mM), as the sole organic carbon source"

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: laboratory bioreactor ↗ TaxonMech: Desulfovibrio vulgaris ↗ TraitMech: Desulfovibrio vulgaris ↗ TaxonMech: Methanococcus maripaludis ↗ TraitMech: Methanococcus maripaludis ↗ TaxonMech: Methanosarcina barkeri ↗ TraitMech: Methanosarcina barkeri ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗