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Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community

Community ID CommunityMech:000255
Ecological State PERTURBED
Environment freshwater wetland soil — ontology label: wetland area
ENVO:00000043 · HabitatMech ↗

Freshwater wetland soil microbial microcosms incubated under anoxic non-sulfate, anoxic sulfate-addition, oxic non-sulfate, and oxic sulfate-addition conditions to resolve how climate-linked oxygen and sulfate exposures alter methane and carbon dioxide emissions. The study integrated geochemical measurements, proteogenomics, metaproteomics, and stoichiometric modeling to identify altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Sulfate exposure reduced methane production, oxygen shifted greenhouse gas emissions from CH4 toward CO2, and the combined exposure resembled oxygen exposure alone.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
wetland soil microbial community — ontology label: cellular organisms NCBITaxon:131567 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER SYNTROPHIC_PARTNER
N/A
  • PMID:38961111 - SUPPORT (COMPUTATIONAL)
    "geochemical analysis, proteogenomics, and stoichiometric modeling"
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "wetland soil may be exposed to oxygen (O2) during droughts"
wetland soil methanogenic archaea — ontology label: Archaea NCBITaxon:2157 · TaxonMech · TraitMech
SYNTROPHIC_PARTNER PRIMARY_PRODUCER
N/A
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "hydrogenotrophic methanogenesis more suppressed than acetoclastic"
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "Elevated SO42- reduced CH4 emissions"
wetland soil bacterial guilds — ontology label: Bacteria NCBITaxon:2 · TaxonMech · TraitMech
PRIMARY_DEGRADER SECONDARY_FERMENTER CROSS_FEEDER
N/A
  • PMID:38961111 - SUPPORT (COMPUTATIONAL)
    "identified altered microbial guilds and metabolic processes"
  • PMID:38961111 - SUPPORT (COMPUTATIONAL)
    "converts lactate and SO42- to produce acetate, H2S, and CO2"

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 Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for competition. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Competition
Other

Sulfate Suppression Of Methanogenesis

COMPETITION

Sulfate addition reduced methane accumulation in the wetland microcosms. PARTIAL: metaproteomic markers and fitted fluxes support stronger suppression of hydrogenotrophic than acetoclastic methanogenesis and competition between sulfate-reducing bacterial and methanogenic guilds. This does not measure a universal Bacteria-to-Archaea antagonism or establish direct acetate competition with acetoclastic methanogens.

Source Taxon: wetland soil bacterial guilds

Target Taxon: wetland soil methanogenic archaea

Participating Taxa: wetland soil methanogenic archaea, wetland soil bacterial guilds

Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38961111 - SUPPORT (IN_VITRO)
    "Elevated SO42- reduced CH4 emissions"
  • PMID:38961111 - PARTIAL (COMPUTATIONAL)
    "hydrogenotrophic methanogenesis more suppressed than acetoclastic"
  • PMID:38961111 - PARTIAL (COMPUTATIONAL)
    "SRB outcompeting hydrogenotrophic methanogens"

Oxygen Shift From Methane To Carbon Dioxide

Oxygen-treated soil microcosms accumulated less methane and more carbon dioxide than the anoxic baseline. The combined oxygen-plus-sulfate treatment showed a similar overall gas pattern to oxygen alone, not identity of all microbial responses. This abiotic treatment effect is not an organism-to-organism niche-partitioning interaction; residual methane in the measurements must not be equated with zero production.

Metabolites: dioxygen (CHEBI:15379 · MediaIngredientMech · CMMMech), methane (CHEBI:16183 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38961111 - SUPPORT (IN_VITRO)
    "Elevated O2 shifted the greenhouse gas emissions from CH4 to CO2"
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone"

Modeled lactate-sulfate carbon and sulfur subnetwork

PARTIAL: a nine-reaction stoichiometric model fitted to measured metabolite amounts supports sulfidogenic lactate oxidation producing acetate, H2S and CO2 in the oxic sulfate treatment. Fitted fluxes and concordant protein abundances are not directly measured interspecies transfer or unique donor-recipient cross-feeding. Oxygen also suppressed sulfate-reduction activity relative to anoxic sulfate treatment, so this subnetwork is not evidence of universally enhanced sulfate reduction under oxygen.

Source Taxon: wetland soil bacterial guilds

Participating Taxa: wetland soil bacterial guilds

Metabolites: lactate (CHEBI:24996 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), hydrogen sulfide (CHEBI:16136 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:38961111 - PARTIAL (COMPUTATIONAL)
    "Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism"
  • PMID:38961111 - PARTIAL (COMPUTATIONAL)
    "converts lactate and SO42- to produce acetate, H2S, and CO2"
  • PMID:38961111 - PARTIAL (COMPUTATIONAL)
    "The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate, H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation."

Associated Datasets

Dataset Type Repository Accession
Wetland oxygen-sulfate metagenome BioProject
NCBI BioProject for metagenome data from the wetland soil incubation treated with sulfate and oxygen. 		METAGENOMICS NCBI_BIOPROJECT PRJNA1112840
Wetland oxygen-sulfate metaproteome dataset
ProteomeXchange/PRIDE dataset linked to the wetland soil incubation treated with sulfate and oxygen. 		METAPROTEOMICS OTHER PXD047453

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which guild-resolved transfers and causal dependencies are uniquely established beyond the fitted wetland model?

Measured standing metabolites and endpoint metaproteomes constrain a nine-reaction model but do not isolate donor-recipient fluxes or establish the two removed response-to-model arrows. Source results/discussion also differ in statements about additivity and some oxygen-linked routes, so no stronger route-specific or universal-zero conclusion is added. Model-code, raw-data and perturbation review would be needed to resolve those dependencies.

Attaches to: ecological_interactions#Sulfate Suppression Of Methanogenesis, ecological_interactions#Oxygen Shift From Methane To Carbon Dioxide, ecological_interactions#Modeled lactate-sulfate carbon and sulfur subnetwork

1 evidence item(s)
PMID:38961111

The fluxes of these reactions were fitted to the cumulative amounts of acetate, lactate, butyrate, H2, CO2, CH4, and H2S produced or consumed over the 30 days of incubation.

External Resources

Name Repository Resource ID
Primary publication for wetland oxygen-sulfate greenhouse gas microcosms
PubMed record for the npj Biofilms and Microbiomes article reporting metaproteomics-informed stoichiometric modeling of wetland microbial community responses to oxygen and sulfate exposure. 		OTHER PMID:38961111
  • PMID:38961111 - SUPPORT (OTHER)
    "Metaproteomics-informed stoichiometric modeling reveals the responses"
DOI landing page
DOI landing page for the npj Biofilms and Microbiomes publication. 		OTHER doi:10.1038/s41522-024-00525-5
  • PMID:38961111 - SUPPORT (OTHER)
    "doi: 10.1038/s41522-024-00525-5"

Environmental Factors

Factor Value Unit
Oxygen exposure oxic microcosm treatment N/A
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "wetland soil may be exposed to oxygen (O2) during droughts"
Sulfate exposure elevated sulfate microcosm treatment N/A
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "to sulfate (SO42-) as a result of sea level rise"
Greenhouse gas emissions methane and carbon dioxide N/A
  • PMID:38961111 - SUPPORT (IN_VITRO)
    "microbial methane (CH4) and carbon dioxide (CO2) emissions"

Growth Media

freshwater wetland soil slurry, with sulfate and oxygen as the manipulated variables

Temperature 30 °C
Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
sulfate (added treatments only) · MediaIngredientMech 7.2 mM CHEBI:16189
dioxygen (oxic treatments only, as sterile air replacing half the gas phase) · MediaIngredientMech N/A N/A CHEBI:15379

Preparation notes: Cores were sealed air-tight on removal to preserve redox state and processed immediately. Bottles were filled inside an anaerobic chamber, preincubated five days at room temperature, then held at 30 C for 30 days. Four treatments dosed every two days: anoxic no-sulfate (S-O-), anoxic sulfate (S+O-, final ~7.2 mM), oxic no-sulfate (S-O+, half the gas phase replaced by sterile air) and oxic sulfate (S+O+). atmosphere is ANAEROBIC because that is the base condition the microcosms were built and held under; the oxic arms are a perturbation applied every two days, recorded in headspace_gas rather than by relabelling the whole record aerobic. No pH is reported.

Evidence

PMID:38961111

"Triplicate soil samples were collected from a seasonally flooded urban freshwater wetland connected to Lake Washington in Seattle, WA, USA (Coordinates: 47.642196oN, -122.296236oW) in May 2022"

PMID:38961111

"The cores were sealed air-tight upon removal from the natural habitat, to protect the redox state of samples. Samples were then transported to the lab on ice, for immediate processing."

PMID:38961111

"Microcosms were set up by filling 160 mL bottles with 40 g fresh sediment soil slurry in an anaerobic chamber. The chamber gas contained N2 : H2 (97:3)."

PMID:38961111

"All bottles were preincubated for five days at room temperature and then incubated at 30 °C for 30 days."

PMID:38961111

"Soil microcosms were divided into four groups, with each group receiving specific treatments every two days: anoxic non-sulfate-addition, anoxic sulfate-addition (resulting in a final SO42- concentration of approximately 7.2 mM), oxic non-sulfate-addition (where half of the gas phase was replaced by sterile air), and oxic sulfate-addition, which was treated with both SO42- and sterile air."

Cross-Mech Suite Links

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

HabitatMech: freshwater wetland soil ↗ TaxonMech: wetland soil microbial community ↗ TraitMech: wetland soil microbial community ↗ TaxonMech: wetland soil methanogenic archaea ↗ TraitMech: wetland soil methanogenic archaea ↗ TaxonMech: wetland soil bacterial guilds ↗ TraitMech: wetland soil bacterial guilds ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗