Natural wetland sediment microbial and viral communities from the Prairie Pothole Region of North America, curated around genome-resolved metagenomic evidence for high-rate sulfur and carbon cycling. The study recovered sulfate-reduction marker genes, candidate sulfate-reducing genomes, methanogenesis marker genes, putative methanogen genomes, and abundant novel viral populations predicted to target dominant sulfate reducers and methanogens. The community is DOE-relevant because DNA sequencing and analysis were conducted by the DOE Joint Genome Institute and because the system links wetland methane emissions, sulfate reduction, carbon mineralization, and virus-host controls.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Prairie Pothole wetland sediment microbial community — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
SYNTROPHIC_PARTNER
|
N/A |
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| Prairie Pothole candidate sulfate reducers — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
|
COMMON |
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| Prairie Pothole methanogens — ontology label: Archaea | NCBITaxon:2157 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
PRIMARY_PRODUCER
|
COMMON |
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| Prairie Pothole wetland sediment viruses — ontology label: Viruses | NCBITaxon:10239 · TaxonMech · TraitMech | COMMON | |
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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.
Diverse Sulfate-Reduction Guild
Candidate sulfate-reducer marker genes and MAGs support diverse genomic potential. PARTIAL: predicted donor use and reaction direction are not measured fluxes or experimentally confirmed sulfate reduction for each genome.
Participating Taxa: Prairie Pothole candidate sulfate reducers
Metabolites: sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech), methanol (CHEBI:17790 · MediaIngredientMech · CMMMech), ethanol (CHEBI:16236 · MediaIngredientMech · CMMMech)
Biological Processes:
- sulfate reduction (GO:0019420 · PathwayMech)
- organic substance catabolic process (GO:0009056 · PathwayMech)
HYPOTHESIZED: metabolic versatility may allow sulfate-reducing guilds to occupy different sediment niches and contribute to high cycling rates; substrate partitioning and its effect on ecosystem rates were not experimentally isolated.
Evidence
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PMID:30086797 - SUPPORT (COMPUTATIONAL)"recovered 162 dsrA and 206 dsrD sequences"
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PMID:30086797 - SUPPORT (COMPUTATIONAL)"utilizing a wide variety of electron donors, such as methanol and other alcohols"
Alcohol-Linked Methanogenesis Potential
HYPOTHESIZED: methanogen markers, putative alcohol dehydrogenases and porewater alcohols suggest alcohol-fueled methanogenesis. These findings do not identify an interspecies producer-to-consumer transfer route or quantify its contribution.
Participating Taxa: Prairie Pothole methanogens
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), ethanol (CHEBI:16236 · MediaIngredientMech · CMMMech), carbon dioxide (CHEBI:16526 · MediaIngredientMech · CMMMech)
Biological Processes:
- methanogenesis (GO:0015948 · PathwayMech)
Evidence
-
PMID:30086797 - SUPPORT (COMPUTATIONAL)"identified 37 mcrA sequences spanning five orders"
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PMID:30086797 - SUPPORT (COMPUTATIONAL)"these alcohols may drive a significant fraction of methanogenesis"
Predicted Viral Links to Sulfate Reducers and Methanogens
Metagenomic analyses predict virus-host links. HYPOTHESIZED: infection could affect these guilds, but host predictions can be false positives and do not establish current lysis or its effect on sulfur and carbon cycling.
Participating Taxa: Prairie Pothole candidate sulfate reducers, Prairie Pothole methanogens, Prairie Pothole wetland sediment viruses
Biological Processes:
- virus-host interaction (GO:0044003 · PathwayMech)
HYPOTHESIZED: host lysis may open niche space and release substrates, potentially changing diversity and cycling. Host suppression and substrate release could have opposing effects, so this existing direction has no established net sign.
Evidence
-
PMID:30086797 - SUPPORT (COMPUTATIONAL)"viral populations were predicted to target dominant sulfate reducers and methanogens"
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PMID:30086797 - SUPPORT (COMPUTATIONAL)"approximately 80% of viral populations being unclassified"
Niche Differentiation In Heterogeneous Wetland Sediment
HYPOTHESIZED: diversity, metabolic versatility, local geochemistry and viral activity may jointly explain heterogeneous niches and high cycling rates. The study does not resolve their causal contributions.
Participating Taxa: Prairie Pothole wetland sediment microbial community, Prairie Pothole candidate sulfate reducers, Prairie Pothole methanogens, Prairie Pothole wetland sediment viruses
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech), sulfate (CHEBI:16189 · MediaIngredientMech · CMMMech)
Biological Processes:
- methanogenesis (GO:0015948 · PathwayMech)
- sulfate reduction (GO:0019420 · PathwayMech)
Evidence
-
PMID:30086797 - SUPPORT (COMPUTATIONAL)"diversity is likely key to extremely high rates of methanogenesis and sulfate reduction"
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PMID:30086797 - SUPPORT (COMPUTATIONAL)"modulating carbon and sulfur cycling in this ecosystem"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Prairie Pothole sulfur-cycling metagenomes
DOE JGI Genome Portal project for raw reads, trimmed reads, assemblies, and quality-control reports from "Seasonal Sulfur Cycling as a Control on Methane Flux in Carbon-Rich Prairie Pothole Sediment Ecosystems." |
METAGENOMICS | OTHER | JGI proposal ID 2025 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which predicted activities and viral effects control measured ecosystem rates?
Retain the genomic findings and both proposed directions. Candidate genomes do not guarantee sulfate-reduction direction; alcohol use and viral host links remain inferred. Viral suppression versus release of labile substrates could lower or raise cycling rates. Exact activities, lysis and net effects need experiments; no new arrows were added.
Attaches to: ecological_interactions#Diverse Sulfate-Reduction Guild, ecological_interactions#Alcohol-Linked Methanogenesis Potential, ecological_interactions#Predicted Viral Links to Sulfate Reducers and Methanogens, ecological_interactions#Niche Differentiation In Heterogeneous Wetland Sediment
2 evidence item(s)
these alcohols may drive a significant fraction of methanogenesis
Supports the alcohol-linked methanogenesis hypothesis in this ecosystem.
viral populations were predicted to target dominant sulfate reducers and methanogens
Supports virus-host targeting of key sulfur- and methane-cycling guilds.
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
Primary publication for Prairie Pothole wetland sulfur-carbon virus-host community
PubMed record for the Microbiome paper reporting viral and metabolic controls on high rates of microbial sulfur and carbon cycling in Prairie Pothole wetland ecosystems. |
OTHER | PMID:30086797 |
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DOI landing page
DOI for the open-access Microbiome publication. |
OTHER | doi:10.1186/s40168-018-0522-4 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Prairie Pothole wetland sediment | North American Prairie Pothole Region | N/A |
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| High sulfate reduction | high sulfate reduction rates in wetland sediment | N/A |
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| Methane emissions | high wetland methane flux | N/A |
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| Dissolved organic carbon and sulfur species | high pore-water sulfur species and dissolved organic carbon | N/A |
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