A multi-site terrestrial freshwater wetland microbial community synthesis curated around the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. The study integrates 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux measurements across nine wetlands to link microbial community structure, methane-cycling guilds, decomposition networks, and methane emissions. It identifies eight methane-cycling genera shared across wetlands, highlights wetland-specific metabolic interactions in marshes, and reports Methanoregula as a hub methanogen and predictor of methane flux. The record is DOE-relevant because the study was supported by DOE Office of Science BER awards and included metagenomic and metatranscriptomic sequencing at the DOE Joint Genome Institute.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| MUCC freshwater wetland microbial community — ontology label: cellular organisms | NCBITaxon:131567 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
SECONDARY_FERMENTER
SYNTROPHIC_PARTNER
|
N/A |
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| MUCC wetland methanogens — ontology label: Archaea | NCBITaxon:2157 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
PRIMARY_PRODUCER
|
COMMON |
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| Methanoregula | NCBITaxon:395331 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
PRIMARY_PRODUCER
|
COMMON |
|
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| MUCC wetland methanotrophs — ontology label: Bacteria | NCBITaxon:2 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
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.
Conserved Methane-Cycling Genera Across Wetlands
MUCC combines nine wetland sites; five high-emitting marsh and swamp sites share five methanogen and three methanotroph genera under the authors occupancy definition. Core means present in at least one sample at every site in this subset, not present in every sample or a demonstrated stable mutualistic consortium. The canonical whole-community aggregate and Archaea/Bacteria guild participants are contextual placeholders, not all eight resolved genera. Genus occupancy and relative abundance do not establish niche partitioning or metabolic dependence.
Participating Taxa: MUCC freshwater wetland microbial community, MUCC wetland methanogens, MUCC wetland methanotrophs
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Evidence
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PMID:39843444 - SUPPORT (COMPUTATIONAL)"identify eight methane-cycling genera shared across wetlands"
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PMID:39843444 - PARTIAL (COMPUTATIONAL)"Microorganisms drive methane cycling"
Wetland Methanogen Co-occurrence Networks
Positive Spearman genus co-occurrence networks used 12 late-season samples per site, four per depth category, at JLA, LA2, OWC, PPR P7 and PPR P8. JLA is a swamp despite shorthand marsh wording. Fewer methanogen-associated nodes and methanogen-methanotroph connections were associated with greater methane flux; whole-community network structure did not show the same relationship. MAG-derived metabolic categories were matched at genus level, providing potential cross-feeding interpretations rather than direct exchange measurements. Shared environmental responses, relative-abundance effects and incomplete genome coverage remain alternatives. Broad canonical guilds do not identify every network member or a directed donor-recipient pair.
Participating Taxa: MUCC wetland methanogens, MUCC wetland methanotrophs
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Evidence
-
PMID:39843444 - PARTIAL (COMPUTATIONAL)"wetland-specific metabolic interactions in marshes"
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PMID:39843444 - PARTIAL (COMPUTATIONAL)"low connections between methanogens and methanotrophs in high-emitting wetlands"
Methanoregula Hub Methanogen And Flux Predictor
Methanoregula was a core network member, and its fraction within methanogens predicted methane flux across nine sites; temperature plus this dominance measure improved the reported fit. These are cross-site associations, not evidence that removing or adding Methanoregula changes flux or that it is an obligate syntrophic hub. OWC MAG/genus transcription supplies an activity proxy, not methane-production flux. Methods describe 2018 transcriptomes and production estimates using 2015 flux/porewater inputs; temporal alignment needs reconciliation before treating the VIP analysis as a matched contemporaneous test. The single canonical participant identifies the focal genus, not its partners.
Participating Taxa: Methanoregula
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Evidence
-
PMID:39843444 - SUPPORT (COMPUTATIONAL)"Methanoregula emerged as a hub methanogen across networks"
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PMID:39843444 - SUPPORT (COMPUTATIONAL)"strong predictor of methane flux"
Methylotrophic Methanogenesis Potential
Some of 107 dereplicated Methanoregula MAGs encoded candidate methylotrophic machinery for methylated sulfides and methoxylated compounds alongside broadly conserved hydrogenotrophic potential. Genomic annotation, phylogenetic placement and synteny support metabolic potential, not confirmed substrate use, enzyme activity or pathway-specific methane flux in these wetlands. This does not establish methanol use by the curated genus or experimentally demonstrated niche partitioning. Physiological validation is needed to assign the proposed expanded substrate range.
Participating Taxa: Methanoregula
Metabolites: methane (CHEBI:16183 · MediaIngredientMech · CMMMech)
Evidence
-
PMID:39843444 - PARTIAL (COMPUTATIONAL)"functional potential for methylotrophic methanogenesis"
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PMID:39843444 - PARTIAL (COMPUTATIONAL)"highlighting the importance of this pathway"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
MUCC v2.0.0 Zenodo database
Zenodo archive for MUCC v2.0.0 processed MAGs, 16S rRNA tables, metatranscriptomic abundance tables, DRAM annotations, and analysis files. |
OTHER | ZENODO | 10.5281/zenodo.14532347 |
|
MUCC BioProject PRJNA330672
NCBI BioProject listed by the MUCC v2.0.0 Nature Communications data availability statement. |
OTHER | NCBI_BIOPROJECT | PRJNA330672 |
|
MUCC BioProject PRJNA1007388
NCBI BioProject listed by the MUCC v2.0.0 Nature Communications data availability statement. |
OTHER | NCBI_BIOPROJECT | PRJNA1007388 |
|
MUCC BioProject PRJNA216952
NCBI BioProject listed by the MUCC v2.0.0 Nature Communications data availability statement. |
OTHER | NCBI_BIOPROJECT | PRJNA216952 |
|
MUCC BioProject PRJNA638786
NCBI BioProject listed by the MUCC v2.0.0 Nature Communications data availability statement. |
OTHER | NCBI_BIOPROJECT | PRJNA638786 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which wetland associations correspond to causal metabolic exchange?
Retain four observations and zero arrows, preserving the prior three workflow-edge removals. Genus co-occurrence and MAG potential do not establish pairwise transfer or obligate syntrophy; flux prediction does not establish a perturbed driver. Validate candidate methylated-sulfide/methoxylated-compound use rather than substituting methanol. Temporal alignment of 2018 expression and 2015 modeled production, transcriptome counts and roster/metadata ambiguities remain under #1574. Complete primary main text read, not original figure pixels, separate supplements, raw data or executable models.
Attaches to: ecological_interactions#Conserved Methane-Cycling Genera Across Wetlands, ecological_interactions#Wetland Methanogen Co-occurrence Networks, ecological_interactions#Methanoregula Hub Methanogen And Flux Predictor, ecological_interactions#Methylotrophic Methanogenesis Potential
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
Primary publication for MUCC freshwater wetland methane networks
PubMed record for the Nature Communications paper describing MUCC v2.0.0 and metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands. |
OTHER | PMID:39843444 |
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DOI landing page
DOI for the Nature Communications publication. |
OTHER | doi:10.1038/s41467-025-56133-0 |
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USGS Publications Warehouse record
USGS Publications Warehouse record for the Nature Communications MUCC v2.0.0 wetland methane-cycling article. |
OTHER | USGS:70268258 |
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Wetland type | marsh, swamp, fen, and bog | N/A |
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| Annual methane flux | annual methane flux data | N/A |
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| High methane-emitting wetlands | high methane emission context | N/A |
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