DOE OSTI · 3382668
Mapping the soil microbiome functions shaping wetland methane emissions
Abstract
Accounting for only 8% of Earth’s land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.
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Borton, Mikayla A. [Colorado State Univ., Fort Collins, CO (United States)] (ORCID:0000000180374253), Oliverio, Angela M. [Colorado State Univ., Fort Collins, CO (United States); Syracuse Univ., NY (United States)], Narrowe, Adrienne B. [Colorado State Univ., Fort Collins, CO (United States)], Villa, Jorge A. [Univ. of Louisiana, Lafayette, LA (United States)], Rinke, Christian [Univ. Innsbruck (Austria)], Hoyt, David W. [Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)], Liu, Pengfei [Colorado State Univ., Fort Collins, CO (United States); Lanzhou Univ. (China)], McGivern, Bridget B. [Colorado State Univ., Fort Collins, CO (United States)] (ORCID:0000000190230018), Bechtold, Emily K. [Colorado State Univ., Fort Collins, CO (United States)], Ellenbogen, Jared B. [Colorado State Univ., Fort Collins, CO (United States)] (ORCID:0000000316929044), Daly, Rebecca A. [Colorado State Univ., Fort Collins, CO (United States)], Smith, Garrett J. [The Ohio State Univ., Columbus, OH (United States)] (ORCID:0000000210145102), Angle, Jordan C. [The Ohio State Univ., Columbus, OH (United States)] (ORCID:0000000232605851), Flynn, Rory M. [Colorado State Univ., Fort Collins, CO (United States)], Freiburger, Andrew P. [Argonne National Laboratory (ANL), Argonne, IL (United States)] (ORCID:000000027288535X), Louie, Katherine B. [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)], Stemple, Brooke [Colorado State Univ., Fort Collins, CO (United States)], Northen, Trent R. [USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)] (ORCID:0000000184043259), Henry, Christopher [Argonne National Laboratory (ANL), Argonne, IL (United States)], Miller, Christopher S. [Univ. of Colorado, Boulder, CO (United States)] (ORCID:0000000294488144), Morin, Timothy H. [State Univ. of New York (SUNY), Syracuse, NY (United States)], Bohrer, Gil [The Ohio State Univ., Columbus, OH (United States)] (ORCID:0000000292099540), Wrighton, Kelly C. [Colorado State Univ., Fort Collins, CO (United States)] (ORCID:0000000304344217). 2026-06-23. Mapping the soil microbiome functions shaping wetland methane emissions. https://doi.org/10.1128/msystems.00680-25
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