Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

Katherine Duchesneau; Borja Aldeguer-Riquelme; Caitlin Petro; Ghiwa Makke; Madison Green; Malak Tfaily; Rachel Wilson; Spencer W. Roth; Eric R. Johnston; Laurel A. Kluber; Christopher W. Schadt; Jesse B. Trejo; Stephen J. Callister; Samuel O. Purvine; Jeffrey P. Chanton; Paul J. Hanson; Susannah Tringe; Emiley Eloe-Fadrosh; Tijana Glavina del Rio; Konstantinos T. Konstantinidis; Joel E. Kostka

doi:10.1038/s41467-025-61664-7

Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

Katherine Duchesneau, Borja Aldeguer-Riquelme, Caitlin Petro, Ghiwa Makke, Madison Green, Malak Tfaily, Rachel Wilson, Spencer W. Roth, Eric R. Johnston, Laurel A. Kluber, Christopher W. Schadt, Jesse B. Trejo, Stephen J. Callister, Samuel O. Purvine, Jeffrey P. Chanton, Paul J. Hanson, Susannah Tringe, Emiley Eloe-Fadrosh, Tijana Glavina del Rio, Konstantinos T. KonstantinidisJoel E. Kostka

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Abstract

The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.

Original language	English
Article number	6869
Journal	Nature Communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-61664-7
State	Published - Dec 2025

Funding

We are thankful to the editor and reviewers for their attentive and considerate comments. This study was funded by the Office of Biological and Environmental Research, Terrestrial Ecosystem Science Program and Genomic Science programs, under US Department of Energy (DOE) Contract DE-SC0023297 (JEK). The work (proposal: 10.46936/10.25585/60001027) conducted by the U.S. Department of Energy Joint Genome Institute ( https://ror.org/04xm1d337 ), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. A portion of this research was performed on a project award ( https://doi.org/10.46936/sthm.proj.2016.49279/60005943 ) from the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The SPRUCE experiment is funded by the Biological and Environmental Research program in the U.S. Department of Energy’s Office of Science. We also acknowledge the important SPRUCE onsite contributions made by W. Robert Nettles and Jeff Riggs who managed and sustained the SPRUCE experimental and warming treatments, and environmental monitoring systems. We would also like to acknowledge Karl K. Weitz from the Biological Sciences Division at PNNL for running the proteomic samples on the mass spectrometer.

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Duchesneau, K., Aldeguer-Riquelme, B., Petro, C., Makke, G., Green, M., Tfaily, M., Wilson, R., Roth, S. W., Johnston, E. R., Kluber, L. A., Schadt, C. W., Trejo, J. B., Callister, S. J., Purvine, S. O., Chanton, J. P., Hanson, P. J., Tringe, S., Eloe-Fadrosh, E., Glavina del Rio, T., ... Kostka, J. E. (2025). Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter. Nature Communications, 16(1), Article 6869. https://doi.org/10.1038/s41467-025-61664-7

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title = "Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter",

abstract = "The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7\% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.",

author = "Katherine Duchesneau and Borja Aldeguer-Riquelme and Caitlin Petro and Ghiwa Makke and Madison Green and Malak Tfaily and Rachel Wilson and Roth, \{Spencer W.\} and Johnston, \{Eric R.\} and Kluber, \{Laurel A.\} and Schadt, \{Christopher W.\} and Trejo, \{Jesse B.\} and Callister, \{Stephen J.\} and Purvine, \{Samuel O.\} and Chanton, \{Jeffrey P.\} and Hanson, \{Paul J.\} and Susannah Tringe and Emiley Eloe-Fadrosh and \{Glavina del Rio\}, Tijana and Konstantinidis, \{Konstantinos T.\} and Kostka, \{Joel E.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2025.",

year = "2025",

month = dec,

doi = "10.1038/s41467-025-61664-7",

language = "English",

volume = "16",

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Duchesneau, K, Aldeguer-Riquelme, B, Petro, C, Makke, G, Green, M, Tfaily, M, Wilson, R, Roth, SW, Johnston, ER, Kluber, LA, Schadt, CW, Trejo, JB, Callister, SJ, Purvine, SO, Chanton, JP, Hanson, PJ, Tringe, S, Eloe-Fadrosh, E, Glavina del Rio, T, Konstantinidis, KT & Kostka, JE 2025, 'Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter', Nature Communications, vol. 16, no. 1, 6869. https://doi.org/10.1038/s41467-025-61664-7

TY - JOUR

T1 - Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

AU - Duchesneau, Katherine

AU - Aldeguer-Riquelme, Borja

AU - Petro, Caitlin

AU - Makke, Ghiwa

AU - Green, Madison

AU - Tfaily, Malak

AU - Wilson, Rachel

AU - Roth, Spencer W.

AU - Johnston, Eric R.

AU - Kluber, Laurel A.

AU - Schadt, Christopher W.

AU - Trejo, Jesse B.

AU - Callister, Stephen J.

AU - Purvine, Samuel O.

AU - Chanton, Jeffrey P.

AU - Hanson, Paul J.

AU - Tringe, Susannah

AU - Eloe-Fadrosh, Emiley

AU - Glavina del Rio, Tijana

AU - Konstantinidis, Konstantinos T.

AU - Kostka, Joel E.

PY - 2025/12

Y1 - 2025/12

N2 - The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.

AB - The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.

UR - https://www.scopus.com/pages/publications/105011766738

U2 - 10.1038/s41467-025-61664-7

DO - 10.1038/s41467-025-61664-7

M3 - Article

C2 - 40715043

AN - SCOPUS:105011766738

SN - 2041-1723

VL - 16

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 6869

ER -

Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter

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