IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-61664-7.html
   My bibliography  Save this article

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

Author

Listed:
  • Katherine Duchesneau

    (Georgia Institute of Technology)

  • Borja Aldeguer-Riquelme

    (Georgia Institute of Technology)

  • Caitlin Petro

    (Georgia Institute of Technology)

  • Ghiwa Makke

    (University of Arizona)

  • Madison Green

    (Georgia Institute of Technology)

  • Malak Tfaily

    (University of Arizona)

  • Rachel Wilson

    (Florida State University)

  • Spencer W. Roth

    (Oak Ridge National Laboratory)

  • Eric R. Johnston

    (Oak Ridge National Laboratory)

  • Laurel A. Kluber

    (Oak Ridge National Laboratory)

  • Christopher W. Schadt

    (Oak Ridge National Laboratory)

  • Jesse B. Trejo

    (US Department of Energy)

  • Stephen J. Callister

    (US Department of Energy)

  • Samuel O. Purvine

    (US Department of Energy)

  • Jeffrey P. Chanton

    (Florida State University)

  • Paul J. Hanson

    (Oak Ridge National Laboratory)

  • Susannah Tringe

    (Lawrence Berkeley National Laboratory)

  • Emiley Eloe-Fadrosh

    (Lawrence Berkeley National Laboratory)

  • Tijana Glavina del Rio

    (Lawrence Berkeley National Laboratory)

  • Konstantinos T. Konstantinidis

    (Georgia Institute of Technology)

  • Joel E. Kostka

    (Georgia Institute of Technology)

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.

Suggested Citation

  • 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. Sch, 2025. "Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61664-7
    DOI: 10.1038/s41467-025-61664-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-61664-7
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-025-61664-7?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Himel Mallick & Ali Rahnavard & Lauren J McIver & Siyuan Ma & Yancong Zhang & Long H Nguyen & Timothy L Tickle & George Weingart & Boyu Ren & Emma H Schwager & Suvo Chatterjee & Kelsey N Thompson & Je, 2021. "Multivariable association discovery in population-scale meta-omics studies," PLOS Computational Biology, Public Library of Science, vol. 17(11), pages 1-27, November.
    2. A. M. Hopple & R. M. Wilson & M. Kolton & C. A. Zalman & J. P. Chanton & J. Kostka & P. J. Hanson & J. K. Keller & S. D. Bridgham, 2020. "Massive peatland carbon banks vulnerable to rising temperatures," Nature Communications, Nature, vol. 11(1), pages 1-7, December.
    3. Chirag Jain & Luis M. Rodriguez-R & Adam M. Phillippy & Konstantinos T. Konstantinidis & Srinivas Aluru, 2018. "High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    4. Stefan Dyksma & Michael Pester, 2023. "Publisher Correction: Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium," Nature Communications, Nature, vol. 14(1), pages 1-1, December.
    5. Martin Steinegger & Johannes Söding, 2018. "Clustering huge protein sequence sets in linear time," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    6. Carmody K. McCalley & Ben J. Woodcroft & Suzanne B. Hodgkins & Richard A. Wehr & Eun-Hae Kim & Rhiannon Mondav & Patrick M. Crill & Jeffrey P. Chanton & Virginia I. Rich & Gene W. Tyson & Scott R. Sal, 2014. "Methane dynamics regulated by microbial community response to permafrost thaw," Nature, Nature, vol. 514(7523), pages 478-481, October.
    7. Rhiannon Mondav & Ben J. Woodcroft & Eun-Hae Kim & Carmody K. McCalley & Suzanne B. Hodgkins & Patrick M. Crill & Jeffrey Chanton & Gregory B. Hurst & Nathan C. VerBerkmoes & Scott R. Saleska & Philip, 2014. "Discovery of a novel methanogen prevalent in thawing permafrost," Nature Communications, Nature, vol. 5(1), pages 1-7, May.
    8. Valero-Mora, Pedro M., 2010. "ggplot2: Elegant Graphics for Data Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 35(b01).
    9. Ben J. Woodcroft & Caitlin M. Singleton & Joel A. Boyd & Paul N. Evans & Joanne B. Emerson & Ahmed A. F. Zayed & Robert D. Hoelzle & Timothy O. Lamberton & Carmody K. McCalley & Suzanne B. Hodgkins & , 2018. "Genome-centric view of carbon processing in thawing permafrost," Nature, Nature, vol. 560(7716), pages 49-54, August.
    10. Stefan Dyksma & Michael Pester, 2023. "Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    11. Francesco Asnicar & Andrew Maltez Thomas & Francesco Beghini & Claudia Mengoni & Serena Manara & Paolo Manghi & Qiyun Zhu & Mattia Bolzan & Fabio Cumbo & Uyen May & Jon G. Sanders & Moreno Zolfo & Evg, 2020. "Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Brooke C. Wilson & Michele Zuppi & José G. B. Derraik & Benjamin B. Albert & Ry Y. Tweedie-Cullen & Karen S. W. Leong & Kathryn L. Beck & Tommi Vatanen & Justin M. O’Sullivan & Wayne S. Cutfield, 2025. "Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    2. Emily K. Bechtold & Jared B. Ellenbogen & Jorge A. Villa & Djennyfer K. Melo Ferreira & Angela M. Oliverio & Joel E. Kostka & Virginia I. Rich & Ruth K. Varner & Sheel Bansal & Eric J. Ward & Gil Bohr, 2025. "Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    3. Minghui Cheng & Yingjie Xu & Xiao Cui & Xin Wei & Yundi Chang & Jun Xu & Cheng Lei & Lei Xue & Yifan Zheng & Zhang Wang & Lingtong Huang & Min Zheng & Hong Luo & Yuxin Leng & Chao Jiang, 2024. "Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    4. Jean-Sebastien Gounot & Minghao Chia & Denis Bertrand & Woei-Yuh Saw & Aarthi Ravikrishnan & Adrian Low & Yichen Ding & Amanda Hui Qi Ng & Linda Wei Lin Tan & Yik-Ying Teo & Henning Seedorf & Niranjan, 2022. "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Jiandui Mi & Xiaoping Jing & Chouxian Ma & Fuyu Shi & Ze Cao & Xin Yang & Yiwen Yang & Apurva Kakade & Weiwei Wang & Ruijun Long, 2024. "A metagenomic catalogue of the ruminant gut archaeome," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Xinwei Song & Yiling Wang & Youjing Wang & Kankan Zhao & Di Tong & Ruichuan Gao & Xiaofei Lv & Dedong Kong & Yunjie Ruan & Mengcen Wang & Xianjin Tang & Fangbai Li & Yongming Luo & Yongguan Zhu & Jian, 2025. "Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    7. Karen D. Corbin & Elvis A. Carnero & Blake Dirks & Daria Igudesman & Fanchao Yi & Andrew Marcus & Taylor L. Davis & Richard E. Pratley & Bruce E. Rittmann & Rosa Krajmalnik-Brown & Steven R. Smith, 2023. "Host-diet-gut microbiome interactions influence human energy balance: a randomized clinical trial," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    8. Maren Jenrich & Michael Angelopoulos & Susanne Liebner & Claire Treat & Christian Knoblauch & Sizhong Yang & Guido Grosse & Fiona Giebeler & Loeka L. Jongejans & Mikhail Grigoriev & Jens Strauss, 2025. "Greenhouse Gas Production and Microbial Response During the Transition From Terrestrial Permafrost to a Marine Environment," Permafrost and Periglacial Processes, John Wiley & Sons, vol. 36(1), pages 63-82, January.
    9. Congmin Zhu & Linwei Wu & Daliang Ning & Renmao Tian & Shuhong Gao & Bing Zhang & Jianshu Zhao & Ya Zhang & Naijia Xiao & Yajiao Wang & Mathew R. Brown & Qichao Tu & Feng Ju & George F. Wells & Jianhu, 2025. "Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    10. Thomas C. A. Hitch & Johannes M. Masson & Charlie Pauvert & Johanna Bosch & Selina Nüchtern & Nicole S. Treichel & Marko Baloh & Soheila Razavi & Afrizal Afrizal & Ntana Kousetzi & Andrea M. Aguirre &, 2025. "HiBC: a publicly available collection of bacterial strains isolated from the human gut," Nature Communications, Nature, vol. 16(1), pages 1-20, December.
    11. Sudakow, Ivan & Savenkova, Elena & Kondrashov, Dmitri & Vakulenko, Sergey A. & Sashina, Elena, 2023. "Diverse soil microbial communities may mitigate climate system bifurcation," Chaos, Solitons & Fractals, Elsevier, vol. 177(C).
    12. Bin Ma & Caiyu Lu & Yiling Wang & Jingwen Yu & Kankan Zhao & Ran Xue & Hao Ren & Xiaofei Lv & Ronghui Pan & Jiabao Zhang & Yongguan Zhu & Jianming Xu, 2023. "A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    13. Guillermo Guerrero-Egido & Adrian Pintado & Kevin M. Bretscher & Luisa-Maria Arias-Giraldo & Joseph N. Paulson & Herman P. Spaink & Dennis Claessen & Cayo Ramos & Francisco M. Cazorla & Marnix H. Mede, 2024. "bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    14. Zhen Li & William J. Riley & Gianna L. Marschmann & Ulas Karaoz & Ian A. Shirley & Qiong Wu & Nicholas J. Bouskill & Kuang-Yu Chang & Patrick M. Crill & Robert F. Grant & Eric King & Scott R. Saleska , 2025. "A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    15. Juan Pedro Rodríguez-López & Chihua Wu & Tatiana A. Vishnivetskaya & Julian B. Murton & Wenqiang Tang & Chao Ma, 2022. "Permafrost in the Cretaceous supergreenhouse," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    16. Ruairi C. Robertson & Thaddeus J. Edens & Lynnea Carr & Kuda Mutasa & Ethan K. Gough & Ceri Evans & Hyun Min Geum & Iman Baharmand & Sandeep K. Gill & Robert Ntozini & Laura E. Smith & Bernard Chasekw, 2023. "The gut microbiome and early-life growth in a population with high prevalence of stunting," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    17. Bong Gu Kang & Kyung-Min Seo & Tag Gon Kim, 2018. "Communication Analysis of Network-Centric Warfare via Transformation of System of Systems Model into Integrated System Model Using Neural Network," Complexity, Hindawi, vol. 2018, pages 1-16, June.
    18. Hidenori Shimizu & Junki Miyamoto & Keiko Hisa & Ryuji Ohue-Kitano & Hiromi Takada & Mayu Yamano & Akari Nishida & Daiki Sasahara & Yuki Masujima & Keita Watanabe & Shota Nishikawa & Sakura Takahashi , 2025. "Sucrose-preferring gut microbes prevent host obesity by producing exopolysaccharides," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    19. Emily A. Kaelin & Caroline Mitchell & Jaime Soria & Alberto La Rosa & Eduardo Ticona & Robert W. Coombs & Lisa M. Frenkel & Marta E. Bull & Efrem S. Lim, 2025. "Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    20. Shanlin Ke & Scott T. Weiss & Yang-Yu Liu, 2022. "Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61664-7. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.