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Methane dynamics regulated by microbial community response to permafrost thaw

Nature volume 514, pages 478481 (23 October 2014) | Download Citation


Permafrost contains about 50% of the global soil carbon1. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions2,3. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown3 and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ13C signature (10–15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden4,5 as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus ‘Methanoflorens stordalenmirensis6 is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models3,7. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

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Sequence Read Archive

Data deposits

Amplicon sequencing data are deposited in the NCBI Sequence Read Archive with accession number SRP042265.


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We thank the Abisko Scientific Research Station for infrastructure and logistical support; T. Logan and N. Rakos for their assistance in the field; and S. Wofsy and S. Frolking for feedback on a draft of this paper. This work was supported by the US Department of Energy Office of Biological and Environmental Research (award DE-SC0004632), and by the University of Arizona Technology and Research Initiative Fund, through the Water, Environmental and Energy Solutions Initiative. R.M. was supported by an Australian Postgraduate Award Scholarship.

Author information

Author notes

    • Carmody K. McCalley
    •  & Rhiannon Mondav

    Present addresses: Earth Systems Research Center, University of New Hampshire, Durham, New Hampshire 03824, USA (C.K.M.); Department of Ecology and Genetics, Uppsala University, Uppsala 75 236, Sweden (R.M.).


  1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA

    • Carmody K. McCalley
    • , Richard A. Wehr
    •  & Scott R. Saleska
  2. Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Queensland, Australia

    • Ben J. Woodcroft
    • , Rhiannon Mondav
    •  & Gene W. Tyson
  3. Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida 32306, USA

    • Suzanne B. Hodgkins
    •  & Jeffrey P. Chanton
  4. Department of Soil, Water and Environmental Science, University of Arizona, Tucson, Arizona 85721, USA

    • Eun-Hae Kim
    •  & Virginia I. Rich
  5. Department of Geological Sciences, Stockholm University, Stockholm 106 91, Sweden

    • Patrick M. Crill


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S.R.S., V.I.R., P.M.C., J.C. and G.W.T. designed the study. C.K.M., S.B.H., R.A.W., P.M.C., J.C. and S.R.S. designed and/or performed flux/porewater/isotope measurements and laboratory incubations. C.K.M., B.J.W., R.M., E.-H.K., S.R.S., V.I.R. and G.W.T. designed and/or performed analyses integrating bioinformatics and biogeochemistry. C.K.M., V.I.R. and S.R.S. wrote the paper in consultation with B.J.W., S.B.H., J.C., P.M.C., E.-H.K., R.M. and G.W.T.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Carmody K. McCalley or Scott R. Saleska.

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  1. 1.

    Supplementary Data

    Operational taxonomic unit (OTU) table from 16S rRNA gene amplicon analysis. Each row represents an OTU. The first set of columns show the number of that 16S rRNA gene amplicon found in each sample. The rightmost columns show the taxonomy of that OTU predicted with BLAST. The samples presented in this study represent a subset of a larger sampling campaign (eg. Mondav et al 2014) therefore not all OTU's identified in the larger sample-set are present in this table.

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