Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere1. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils2,3,4 and a rapid shift in functional gene composition during short-term thaw experiments3. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales5,6. Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.
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Sequence Read Archive
We thank R. Hettich and the Organic and Biological Mass Spectrometry group at Oak Ridge National Laboratory for access to mass spectrometry instrumentation. M. Haw, K. Li, K. Chavarria and R. Lamendella are acknowledged for help with pre-processing frozen samples. We thank K. Billis for help with RNA sequence preprocessing. This work was partly supported by the Director, Office of Science, Office of Biological and Environmental Research, Climate and Environmental Science Division, of the US Department of Energy, Terrestrial Ecosystem Science-Scientific Focus Area (TES-SFA), through a Community Sequencing Project at the DOE Joint Genome Institute (JGI CSP - 152) and by a Lawrence Berkeley National Laboratory Laboratory Directed Research & Development (LDRD) grant, all under contract number DE-AC02-05CH11231; by the Pacific Northwest National Laboratory under contract number DE-AC05-76RL01830; and by the Danish National Research Foundation (CENPERM DNRF100). The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. Additional funding and considerable logistic support were provided by the Bonanza Creek Long-Term Ecological Research Program, which is jointly funded by National Science Foundation (DEB 1026415) and the US Department of Agriculture Forest Service, Pacific Northwest Research Station (PNW01-JV112619320-16). Support was also received from the US Geological Survey Climate R&D Program and Alaska Climate Science Center. J.Hu. was supported by Academy of Finland grant number 135669.
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Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic
Journal of Microbiology (2019)