Abstract

The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from −10 to −2 °C or when freezing from −2 to −10 °C. In contrast, within a few days we observed changes when warming from −2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria—collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.

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Data availability

Complete OTU tables are available in the Supplementary datasheet. Sequence data generated in this study was deposited in the NCBI Sequence Read Archive and are accessible through accession number SRP124869.

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Acknowledgements

This work was supported by the Danish National Research Foundation (CENPERM DNRF100), Danish Geocenter for sequencing funding, Danish Council for Independent Research (DFF-4002-00274) and the EU MSC Action 675546: MicroArctic. The authors thank Pia Bach Jacobsen for help and technical support in the laboratory, Samuel Faucherre for sampling the soil core, and Annelise Kjøller for discussions on the fungal community changes. The authors would also like to thank Martin Asser Hansen for bioinformatics support.

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Affiliations

  1. Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark

    • Morten Schostag
    • , Anders Priemé
    •  & Carsten Suhr Jacobsen
  2. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    • Morten Schostag
    • , Anders Priemé
    • , Samuel Jacquiod
    • , Jakob Russel
    •  & Flemming Ekelund
  3. Geological Survey of Denmark and Greenland, Copenhagen, Denmark

    • Morten Schostag
    •  & Carsten Suhr Jacobsen
  4. INRA Dijon, UMR1347 Agroécologie, Dijon, France

    • Samuel Jacquiod
  5. Department of Environmental Science, Aarhus University, Roskilde, Denmark

    • Carsten Suhr Jacobsen

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https://doi.org/10.1038/s41396-019-0351-x