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Front Microbiol. 2015 Apr 30;6:399. doi: 10.3389/fmicb.2015.00399. eCollection 2015.

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses.

Author information

1
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark ; Department of Biology, University of Copenhagen Copenhagen, Denmark.
2
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark.
3
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Geological Survey of Denmark and Greenland (GEUS) Copenhagen, Denmark ; Department of Environmental Sciences, Aarhus University Denmark.
4
Department of Environmental Sciences, Aarhus University Denmark.
5
Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
6
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark.
7
Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.
8
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Department of Arctic and Marine Biology, University of Tromsø Tromsø, Norway.
9
Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen Copenhagen, Denmark ; Department of Biology, University of Copenhagen Copenhagen, Denmark.

Abstract

The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

KEYWORDS:

16S rRNA gene; Arctic; bacterial community structure; permafrost active layer; seasonal variation

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