Article

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage

  • Nature Microbiology 1, Article number: 16063 (2016)
  • doi:10.1038/nmicrobiol.2016.63
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Abstract

The identification and functional characterization of microbial communities remains a prevailing topic in microbial oceanography as information on environmentally relevant pelagic prokaryotes is still limited. The Roseobacter group, an abundant lineage of marine Alphaproteobacteria, can constitute large proportions of the bacterioplankton. Roseobacters also occur associated with eukaryotic organisms and possess streamlined as well as larger genomes from 2.2 to >5 Mpb. Here, we show that one pelagic cluster of this group, CHAB-I-5, occurs globally from tropical to polar regions and accounts for up to 22% of the active North Sea bacterioplankton in the summer. The first sequenced genome of a CHAB-I-5 organism comprises 3.6 Mbp and exhibits features of an oligotrophic lifestyle. In a metatranscriptome of North Sea surface waters, 98% of the encoded genes were present, and genes encoding various ABC transporters, glutamate synthase and CO oxidation were particularly upregulated. Phylogenetic gene content analyses of 41 genomes of the Roseobacter group revealed a unique cluster of pelagic organisms distinct from other lineages of this group, highlighting the adaptation to life in nutrient-depleted environments.

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Acknowledgements

The authors thank J. Orchard, A. Neumann and O. Thomsen for their help in the laboratory, J. Lucas for the water sample from Helgoland and the crews of RV Heincke (grant no. AWI-HE361_00) and RV Polarstern (grant nos. AWI-PS ANT28-2_00, AWI-PS ANT28-4_00 and AWI-PS ANT28-5_00) for their support on board ship. The EAGER 2011 cruise was organized by the Continental Shelf Project of the Kingdom of Denmark and the Galathea 3 expedition was under the auspices of the Danish Expedition Foundation. This work was supported by the Deutsche Forschungsgemeinschaft (DFG) within the Transregional Collaborative Research Centre ‘Roseobacter’ (TRR 51).

Author information

Affiliations

  1. Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg D-26111, Germany

    • Sara Billerbeck
    • , Helge-Ansgar Giebel
    • , Thorsten Brinkhoff
    •  & Meinhard Simon
  2. Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen D-37077, Germany

    • Bernd Wemheuer
    • , Sonja Voget
    • , Anja Poehlein
    •  & Rolf Daniel
  3. Department of Systems Biology, Technical University of Denmark, Lyngby DK-2800 Kgs, Denmark

    • Lone Gram
  4. Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida 32514, USA

    • Wade H. Jeffrey

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Contributions

S.B., T.B. and M.S. designed the study. S.B. carried out the analyses of the phylogenetic cluster, biogeography and qPCR, and isolation of strain SB2. H.A.G. participated in sampling and provided data on chlorophyll and bacterial abundance in the North Sea. B.W., S.V., A.P. and R.D. carried out the genomic, metagenomic and metatranscriptomic analyses. L.G. and W.H.J. provided samples from various oceans. S.B. and M.S. wrote the major parts of the manuscript and all authors contributed to writing and revising it.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Meinhard Simon.

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    Supplementary information

    Supplementary Text, Supplementary Figures 1-4, Supplementary Tables 1-6 and 8-10, Supplementary Table 7 Legend and Supplementary References.

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