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Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures

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Abstract

Antarctic lake ecosystems provide a rare opportunity to study the evolution and adaptation of microorganisms to extreme conditions, as well as to discover new species useful for biotechnological applications. Four water samples were collected from various layers of the water column of freshwater Lake Radok in East Antarctica. Two regions (v3-v5 and v4-v8) of the 16S rRNA gene were amplified by PCR and sequenced. Twenty dominant phylotypes were detected representing five bacterial phyla (Actinobacteria, α, β and δ Proteobacteria, Bacteroidetes, Planctomycetes, OD1) and two eukaryotic divisions (stramenopiles and green algae). Of these, 16 phylotypes demonstrated ≤98 % identity to the nearest taxa in GenBank and were therefore classified as new unknown species. Seven phylotypes demonstrated ≤90 % identity and thus remained unidentified. Actinobacteria was the most abundant phylum with 157 clones (41 % of the total number) representing 5 phylotypes. A species complex (3 clades from acI-A subgroup) of Candidatus Planktophila limnetica was prevalent in all layers. Representatives of the OD1 phylum and δ-proteobacteria were discovered by sequencing of the v3-v5 region of 16S rRNA, while Planctomycetes, β-proteobacteria and mtDNA of stramenopiles were discovered by sequencing of the v4-v8 region. This highlights the necessity of sequencing at least two 16S rRNA gene regions to gain more data on microbial community characterization. In general, despite the uniformity in the physical and chemical properties in the water column, a prominent stratification of microbial groups was observed, at the levels of both divisions and phylotypes.

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Acknowledgments

We would like to thank the team of the 50th Russian Antarctic Expedition and personally V.L. Kuznetsov, M.P. Andreev and A.I. Kutsuruba for lake water sampling and for transportation of frozen samples (on RV ‘Fedorov’) to Bremerhaven; LGGE (Grenoble, France) for delivery of the samples from Bremerhaven to Grenoble; and Olga Neveykina and especially Ian Probert for English language editing. We are also very grateful for the time and energy the reviewers extended to help us improve the paper. The research was partially supported by the Russian Foundation for Basic Research (RFBR), Research Project No. 07-04-00646, as well as the Act 211 Government of the Russian Federation, Agreement No. 02.A03.21.0006.

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Authors and Affiliations

  1. National Research Centre “Kurchatov Institute” B.P. Konstantinov, Petersburg Nuclear Physics Institute, Gatchina, Russia

    Denis S. Karlov, Danil A. Sumbatyan & Sergey A. Bulat

  2. Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France

    Dominique Marie

  3. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia

    Maria S. Chuvochina

  4. S.N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia

    Irina S. Kulichevskaya

  5. Arctic and Antarctic Research Institute, St. Petersburg, Russia

    Irina A. Alekhina

  6. Institute of Physics and Technology, Ural Federal University, Ekaterinburg, Russia

    Sergey A. Bulat

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  1. Denis S. Karlov
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Correspondence to Denis S. Karlov or Sergey A. Bulat.

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Karlov, D.S., Marie, D., Sumbatyan, D.A. et al. Microbial communities within the water column of freshwater Lake Radok, East Antarctica: predominant 16S rDNA phylotypes and bacterial cultures. Polar Biol 40, 823–836 (2017). https://doi.org/10.1007/s00300-016-2008-9

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