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Phylogenetic diversity of bacteria in soda lake stratified sediments

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Abstract

Various previously developed techniques for DNA extraction from samples with complex physicochemical structure (soils, silts, and sediments) and modifications of these techniques developed in the present work were tested. Their usability for DNA extraction from the sediments of the Kulunda Steppe hypersaline soda lakes was assessed, and the most efficient procedure for indirect (two-stage) DNA extraction was proposed. Almost complete separation of the cell fraction was shown, as well as the inefficiency of nested PCR for analysis of the clone libraries obtained from washed sediments by amplification of the 16S rRNA gene fragments. Analysis of the clone library obtained from the cell fractions of stratified sediments (upper, medium, and lower layers) revealed that in the sediments of Bitter Lake 3 most eubacterial phylotypes belonged to the class Clostridia, phylum Firmicutes. They were probably specific for this habitat and formed a new, presently unknown high-rank taxon. The data obtained revealed no pronounced stratification of the species diversity of the eubacterial component of the microbial community inhabiting the sediments (0–20 cm) in the inshore zone of Bitter Lake 3.

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Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow, 117312, Russia

    T. P. Tourova & D. Yu. Sorokin

  2. Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia

    T. P. Tourova & M. A. Grechnikova

  3. Centre “Bioengineering, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 1, Moscow, 117312, Russia

    M. A. Grechnikova & B. B. Kuznetsov

  4. Department of Biotechnology, TU Delft, Delft, The Netherlands

    D. Yu. Sorokin

Authors
  1. T. P. Tourova
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  2. M. A. Grechnikova
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  3. B. B. Kuznetsov
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  4. D. Yu. Sorokin
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Correspondence to T. P. Tourova.

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Original Russian Text © T.P. Tourova, M.A. Grechnikova, B.B. Kuznetsov, D.Yu. Sorokin, 2014, published in Mikrobiologiya, 2014, Vol. 83, No. 6, pp. 730–742.

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Tourova, T.P., Grechnikova, M.A., Kuznetsov, B.B. et al. Phylogenetic diversity of bacteria in soda lake stratified sediments. Microbiology 83, 869–879 (2014). https://doi.org/10.1134/S0026261714060186

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  • DOI: https://doi.org/10.1134/S0026261714060186

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