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Composition of the microbial communities of bituminous constructions at natural oil seeps at the bottom of Lake Baikal

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Abstract

Microbial communities of two bituminous constructions at the bottom of Lake Baikal in the region of natural oil seeps at a depth of 900 m have been investigated. Construction 8 contained biodegraded hydrocarbons, and construction 3, through which oil seeped, contained material that experienced biodegradation to a lesser degree. The composition of the microbial communities was studied by means of pyrosequencing of 16S rRNA gene fragments. Most of the bacterial 16S rRNA gene sequences identified in both bituminous constructions were attributed to proteobacteria, along with which Actinobacteria, Acidobacteria, Bacteroidetes, and TM7 were revealed. About 40% of the bacterial sequences in bituminous construction 3 belonged to representatives of uncultured groups within the classes Alphaproteobacteria and Betaproteobacteria and the phylum Bacteroidetes. The 16S rRNA gene sequences of archaea belonged to aceticlastic and hydrogenotrophic methanogens of the orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales. The 16S rRNA genes of various groups of bacteria carrying out aerobic biodegradation of aromatic compounds and n-alkanes were found; their compositions differed between the constructions. Neither known groups of denitrifying betaproteobacteria nor known groups of sulfate-reducing deltaproteobacteria capable of carrying out anaerobic degradation of n-alkanes were found, which agrees with the low content of nitrate and sulfate in the water. In the anaerobic zone of bituminous constructions, the processes of biodegradation of hydrocarbons are probably carried out in the absence of alternative electron acceptors by the syntrophic community, including deltaproteobacteria of the genus Syntrophus and methanogenic archaea.

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References

  1. De Batist, M., Klerkx, J., Van Rensbergen, P.V., Vanneste, M., Poort, J., Golmshtok, A.Y., Kremlev, A., Khlystov, O.M., and Krinitsky, P., Active hydrate destabilization in Lake Baikal, Siberia, Terra Nova, 2002, vol. 14, pp. 436–442.

    Article  Google Scholar 

  2. Khlystov, O., De Batist, M., Shoji, H., Hachikubo, A., Nishio, S., Naudts, L., Poort, J., Khabuev, A., Belousov, O., Manakov, A., and Kalmychkov, G., Gas hydrate of Lake Baikal: discovery and varieties, J. Asian Earth Sci., 2013, vol. 62, no. 1, pp. 162–166.

    Article  Google Scholar 

  3. Simoneit, B.R.T., Aboul-Kassim, T.A.T., and Tiercelin, J.J., Hydrothermal petroleum from lacustrine sedimentary organic matter in the East African Rift, Appl. Geochem., 2000, vol. 15, pp. 355–368.

    Article  PubMed  CAS  Google Scholar 

  4. Zárate-del Valle, P.F. and Simoneit, B.R.T., Hydrothermal bitumen generated from sedimentary organic matter of rift lakes-Lake Chapala, Citala Rift, Western Mexico, Appl. Geochem., 2005, vol. 20, pp. 2343–2350.

    Article  Google Scholar 

  5. Khlystov, O.M., Gorshkov, A.G., Egorov, A.V., Zemskaya, T.I., Granin, N.G., Kalmychkov, G.V., Vorob’eva, S.S., Pavlova, O.N., Yakup, M.A., Makarov, M.M., Moskvin, V.I., and Grachev, M.A., Oil in the Lake of World Heritage, Dokl. Earth Sci., 2007, vol. 415, pp. 682–685.

    Article  CAS  Google Scholar 

  6. Kashirtsev, V.A., Kontorovich, A.E., Moskvin, V.I., Danilova, V.P., and Melenevskii, V.N., Terpanes from oil shows of Lake Baikal, Pet. Chem., 2006, vol. 46, pp. 217–224.

    Article  Google Scholar 

  7. Khlystov, O.M., Zemskaya, T.I., Sitnikova, T.Ya., Mekhanikova, I.V., Kaigorodova, I.A., Gorshkov, A.G., Timoshkin, O.A., Shubenkova, O.V., Chernitsyna, S.M., Lomakina, A.V., Likhoshvai, A.V., Sagalevich, A.M., Moskvin, V.I., Peresypkin, V.I., Belyaev, N.A., Slipenchuk, M.V., Tulokhonov, A.K., and Grachev, M.A., Bottom bituminous constructions and biota inhabiting them according to investigation of Lake Baikal with the Mir submersible, Dokl. Earth Sci., 2009, vol. 429, pp. 1333–1336.

    Article  CAS  Google Scholar 

  8. Zemskaya, T.I., Pogodaeva, T.V., Shubenkova, O.V., Chernitsina, S.M., Khlystov, O.M., Dagurova, O.P., Buryukhaev, S.P., Namsaraev, B.B., Egorov, A.V., Krylov, A.A., and Kalmychkov, G.V., Geochemical and microbiological characteristics of sediments near the Malenky mud volcano (Lake Baikal, Russia), with evidence of Archaea intermediate between the marine anaerobic methanotrophs ANME-2 and ANME-3, Geo-Mar. Lett., 2010, vol. 30, p. 411–425.

    Article  CAS  Google Scholar 

  9. Shubenkova, O.V., Zemskaya, T.I., Chernitsyna, S.M., Khlystov, O.M., and Triboi, T.I., The first results of a study of the phylogenetic diversity of microorganisms in southern Baikal sediments from the area of subsurface depositions of methane hydrate, Microbiology, 2005, vol. 74, pp. 314–320.

    Article  CAS  Google Scholar 

  10. Springer, E., Sachs, M.S., Woese, C.R., and Boone, D.R., Partial gene sequences for the A subunit of methyl-coenzyme M reductase (McrI) as a phylogenetic tool for the family Methanosarcinaceae, Int. J. Syst. Bacteriol., 1995, vol. 45, p. 554–559.

    Article  PubMed  CAS  Google Scholar 

  11. Kohno, T., Sugimoto, Y., Sei, K., and Mori, K., Design of PCR primers and gene probes for general detection of alkane-degrading bacteria, Microbes and Environments, 2002, vol. 17, pp. 114–121.

    Article  Google Scholar 

  12. Behnke, A., Engel, M., Christen, R., Nebel, M., Klein, R.R., and Stoeck, T., Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions, Environ. Microbiol., 2011, vol. 13, pp. 340–349.

    Article  PubMed  CAS  Google Scholar 

  13. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., Kulam-Syed-Mohideen, A.S., McGarrell, D.M., Marsh, T., Garrity, G.M., and Tiedje, J.M., The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 2009, vol. 37, pp. 141–145.

    Article  Google Scholar 

  14. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G., The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 1997, vol. 24, pp. 4876–4882.

    Article  Google Scholar 

  15. Van de Peer, Y. and De Wachter, R., TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment, Comput. Appl. Biosci., 1994, vol. 10, pp. 569–570.

    PubMed  Google Scholar 

  16. Widdel, F. and Rabus, R., Anaerobic biodegradation of saturated and aromatic hydrocarbons, Curr. Opin. Biotechnol., 2001, vol. 12, pp. 259–276.

    Article  PubMed  CAS  Google Scholar 

  17. Rabus, R., Wilkes, H., Schramm, A., Harms, G., Behrends, A., Amann, R., and Widdel, F., Anaerobic utilization of alkylbenzenes and n-alkanes from crude oil in an enrichment culture of denitrifying bacteria affiliating with the beta-subclass of Proteobacteria, Environ. Microbiol, 1999, vol. 1, pp. 145–157.

    Article  PubMed  CAS  Google Scholar 

  18. Smits, T.H.M., Balada, S.B., Witholt, B., and van Beilen, J.B., Functional analysis of alkane hydroxylases from Gram-negative and Gram-positive bacteria, J. Bacteriol., 2002, vol. 184, pp. 1733–1742.

    Article  PubMed  CAS  Google Scholar 

  19. Nazina, T.N., Tourova, T.P., Poltaraus, A.B., Novikova, E.V., Grigoryan, A.A., Ivanova, A.E., Lysenko, A.M., Petrunyaka, V.V., Osipov, G.A., Belyaev, S.S., and Ivanov, M.V., Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermoglucosidasius and Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. thermocatenulatus, G. thermoleovorans, G. kaustophilus, G. thermoglucosidasius and G. thermodenitrificans, Int. J. Syst. Evol. Microbiol, 2001, vol. 51, pp. 433–446.

    PubMed  CAS  Google Scholar 

  20. Magot, M., Ollivier, B., and Patel, B.K.C., Microbiology of petroleum reservoirs, Antonie van Leeuwenhoek, 2000, vol. 77, pp. 103–116.

    Article  PubMed  CAS  Google Scholar 

  21. Aeckersberg, F., Bak, F., and Widdel, F., Anaerobic oxidation of saturated hydrocarbons to CO2 by a new type of sulfate-reducing bacterium, Arch. Microbiol., 1991, vol. 156, pp. 5–14.

    Article  CAS  Google Scholar 

  22. Schink, B., Energetics of syntrophic cooperation in methanogenic degradation, Microbiol. Mol. Biol. Rev., 1997, vol. 61, pp. 262–280.

    PubMed  CAS  Google Scholar 

  23. Zengler, K., Richnow, H.H., Rossello-Mora, R., Michaelis, W., and Widdel, F., Methane formation from long-chain alkanes by anaerobic microorganisms, Nature, 1999, vol. 401, pp. 266–269.

    Article  PubMed  CAS  Google Scholar 

  24. Anderson, R.T. and Lovley, D.R., Hexadecane decay by methanogenesis, Nature, 2000, vol. 404, pp. 722–723.

    Article  PubMed  CAS  Google Scholar 

  25. Lovley, D.R., Baedecker, M.J., Lonergan, D.J., Cozzarelli, I.M., Phillips, E.J.P., and Siegel, D.I., Oxidation of aromatic contaminants coupled to microbial iron reduction, Nature, 1989, vol. 339, pp. 297–299.

    Article  CAS  Google Scholar 

  26. Nakatsu, C.H., Hristova, K., Hanada, S., Meng, X.Y., Hanson, J.R., Scow, K.M., and Kamagata, Y., Methylibium petroleiphilum gen. nov., sp. nov., a novel methyl tert-butyl ether-degrading methylotroph of the Betaproteobacteria, Int. J. Syst. Evol. Microbiol., 2006, vol. 56, pp. 983–989.

    Article  PubMed  CAS  Google Scholar 

  27. Liu, Y. and Whitman, W.B., Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea, Ann. N. Y. Acad. Sci., 2008, vol. 1125, pp. 171–189.

    Article  PubMed  CAS  Google Scholar 

  28. Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V., Shubenkova, O.V., Pogodaeva, T.V., Zemskaya, T.I., Ravin, N.V., and Skryabin, K.G., Microbial community structure in methane hydrate-bearing sediments of freshwater Lake Baikal, FEMS Microbiol. Ecol., 2012, vol. 79, pp. 348–358.

    Article  PubMed  CAS  Google Scholar 

  29. van Beilen, J.B., Li, Z., Duetz, W.A., Smits, T.H.M., and Witholt, B., Diversity of alkane hydroxylase systems in the environment, Oil Gas Sci. Technol., 2003, vol. 58, pp. 427–440.

    Article  Google Scholar 

  30. Jones, D.M., Head, I.M., Gray, N.D., Adams, J.J., Rowan, A.K., Aitken, C.M., Bennett, B., Huang, H., Brown, A., Bowler, B.F., Oldenburg, T., Erdmann, M., and Larter, S.R., Crude-oil biodegradation via methanogenesis in subsurface petroleum reservoirs, Nature, 2008, vol. 451, pp. 176–180.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

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

    V. V. Kadnikov, A. V. Beletsky, A. V. Mardanov & N. V. Ravin

  2. Limnological Institute, Siberian Branch, Russian Academy of Sciences, ul. Ulan-Batorskaya, 3, Irkutsk, 664033, Russia

    A. V. Lomakina, A. V. Likhoshvai, A. G. Gorshkov, T. V. Pogodaeva & T. I. Zemskaya

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  1. V. V. Kadnikov
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  2. A. V. Lomakina
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  3. A. V. Likhoshvai
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  4. A. G. Gorshkov
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  5. T. V. Pogodaeva
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  6. A. V. Beletsky
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  7. A. V. Mardanov
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  8. T. I. Zemskaya
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  9. N. V. Ravin
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Correspondence to N. V. Ravin.

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Kadnikov, V.V., Lomakina, A.V., Likhoshvai, A.V. et al. Composition of the microbial communities of bituminous constructions at natural oil seeps at the bottom of Lake Baikal. Microbiology 82, 373–382 (2013). https://doi.org/10.1134/S0026261713030168

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  • DOI: https://doi.org/10.1134/S0026261713030168

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