Skip to main content
SpringerLink
Log in

Structure and Metabolic Potential of the Microbiome of Lake Baikal Upper Sediment Layers Determined by Metagenome Analysis

  • SHORT COMMUNICATIONS
  • Published:
Microbiology Aims and scope Submit manuscript

Abstract—

This is the first report on the application of metagenomic analysis of the microbiome of Lake Baikal bottom sediments in order to assess the community structure and metabolic potential of the microorganisms inhabiting the upper sediment horizon at the site of a deep-water station. Compared to the metagenome of near-bottom water, relative abundance of the phyla Methylomirabilota, Chloroflexota, and Acidobacterota was found to increase, as well as that of the genes for the pathways of methane, sulfur, and thiosulfate oxidation and of nitrate reduction. Genomes of members of 12 phyla forming the basis of the studied microbiome were assembled. Reconstruction of the metabolic pathways indicated the possible coexistence of microorganisms capable of gaining carbon and energy due to oxidation of carbohydrates, methane, thiosulfate, and ammonia, as well as via anaerobic processes of fermentation, denitrification, and (to a lesser degree) sulfate reduction.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 1.
Fig. 2.

REFERENCES

  1. Baumann, K.B.L., Thoma, R., Callbeck, C.M., Niederdorfer, R., Schubert, C.J., Müller, B., Lever, M.A., and Bürgmann, H., Microbial nitrogen transformation potential in sediments of two contrasting lakes is spatially structured but seasonally stable, MSphere, 2022, vol. 7, e01013-21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Biessy, L., Pearman, J.K., Waters, S., Vandergoes, M.J., and Wood, S.A., Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes, MBGM, 2022, vol. 6, e79265.

    Google Scholar 

  3. Butina, T.V., Bukin, Y.S., Petrushin, I.S., Tupikin, A.E., Kabilov, M.R., and Belikov, S.I., Extended evaluation of viral diversity in Lake Baikal through metagenomics, Microorganisms, 2021, vol. 9, p. 760.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cabello-Yeves, P.J., Zemskaya, T.I., Rosselli, R., Coutinho, F.H., Zakharenko, A.S., Blinov, V.V., and Rodriguez-Valera, F., Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal, Appl. Env. Microbiol., 2018, vol. 84, e02132-17.

    Article  ADS  Google Scholar 

  5. Cabello-Yeves, P.J., Zemskaya, T.I., Zakharenko, A.S., Sakirko, M.V., Ivanov, V.G., Ghai, R., and Rodriguez-Valera F., Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat, Limnol. Oceanogr., 2020, vol. 65, pp. 1471–1488.

    Article  ADS  CAS  Google Scholar 

  6. Coutinho, F.H., Cabello-Yeves, P.J., Gonzalez-Serrano, R., Rosselli, R., López-Pérez, M., Zemskaya, T.I., Zakharenko, A.S., Ivanov, V.G., and Rodriguez-Valera, F., New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal, Microbiome, 2020, vol. 8, p. 163.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Emerson, J.B., Varner, R.K., Wik, M., Parks, D.H., Neumann, R.B., Johnson, J.E., Singleton, C.M., Woodcroft, B.J., Tollerson, R., Owusu-Dommey, A., Binder, M., Freitas, N.L., Crill, P.M., Saleska, S.R., Tyson, G.W., and Rich, V.I., Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes, Nat. Comm., 2021, vol. 12, p. 5815.

  8. Granina, L.Z., Rannii diagenez donnykh osadkov ozera Baikal (Early Diagenesis of Lake Baikal Bottom Sediments), Novosibirsk: GEO, 2008.

  9. Haro‑Moreno, J.M., Cabello‑Yeves, P.J., Garcillán‑ Barcia, M.P., Zakharenko, A., Zemskaya, T.I., and Rodriguez‑Valera, F., A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long‑read metagenomics, Env. Microbiome, 2023, vol. 18, p. 12.

  10. Khodzher, T.V., Domysheva, V.M., Sorokovikova, L.M., Sakirko, M.V., and Tomberg, I.V., Current chemical composition of Lake Baikal water, Inland Waters, 2017, vol. 7, pp. 250–258.

    Article  CAS  Google Scholar 

  11. Lomakina, A., Bukin, S., Shubenkova, O., Pogodaeva, T., Ivanov, V., Bukin, Y., and Zemskaya, T., Microbial communities in ferromanganese sediments from the northern basin of Lake Baikal (Russia), Microorganisms, 2023, vol. 11, p. 1865.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Nawrocki, E.P., Structural RNA homology search and alignment using covariance models, Ph.D. Thesis, Washington Univ., Saint Louis, School of Medicine. 2009.

  13. Pimenov, N.V. and Bonch-Osmolovskaya, E.A., In situ activity studies in thermal environments, Methods Microbiol., 2006, vol. 35, pp. 29–53.

    Article  CAS  Google Scholar 

  14. Pogodaeva, T.V., Lopatina, I.N., Khlystov, O.M., Egorov, A.V., and Zemskaya, T.I., Background composition of pore waters in Lake Baikal bottom sediments, J. Great Lakes Res., 2017, vol. 43, pp. 1030 –1043.

    Article  CAS  Google Scholar 

  15. Potapov, S.A., Tikhonova, I.V., Krasnopeev, A.Yu., Kabilov, M.R., Tupikin, A.E., Chebunina, N.S., Zhuchenko, N.A., and Belykh, O.I., Metagenomic analysis of virioplankton from the pelagic zone of Lake Baikal, Viruses, 2019, vol. 11, p. 991.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Potapov, S., Krasnopeev, A., Tikhonova, I., Podlesnaya, G., Gorshkova, A., and Belykh, O., The viral fraction metatranscriptomes of Lake Baikal, Microorganisms, 2022, vol. 10, p. 1937. Ravin, N.V., Mardanov, A.V., and Skryabin, K.G., Metagenomics as a tool for the investigation of uncultured microorganisms, Russ. J. Genet., 2015, vol. 51, pp. 431–439.

    Google Scholar 

  17. Riesenfeld, C.S., Schloss, P.D., and Handelsman, J., Metagenomics: genomic analysis of microbial communities, Annu. Rev. Genet., 2004, vol. 38, pp. 525–552.

    Article  CAS  PubMed  Google Scholar 

  18. Rusanov, I.I., Savvichev, A.S., Yusupov, S.K., Pimenov, N.V., and Ivanov, M.V., Production of exometabolites in the microbial oxidation of methane in marine ecosystems, Microbiology (Moscow), 1998, vol. 67, pp. 590–596.

    CAS  Google Scholar 

  19. Ruuskanen, M.O., Colby, G., St.Pierre, K.A., St.Louis, V.L., Aris-Brosou, S., and Poulain, A.J., Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments, Limnol. Oceanogr., 2019, vol. 65, pp. 233–247.

    Google Scholar 

  20. Zakharova, Yu.R., Galachyants, Yu.P., Kurilkina, M.I., Likhoshvay, A.V., Petrova, D.P., Shishlyannikov, S.M., Ravin, N.V., Mardanov, A.V., Beletsky, A.B., and Likhoshway, Ye.V., The structure of microbial community and degradation of diatoms in the deep near-bottom layer of Lake Baikal, PLoS One, 2013, vol. 8, e59977.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zemskaya, T.I., Bukin, S.V., Lomakina, A.V., and Pavlova, O.N., Microorganisms in the sediments of Lake Baikal, the deepest and oldest lake in the world, Microbiology (Moscow), 2021, vol. 90, pp. 298–313.

    Article  CAS  Google Scholar 

  22. Zemskaya, T.I., Cabello-Yeves, P.J., Pavlova, O.N., and Rodriguez-Valera, F., Microorganisms of Lake Baikal—the deepest and most ancient lake on Earth, Appl. Microbiol. Biotechnol., 2020, vol. 104, pp. 6079–6090.

    Article  CAS  PubMed  Google Scholar 

Download references

ACKNOWLEDGMENTS

The authors are grateful to A.V. Khabuev and O.M. Khlystov (Laboratory of Lake Baikal Geology, Limnological Institute, Siberian Branch, Russian Academy of Sciences) and to the crew of RV G.Yu. Vereshchagin for their help in collecting the sediment samples. The authors are also grateful to Jose Manuel Haro-Moreno (Miguel Hernandez University of Elche), for valuable consultations on metagenome analysis. Resource-consuming operations were carried out using the Akademik V.M. Matrosov high-productivity cluster, Irkutsk Supercomputer Center, Siberian Branch, Russian Academy of Sciences.

Funding

The work was supported by the Russian Science Foundation, project no. 22-14-00084.

Author information

Authors and Affiliations

  1. Limnological Institute, Siberian Branch, Russian Academy of Sciences, 664033, Irkutsk, Russia

    S. V. Bukin, A. V. Lomakina, V. G. Ivanov, T. V. Pogodaeva, P. M. Kolesnikov, O. V. Shubenkova, A. S. Zakharenko, Yu. S. Bukin & T. I. Zemskaya

  2. Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    I. I. Rusanov

  3. Miguel Hernandez University of Elche, 03550, Alicante, Spain

    F. Rodriguez-Valera

Authors
  1. S. V. Bukin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Lomakina
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. I. I. Rusanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. V. G. Ivanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. T. V. Pogodaeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. P. M. Kolesnikov
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. O. V. Shubenkova
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. A. S. Zakharenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yu. S. Bukin
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. F. Rodriguez-Valera
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. T. I. Zemskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. V. Bukin.

Ethics declarations

ETHICS APPROVAL AND CONSENT TO PARTICIPATE

This work does not contain any studies involving human and animal subjects.

CONFLICT OF INTEREST

The authors of this work declare that they have no conflicts of interest.

Additional information

Translated by P. Sigalevich

Publisher’s Note.

Pleiades Publishing remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bukin, S.V., Lomakina, A.V., Rusanov, I.I. et al. Structure and Metabolic Potential of the Microbiome of Lake Baikal Upper Sediment Layers Determined by Metagenome Analysis. Microbiology 92 (Suppl 1), S56–S62 (2023). https://doi.org/10.1134/S0026261723603743

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026261723603743

Keywords:

Search

Navigation