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VirusDisease

, Volume 28, Issue 1, pp 18–25 | Cite as

Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis

  • Madina Saparbaevna AlexyukEmail author
  • Aizhan Sabirzhanovna Turmagambetova
  • Pavel Gennadievich Alexyuk
  • Andrey Pavlinovich Bogoyavlenskiy
  • Vladimir Eleazarovich Berezin
Original Article

Abstract

Viruses are the most abundant biological entities on Earth and can be found in a variety of environments. A high prevalence of viruses in marine and freshwater systems was initially reported by Spencer in 1955, but the ecological significance of viruses is insufficiently known even until the present day. Viruses are known to play a key role in the biology of freshwater bacteria: controlling the bacterial abundance, composition of species, and acting as intermediaries in the transfer of genes between bacterial populations. In our study a variety of viromes of the Ile-Balkhash water basin were identified. It was found that the composition of viruses of the Ile-Balkhash region is made up not only of a wide variety of autochthonous viruses typical for phytoplankton hydro ecosystems, but also of representatives of allochthonous viruses—such families as Coronaviridae, Reoviridae and Herpesviridae—indicating anthropogenic pollution of the basin. The research designed to investigate the viral abundance, spread, infectious cycle, seasonal dynamics, composition of the viral community, and the influence of viruses on the bacteria, phytoplankton and recycling of nutrients, as well as the impact of environmental factors on the viral ecology in a variety of marine and freshwater systems is very relevant nowadays.

Keywords

Bacteriophage Metagenomics Viromes Biodiversity Water ecosystems 

Notes

Acknowledgements

This work was supported by Grant 0115PK01095 from the Ministry of Education and Science of the Republic of Kazakhstan. The authors thank the “Genotek” company’s employees for help with the sequencing of the obtained samples.

Supplementary material

13337_2016_353_MOESM1_ESM.tif (1.8 mb)
Map of the Ile-Balkhash region. Ile-Balkhash region is marked by a yellow square (TIFF 1823 kb)
13337_2016_353_MOESM2_ESM.tif (2.6 mb)
Lake Balkhash – place of collection point of water samples. Sample site on the Lake Balkhash is marked by a red flag (TIFF 2620 kb)
13337_2016_353_MOESM3_ESM.tif (2.4 mb)
The Kapchagay water reservoir–place of collection point of water samples. Sample site on the Kapchagay water reservoir is marked by a red flag (TIFF 2450 kb)
13337_2016_353_MOESM4_ESM.tif (2.7 mb)
River Ile – place of collection point of water samples. Sample site on the River Ile is marked by a red flag (TIFF 2748 kb)

References

  1. 1.
    Spencer R. A marine bacteriophage. Nature. 1955;175:690–1.CrossRefPubMedGoogle Scholar
  2. 2.
    Kriss AE, Rukina EA. Bacteriophage in the sea. Rep Acad Sci USSR New Ser. 1947;57(8):833–5.Google Scholar
  3. 3.
    Berg O, Børsheim Y, Bratbak G, Heldal M. High abundance of viruses found in aquatic environments. Nature. 1989;340:467–8.CrossRefGoogle Scholar
  4. 4.
    Fuhrman A. Marine viruses and their biogeochemical and ecological effects. Nature. 1999;399:541–8.CrossRefPubMedGoogle Scholar
  5. 5.
    Noble RT, Middelboe M, Fuhrman JA. The effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton. Aquat Microb Ecol. 1999;18:1–13.CrossRefGoogle Scholar
  6. 6.
    Bratbak G, Heldal M. Viruses rule the waves—the smallest and most abundant members of marine ecosystems. Microbiol Today. 2000;27:171–3.Google Scholar
  7. 7.
    Frede T. Thingstad elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr. 2000;45(6):1320–8.CrossRefGoogle Scholar
  8. 8.
    Jiang SC, Paul JH. Gene transfer by transduction in the marine environment. Appl Environ Microbiol. 1998;64(8):2780–7.PubMedPubMedCentralGoogle Scholar
  9. 9.
    Felts AF, Breitbart MB, Salamon P, Edwards R, et al. The marine viromes of four oceanic regions. PLoS Biol. 2006;4(11):e368.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Weinbauer MG. Ecology of prokaryotic viruses. FEMS Mircobiol Rev. 2004;28:127–81.CrossRefGoogle Scholar
  11. 11.
    Hewson I, Barbosa JG, Brown JM. Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Appl Environ Microbiol. 2012;78(18):6583–91.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Montanié H, et al. Potential effect of freshwater virus on the structure and activity of bacterial communities in the Marennes-Oléron Bay (France). Microb Ecol Febr. 2009;57(2):295–306.CrossRefGoogle Scholar
  13. 13.
    Promoting IWRM and fostering transboundary dialogue in central asia. Report. 2010.Google Scholar
  14. 14.
    Roux S, et al. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife. 2014;3:e03125.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Meyer F, et al. The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform. 2008;9:386.CrossRefGoogle Scholar
  16. 16.
    Gomez-Alvarez V, et al. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 2009;3:1314–7.CrossRefPubMedGoogle Scholar
  17. 17.
    Cox MP, et al. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinform. 2010;11:485.CrossRefGoogle Scholar
  18. 18.
    Rho M, et al. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38(20):e191.CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1.CrossRefPubMedGoogle Scholar
  20. 20.
    Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. 2002;12(4):656–64.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Cairns J, et al. Phage and the origins of molecular biology. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 2000.Google Scholar
  22. 22.
    Rohwer F, Thurber RV. Viruses manipulate the marine environment. Nature. 2009;459:207–12.CrossRefPubMedGoogle Scholar
  23. 23.
    Suttle CA. Marine viruses—major players in the global ecosystem. Nat Rev Microbiol. 2007;5:801–12.CrossRefPubMedGoogle Scholar
  24. 24.
    Wilhelm SW, Suttle CA. Viruses and nutrient cycles in the sea. Bioscience. 1999;49:781–8.CrossRefGoogle Scholar
  25. 25.
    Sano E, et al. Movement of viruses between biomes. Appl Environ Microbiol. 2004;70:5842–6.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Nelson EJ, et al. Cholera transmission: the host, pathogen and bacteriophage dynamic. Nat Rev Microbiol. 2009;7:693–702.CrossRefPubMedGoogle Scholar
  27. 27.
    Reyes A, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466:334–8.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Rho M, et al. Diverse CRISPRs evolving in human microbiomes. PLoS Genet. 2012;8:e1002441.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Mohiuddin M, Schellhorn HE. Spatial and temporal dynamics of virus occurrence in two freshwater lakes captured through metagenomic analysis. Front Microbiol. 2015;6:00960.CrossRefGoogle Scholar
  30. 30.
    Binga EK, Lasken RS, Neufeld JD. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J. 2008;2:233–41.CrossRefPubMedGoogle Scholar
  31. 31.
    Drucker V, Dutova N. Bacteriophages from the Barguzin River and Barguzin Bay of Lake Baikal. Proc Irkutsk State Univ Ser Earth Sci. 2012;2:P111–5.Google Scholar

Copyright information

© Indian Virological Society 2017

Authors and Affiliations

  • Madina Saparbaevna Alexyuk
    • 1
    Email author
  • Aizhan Sabirzhanovna Turmagambetova
    • 1
  • Pavel Gennadievich Alexyuk
    • 1
  • Andrey Pavlinovich Bogoyavlenskiy
    • 1
  • Vladimir Eleazarovich Berezin
    • 1
  1. 1.Institute of Microbiology and VirologyAlmatyKazakhstan

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