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Metagenomics and Culture-Based Diversity Analysis of the Bacterial Community in the Zharkent Geothermal Spring in Kazakhstan

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Abstract

Diversity of the microbial community in the Zharkent geothermal hot spring, located in the southeastern region of Kazakhstan, was assessed using both culture-dependent and -independent approaches. Shotgun metagenomic sequencing of DNA extracted from the spring water yielded 11,061,725 high-quality sequence reads, totaling >1,67 Gb of nucleotide sequences. Furthermore, water samples were enriched in nutrient broth at varying high temperatures, and colonies isolated by being streaked onto nutrient agar. Finally, DNA extraction and amplification, as well as sequencing and phylogenetic analysis, were conducted. Bacteria constituted more than 99.97% of the total prokaryotic abundance, with Archaea contributing only an extremely small component; Firmicutes, Proteobacteria, and Actinobacteria dominated the community. At genus level, Firmicutes reads affiliated with Desmospora, Parageobacillus, Paenibacillus, and Brevibacillus, accounting for more than 60% of total prokaryotic abundance. Eight morphologically distinct, aerobic, endospore-forming thermophilic bacteria were recovered; isolates differed significantly in substrate utilization patterns, as well as their production of thermophilic, extracellular, hydrolytic enzymes for degradation of starch, lipids, cellulose, and protein. Five strains could degrade all four macromolecular types at temperatures ranging from 55 to 75 °C. Phylogenetic analyses based on 16S rRNA gene sequences placed all isolates into the genus Geobacillus with some of them possibly representing novel species. The results indicate that this hot spring represents a rich source of novel thermophilic bacteria and potentially useful thermostable enzymes.

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Data Availability

The datasets generated during and/or analyzed during the current study are available in the GenBank repository, https://www.ncbi.nlm.nih.gov/genbank/. Any data generated or analyzed during this study that are not included in the published article will be available from the corresponding author on reasonable request.

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Acknowledgements

The authors are grateful to the Molecular Imaging Center and the ICP-Laboratory at the University of Bergen for their excellent service in performing electron microscopy and chemical analyses for this study, respectively.

Funding

The research was supported by the Eurasia program of the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (Diku) under Project CPEA-LT-2017/10061.

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Authors and Affiliations

  1. Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan

    Akzhigit Mashzhan, Aida Kistaubayeva & Irina Savitskaya

  2. Department of Biological Sciences, University of Bergen, Bergen, Norway

    Akzhigit Mashzhan, Rubén Javier-López & Nils-Kåre Birkeland

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  1. Akzhigit Mashzhan
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  2. Rubén Javier-López
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Contributions

AM, NKB, AK contributed to conceptualization and methodology; AM, RJL, NKB, and AK were involved in formal analysis and investigation; AM, NKB, AK, IS were involved in writing––original draft preparation; AM and NKB were involved in writing––review and editing; AK and NKB contributed to funding acquisition; AK, IS, and NKB performed supervision.

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Correspondence to Aida Kistaubayeva.

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Mashzhan, A., Javier-López, R., Kistaubayeva, A. et al. Metagenomics and Culture-Based Diversity Analysis of the Bacterial Community in the Zharkent Geothermal Spring in Kazakhstan. Curr Microbiol 78, 2926–2934 (2021). https://doi.org/10.1007/s00284-021-02545-2

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