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Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production

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Abstract

The microbial community of subsurface environments remains understudied due to limited access to deep strata and aquifers. Coal-bed methane (CBM) production is associated with a large number of wells pumping water out of coal seams. CBM wells provide access to deep biotopes associated with coal-bed water. Temperature is one of the key constraints for the distribution and activity of subsurface microorganisms, including sulfate-reducing prokaryotes (SRP). The 16S rRNA gene amplicon sequencing coupled with in situ sulfate reduction rate (SRR) measurements with a radioactive tracer and cultivation at various temperatures revealed that the SRP community of the coal bed water of the Kuzbass coal basin is characterized by an overlapping mesophilic-psychrophilic boundary. The genus Desulfovibrio comprised a significant share of the SRP community. The D. psychrotolerans strain 1203, which has a growth optimum below 20 °C, dominated the cultivated SRP. SRR in coal bed water varied from 0.154 ± 0.07 to 2.04 ± 0.048 nmol S cm−3 day−1. Despite the ambient water temperature of ~ 10–20 °C, an active thermophilic SRP community occurred in the fracture water, which reduced sulfate with the rate of 0.159 ± 0.023 to 0.198 ± 0.007 nmol S cm−3 day−1 at 55 °C. A novel moderately thermophilic “Desulforudis audaxviator”-clade SRP has been isolated in pure culture from the coal-bed water.

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Data Availability

The GenBank accession number for the 16S rRNA gene sequences of Desulfovibrio sp. strain 1203, Desulfomicrobium sp. strain 1260, and Peptococaceae bacterium strain 1190 are OP565011, OP579167, and OP647315, respectively.

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Acknowledgements

We thank Ltd Gazprom Dobycha Kuznetsk for providing access to the coal-bed methane wells and assistance on the sampling site. Special thanks to the editor and anonymous reviewers for comments on improving the manuscript.

Funding

This study was supported by the Russian Science Foundation projects 21–14-00114 to O.V.K. (sampling, sulfate reduction rate measurement, cultivation, 16S rRNA profiling of the enrichments) and 22–14-00178 to N.V.R. (16S rRNA gene profiling).

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Authors and Affiliations

  1. Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, 634050, Russia

    Olga V. Karnachuk, Inna A. Panova, Lilia Schetinina, Marat R. Avakyan, Anstasia P. Lukina & Liubov B. Glukhova

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

    Igor I. Rusanov & Nikolai V. Pimenov

  3. Tomsk Branch of the Trofimuk Institute of Petroleum Geology and Geophysics in the Siberian Branch of the Russian Academy of Sciences, Akademicheskiy 4, 634055, Tomsk, Russia

    Olesya Y. Lepokurova & Evgenia V. Domrocheva

  4. Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prosp, Bld. 33‑2, Moscow, Russia, 119071

    Vitaly V. Kadnikov & Nikolai V. Ravin

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  1. Olga V. Karnachuk
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Contributions

OVK planned the study, prepared and wrote the original draft. NVR wrote the original draft. IAP isolated SRB pure cultures and studied their characteristics. IIR measured the in situ sulfate reduction rate with radioactive tracer. LS isolated SRB pure cultures and studied their characteristics. OYL planned the study. EVD sampled coal-bed water and analyzed physicochemical parameters. LBG isolated and amplified DNA from the cultures. APL sampled coal-bed water and analyzed physicochemical parameters. NVP planned the study and measured the in situ sulfate reduction rate with radioactive tracer. VVK sequenced DNA and performed 16S rRNA gene profiling. MRA carried out phylogenetic analysis. All the authors have read and agreed to the published version of the manuscript.

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Correspondence to Olga V. Karnachuk.

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Karnachuk, O.V., Panova, I.A., Rusanov, I.I. et al. Coexistence of Psychrophilic, Mesophilic, and Thermophilic Sulfate-Reducing Bacteria in a Deep Subsurface Aquifer Associated with Coal-Bed Methane Production. Microb Ecol 86, 1934–1946 (2023). https://doi.org/10.1007/s00248-023-02196-9

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