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Effect of Methanol and Mineral Nitrogen Compounds on the Composition of Methanotrophic Enrichments from the Sediments of a Lake Baikal Methane Seep

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Abstract

Diversity of methano- and methylotrophic bacteria in enrichments from the oxidized sediment layer maintained at 10°C in mineral media with nitrogen compounds (\({\text{NO}}_{3}^{ - }\) and \({\text{NH}}_{4}^{ + }\)) and methanol was studied using high-throughput sequencing of the V2–V3 region of the 16S rRNA gene. Methanotrophs of the bottom sediment belonged to the order Methylococcales, with predominance of the genus Methylobacter (6.4 and 4.6% of the total number of sequences, respectively). Members of the methylotrophic community belonged to the genus Methylotenera (family Methylophilaceae). Enrichments in the medium with ammonium and methane were characterized by the highest diversity of methanotrophs, containing 22 OTUs of the family Methylococcaceae, nine of which were not detected under other cultivation conditions. Altogether, only six out of 28 OTUs of methanotrophic bacteria exhibited similarity to cultured members of Methylobacter, Metyloglobulus, and Methylomicrobium, while others showed different levels of similarity (94–99%) to uncultured members of the family Methylococcaceae. The presence of 0.01% methanol promoted preferential development of methylotrophic bacteria, while 0.5% methanol suppressed the growth of methanotrophic bacteria irrespective of the nitrogen source added.

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ACKNOWLEDGMENTS

The authors are grateful to the Irkutsk Supercomputing Center of the Siberian Branch of the Russian Academy of Sciences for the provided access to the HPC cluster Academician V.M. Matrosov.

Funding

This work was conducted according to the State Assignment theme no. 0279-2021-0006 with financial support of the Russian Foundation for Basic Research, project no. ofi_m 17-29-05040.

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Authors and Affiliations

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

    O. V. Shubenkova, A. S. Zakharenko, Yu. P. Galach’yants, V. G. Ivanov, A. V. Khabuev, T. V. Pogodaeva, S. M. Chernitsyna & T. I. Zemskaya

  2. Vinogradov Institute of Geochemistry, Siberian Branch of the Russian Academy of Sciences, 650033, Irkutsk, Russia

    G. V. Kalmychkov

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  1. O. V. Shubenkova
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Shubenkova, O.V., Zakharenko, A.S., Galach’yants, Y.P. et al. Effect of Methanol and Mineral Nitrogen Compounds on the Composition of Methanotrophic Enrichments from the Sediments of a Lake Baikal Methane Seep. Microbiology 90, 443–454 (2021). https://doi.org/10.1134/S0026261721040123

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