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Structure and Seasonal Variability of Microbial Communities of Groundwater in the City of Moscow

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Abstract—

Groundwater, which appears on the surface in the form of springs, is an important ecologically significant component of the aquatic ecosystem, sensitive to changes in environmental conditions. The anthropogenic impact associated with urbanization leads to a change in the characteristics of groundwater, which, in turn, affects the composition of microbial communities in spring waters. Using high-throughput sequencing of the 16S ribosomal RNA gene fragments, we characterized the composition of microbial communities in five natural springs in the city of Moscow in the spring, summer, and winter seasons. The microbial communities of each spring in different seasons were similar to each other and clearly differed from the microbiomes of the other springs. Among the Archaea, which averaged about 20% of the microbial communities, ammonium-oxidizing Crenarchaeota predominated, as well as Nanoarchaeota. Most of the Bacteria belonged to the phyla Proteobacteria, Patescibacteria, Verrucomicrobiota, Chloroflexi, and Bacteroidota. Autotrophic bacteria, including iron-oxidizing bacteria of the family Gallionellaceae and nitrifiers, as well as methanotrophs, accounted for significant proportions in the microbial communities of the springs with a presumably deeper water source. Chemical and molecular analyses did not reveal contamination of spring waters with toxic substances and oil-derived products, as well as the presence of pathogenic microorganisms and indicators of fecal pollution. However, during the spring season, the proportions of halophilic and hydrocarbon-oxidizing bacteria increased in water microbiomes, which may reflect the entry into groundwater after snow thawing of deicing reagents and hydrocarbons, which are successfully biodegraded in the soil.

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Funding

The study was supported by the Russian Foundation for Basic Research and the Government of Moscow, project no. 21-34-70027, and the Ministry of Science and Higher Education of the Russian Federation.

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  1. Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071, Moscow, Russia

    E. V. Gruzdev, Sh. A. Begmatov, A. V. Beletsky, A. V. Mardanov, N. V. Ravin & V. V. Kadnikov

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  1. E. V. Gruzdev
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  2. Sh. A. Begmatov
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  3. A. V. Beletsky
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  4. A. V. Mardanov
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Contributions

Collection of water samples and their physicochemical characterization, as well as isolation of metagenomic DNA, were carried out by E.V. Gruzdev and V.V. Kadnikov. 16S rRNA gene libraries were sequenced by A.V. Mardanov. Analysis of 16S rRNA gene sequencing results was performed by Sh.A. Begmatov and A.V. Beletsky. Data were analyzed and the article was prepared by E.V. Gruzdev, V.V. Kadnikov, and N.V. Ravin. The project was managed by V.V. Kadnikov. All authors participated in the discussion of the results.

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Correspondence to V. V. Kadnikov.

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Gruzdev, E.V., Begmatov, S.A., Beletsky, A.V. et al. Structure and Seasonal Variability of Microbial Communities of Groundwater in the City of Moscow. Microbiology 92, 192–203 (2023). https://doi.org/10.1134/S0026261722603293

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