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

Abstract

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 other springs. Among the Archaea, which averaged about 20% of 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 microbial communities in the springs with a presumably deeper water source. Chemical and molecular analyzes 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 entry into groundwater after snow thawing of deicin reagents and hydrocarbons, which are successfully biodegraded in the soil.