Microbial Community Composition of Floodplains Shallow-Water Seeps in the Bolshaya Rechka Floodplain, Western Siberia

Recently discovered fields of seeps in western Siberia are an important, previously unknown source of methane. Seeps are located in the floodplains of small rivers and vary in shape, size and localization. Methane fluxes from seeps may be high, making them the sources of high regional importance. However, the data on the seep bacterial community composition are scarce, concentrating mainly on methanotrophic bacteria. In the present work, the overall bacterial diversity in the sediments of shallow-water seeps at the floodplain of the Bolshaya Rechka River was studied using high-throughput 16S rRNA gene sequencing. Molecular analysis revealed that Gammaproteobacteria and Actinobacteria were the most abundant bacterial groups (28.5–33.8 and 11–13.2% of total 16S rRNA genes, respectively). A significant part of the sequences belonged to Chloroflexi, Desulfobacterota, and Bacteroidota. Acidobacteriota and Verrucomicrobiota were responsible for 1.5–2.7 and 1.0–1.9%, respectively. The methanotrophic community was dominated by bacteria of the genus Methylobacter. The most numerous species-level OTU (8% of all 16S rRNA gene sequences) belonged to Methylobacter tundripaludum (97% identity). Methanotrophic Alphaproteobacteria were not detected in the seeps. Our results confirm the presence of an active bacterial community in the sediments of shallow-water seeps, with predominance of methanotrophic Gammaproteobacteria.