Phylogenetic Diversity and Potential Activity of Bacteria and Fungi in the Deep Subsurface Horizons of an Uranium Deposit

The composition of microbial communities in rock samples, reservoir water, and enrichment cultures from subsurface horizons of an uranium deposit (Russia) was determined. The studied horizons were located in the zone of hindered water exchange at a depth of 513–544 m, characterized by moderate salinity (up to 15 g/L) of reservoir water and the presence of charry plant organic matter. The biodiversity of autochthonous subsurface prokaryotes was determined by high-throughput sequencing of the V4 region of the 16S rRNA gene. Bacterial phyla predominant in the rock samples were Firmicutes (24.2%), Fusobacteriota (23.0%), Proteobacteria (18.7%), Actinobacteriota (15.5%) and Bacteroidota (9.0%). The predominant bacterial phylum in the reservoir water was Proteobacteria (90.7%), including representatives of the genera Methylophaga, Porphyrobacter, Roseovarius, Pseudomonas, and Methylococcus. Sequencing of the internal transcribed spacer (ITS) revealed occurrence of lower fungi of the genera Mucor and Thamnidium (phylum Mucoromycota) and of the genus Penicillium (phylum Ascomycota) in the rock samples; members of these genera are known for their resistance to heavy metals and the ability to use complex organic substrates. The functional characteristics of bacterial communities of the rock and reservoir water samples, predicted by the iVicodak program and the KEGG database, showed that reservoir water bacteria had a higher potential ability to carry out the pathways of carbohydrate, nitrogen, and sulfur metabolism, degradation of xenobiotics, benzoate, polycyclic aromatic hydrocarbons and chlorinated organic compounds than the rock microbiota. Enrichment cultures of iron-reducing and sulfate-reducing bacteria and pure cultures of denitrifying bacteria of the genera Bacillus, Paenibacillus, and Acinetobacter were obtained. These results indicate the presence of a small but viable microbial community that can participate in the processes of transformations of carbon, nitrogen, sulfur, and metals in the subsurface horizon when water exchange is activated.