Diversity of Microbial Communities in the Soils of Different Natural and Technogenic Ecosystems of the Meshchera Lowland

Understanding the relationship between the conditions prevailing in anthropogenically altered soils and the diversity of the soil microbiome can provide important information for assessing the state and solving the problem of maintaining the stability of natural and technogenic ecosystems. Using high-throughput Illumina sequencing, the diversity and composition of bacteria, archaea, and fungi in the soils of five different phytocenoses within the Meshchera Lowland (southern Moscow region) (one of the most industrially saturated regions in the country) are analyzed. The results show a reduction in taxonomic richness and a decrease in phylogenetic diversity and alignment of microbial communities during the transition from the soil of a conventionally background site to soils of secondary phytocenoses and soils associated with technogenic objects—an overgrown phosphogypsum dump and an industrial wastewater discharge site. Representatives of 28 bacterial and 1 archaeal phylum are identified in the prokaryotic component of the microbiomes of the studied soils. The dominant position is occupied by the phylum Actinomycetota (relative abundance 21–30%) and Pseudomonadota (16–19%). The taxonomic composition of the fungal component of the communities is dominated by Ascomycota (53–74%), represented by the classes Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Representatives of Basidiomycota in the soils of different phytocenoses accounted for 16 to 29% of all identified fungal taxa. The classes Tremellomycetes, Agaricomycetes, and Microbotryomycetes were the most numerous among the basidiomycetes. Using the FAPROTAX software package for predicting the ecological functions of bacterial and archaeal taxa obtained by sequencing 16S rRNA amplicons, as well as the automatic FUNGuild algorithm for sorting by ecologically significant categories of the fungal taxa identified during ITS amplicon sequencing, the ecological profiles of the studied microbial communities were characterized. The data can be used in the environmental monitoring system of impact zones of industrial enterprises.