The paper presents the result of the research of the microbiome of the typical chernozem. The anthropic load of the soil, the agricultural management system influenced the formation of the communities of Archaea and Bacteria in the soil at the Experimental Base Biotron. The experimental plots were arable land, occupied with plants of two contrasting fodder crop rotations (with and without alfalfa) in three variants: 1 - non-fertilized background (control); 2 - mineral fund (mineral fertilizers); 3 - organic background (cattle manure).The type of soil fertilization and crop rotation are essential factors influencing the abundance and diversity of soil microorganisms. As a result of metagenomic research, about 19 phyla, 38 classes, 97 orders, 146 families and 305 genera of prokaryotes were identified. To characterize the diversity of soil microorganisms according to agricultural practices, the Shannon Diversity Index was determined. The diversity of different soil microbiocenosis taxa was influenced differently by crop rotation and fertilization type. The highest Shannon diversity index of genera within phyla was recorded for the Proteobacteria phylum of the Bacteria domain in the no-alfalfa crop rotation, control variants (3.42) and mineral fertilization (3.35).