Microbiomes were analyzed in samples of the major soil types of Russia and Western Kazakhstan region from different plant communities (fallow, forest, agrophytocenosis). The representatives of 42 bacterial and 2 archaeal phyla were identified in the samples, among which the dominant positions were occupied by representatives of ten phyla: nine bacterial (Actinobacteria (33.5%), Proteobacteria (28.4%), Acidobacteria (8.3%), Verrucomicrobia (7.7%), Bacteroidetes (4.2%), Chloroflexi (3.0%), Gemmatimonadetes (2.3%), Firmicutes (2.1%), Planctomycetes (2.0%)) and one archaeal Crenarchaeota (2.6%). Data analysis by the methods of multivariate statistics suggests that the taxonomic structure of microbiota is formed under the action of two main factors: the strongest factor is soil acidity, which determines the dynamics of the microbiome at the level of major taxa such as phylum, and the weaker factor is the type of vegetation, which determines the community structure at lower taxonomic level (order, family, genus). Detailed analysis of the samples of podzolic soil in Leningrad Region made it possible to identify bacterial taxa specifically associated both with the type of biome (fallow, forest, agrophytocenosis) and with the specific plant community (specific composition of plant synusia).