Microbial communities – microbiome – are responsible for the most functions in natural and agricultural soils and govern transformations of organic matter. Localization of microorganisms at microscale – in pores and aggregates, as well as at the scale of soil profile define the fluxes of water, organic substances and nutrients, and so, determine the composition and functions of soil microbiome. Understanding the exceptional heterogeneity, biodiversity and activity of microbial communities driving the most biogenic processes is impossible without considering the specifics of soil pore space and aggregates structure at microscale. This project aims on specifics of taxonomic and functional composition of soil microbiome by transformation of organic substances of increasing availability depending on their localization on the pores of increasing size in the three dominants soil types of Russia.