The paper presents new data on the physiological status of edaphic microbial communities in long farming conditions of the soil. It has been established that the vast majority of them has an inactive status. Functional activity of microbial communities is determined by the metabolic diversity and ability to assimilate alternative metabolic pathways, as well as by the domination of r-strategies. Preliminary administration of mineral and organic fertilizers leads to the formation of microbial communities with typical biomass for each variant of arable chernozem. The share of active biomass fraction was about 1/3 of the summary in the natural biocenosis, and even less while in the agrocenoses.