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Microbial metabolites and plant exudates are the main regulatory mechanisms of the relationship between agricultural plants and the community of soil microorganisms. The presentation of the report will present experimental materials on the content of bacteria with probiotic properties in the rhizosphere of corn, potatoes and sugar beet anaerobic gg Bifidobacterium and Lactobacillus as the most well-known genera with favorable properties for human health. The dependence of their number on the soil type and their properties, such as acidity and organic matter content, will be considered. It is shown that the number of specific bacteria depends on the yield, apparently, on its root exudates. To study the soil microbial community, a method of microbial diagnostics based on gas chromatography − mass spectrometry of fatty acids, hydroxy acids and fatty aldehydes − was used. Mass spectrometry of the microbial markers method (MSMM) allows you to simultaneously determine more than one hundred microbial fatty acids in situ in clinical, biotechnological or environmental samples without prior cultivation and biochemical analytical materials and primers. This allowed us to quantify 35-40 species of bacteria, including anaerobic bacteria in microbial communities of agricultural soils. Anaerobic bacteria g.g. Bifidobacterium and Lactobacillus did not correlate with the amount of Corg. in the studied soils. Bacteria g. Lactobacillus sp. was identified only in the acidic soils of arable land and bare steam. In separate studies on sandy sod-podzolic sand (humus = 0.8%), lactobacilli (13%) in the NPK + lupine variant prevailed. Bifidobacteria were present in quantities of more than 5% on arable land and on the field. Lactobacilli have not been identified in the maize rhizosphere soil. However, in the maize rhizoplane, the amount of lactobacilli reached 2.6%, while bifidobacteria are ten times less. Thus, the number of specific bacteria depended on the culture cultivated in the rotation. High concentrations of Bifidobacterium were found in the rhizosphere of potatoes in all studied soils. Mycorrhizal fungi of the genus Gigaspora were also found for all cultivated plants. The possibility of including these types of bacteria in agricultural biological products is discussed.