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The method of microbial diagnostic based on gas chromatography – mass spectrometry of fatty acids, hydroxy acids and fatty aldehydes – was used for the study of the soil microbial community. Mass spectrometry of microbial markers (MSMM) method permits simultaneous determination of more than a hundred microbial fatty acids in situ in clinical, biotechnological or environmental samples without precultivation and biochemical test materials and primers. Some beneficial probiotic bacteria in soils microbial community such as Acetobacter diazotroficus, Bacillus sp., Bifidobacterium sp., Clostridium spp., Lactobacillus sp., Rhodococcus sp. and other are discussed in this article. Soil conditions in situ as well as physiological features of these microorganisms allows to present the following trophic chain: hydrocarbons (plant’s exudates and residues) products of their oxidation by actinobacteria (nocardia, rhodococci or mycobacteria) free aminoacids and biomass proteins (metabolism products of nocardia, rhodococci or mycobacteria) products of their fermentation by clostridia (or propionibacteria) volatile fatty acids (acetic, propionic, isobutiric, butyric et all.) and Н2 and CO2. This syntrophic association may be the basis for agricultural ecosystem and can support the compounds of soil’s health and fertility production. Questions concerning the potential effects on soil biofertilization (humus preservation, formation of water-stable aggregates) in agricultural systems are considered. Key words: probiotic bacteria, soil, biofertilization, fatty hydroxy acids biomarkers.