The functioning of well-studied key groups of soil microorganisms depends on the microbial ecosystem in which they function in interaction with species belonging to other ecological groups. An analysis of the composition of the soil microbiota, and the possibility of analyzing the number of representatives of specific species, remains an urgent task of soil microbiology. Such analysis could be performed using modern and expensive methods such as metagenomics and mass-spectrometry, but some questions could also be answered using real-time PCR. This well-known approach is rather cheap for massive analysis and is ready to present reproducible results for practical agricultural applications. Understanding the variability of the primary structure of 16S rRNA is key to the reliable identification of bacterial species and provides an opportunity to choose the optimal pathways for their detection by PCR. In this work, analysis of the sequences of 16S rRNA of two species of soil bacteria, Acinetobacter lwoffii and Paenibacillus taichungensis is carried out. The most variable and most conservative areas on the level of species are detected. It was proved that conventional variable and conservative areas of the gene have on average nearly the same level of variability on the intraspecies level.

Soil microbial communities perform a number of important functions ensuring fertility. They depend on physical and chemical composition of soil and applied agricultural technology. To control the state of the soil, it is necessary to use methods that allow to quickly assess the dynamics of the structure of microbial communities. To develop convenient method for analysis of microbiota the set of taxon-specific primers for RT PCR, recognizing 16S rRNA genes of domain Bacteria, six bacterial phyla and one class was chosen. Calculation of the percentages of lower-order taxa in the upper-order taxon was carried out based on the number of amplification cycles required to achieve the threshold value of fluorescence intensity taking into account the values of amplification factors. Taxonomic structure of the bacterial component of the soil microbial community was analyzed using as an example a sample of the surface layer of arable black soil enriched with regular application of organic fertilizers. The compiled analysis protocol made it possible to obtain data on the percentages of phyla Firmicutes, Bacteroidetes, Actinobacteria, Verrucomicrobia, and of class Gammaproteobacteria belonging to phylum Proteobacteria.

The technology of anaerobic fermentation of organic substrates and especially of organic wastes with rich microbiota needs effective method to observe the microbial community on the different stages of substrate transformation, including its digestion, fermentation and conversion of its products to methane. The fast and cheap method based on taxon-specific RT PCR is developed to assess density of Archaea and Bacteria population in complex microbial communities. The data obtained on the samples from the industrial biogas plant on the different technological stages are consistent with processes that should evolve during fermentation.