The methods of Russian soil biology for the purposes of the investigations of soils microbiome were studied. The most important methods are cross-disciplinary investigations of plant and microbial interactions, the role of microbiome in the forming of soil fertility and carbon cycle. For the purposes of the most complete description of soil microbiome functions we suggest to combine the methods of metagenomics (for the purposes of the assessment of the phylogenic diversity of the microorganisms), biomarkers analysis (for the purposes of determination of the functional diversity) and the changes in the enzyme activity (for the purposes of the assessment of the actual functioning of soils). The investigation of correlation of the structural soil hierarchy (from aggregates and microloci to the soil areas) and levels of microbial community organization (from microbial populations to bio-geographic regularities) will allow us to understand better the distribution and common specificities of soil and microorganisms interactions. Along with the investigation of spatial organization we suggest to study the dynamics of the soil microbiomes on different time lines: short-term changes (on the field monitoring areas), transformation during the soil forming process (on the “chronosequences” of the soil of a different age) and at the geologic time scale (on the example of buried soils). In this paper we consider the importance of the investigation of the diversity of the soil microorganisms as a source of the suppressing activity of soils as the largest depository of genetic information, important agent of the emission and fixation of atmospheric carbon. The comparative analysis of microbial diversity of disturbed and undisturbed soils and the assessment of outer impact on the soil microbiome is necessary for the preservation of soil biodiversity as one of the most valuable ecologic and biotechnologic resource.