The study was carried out in the Kivach Strict Nature Reserve situated in the middle taiga of Karelia. Albic Podzols formed over fluvioglacial sandy deposits in different vegetation microgroups (lichen-, cowberry-, bilberry-, true moss-dominated) within a cowberry-type pine stand were surveyed. The organic and mineral horizons of these soils were examined for the structural and functional setup of the microbial community. The key groups of microorganisms effecting nitrogen and carbon cycling and fluctuations in bacterial numbers were determined in soils formed under the different vegetation microgroups. The composition of the cellulolytic component of the microbial community was identified, and its variation among microgroups was demonstrated. It was found that the main contributor to soil respiration of the biogeocoenosis is microorganisms in the top organic horizon, while the activity of microorganisms in the mineral part of the soil is inhibited. Variations in some ecophysiological parameters of the soil microbiota, such as basal respiration, microbial biomass carbon (Cmic) and nitrogen (Nmic) and others, depend on soil moisture content and forest floor thickness. The data obtained through these integrated studies of the soil microbial community can be used in environmental monitoring.