The stationary multi-factor trial was established in 1974 on experimental station of Borovce. There are 40%, 60% and 80% share of cereals. Grain yield by 40% share of cereals was statistically higher (6,50 t ha -1 ) than by 60 in the crop rotations trial % and 80% share of cereals (6,23 t ha -1 ). Grain yield of spring barley by 80% share of cereals was statistically lower (4,05 t ha -1 ) than by 40% (5,04 t ha -1 ) and 60% share of cereals (5,03 t ha -1 ). Different proportion of cereals in a rotation system had a significant effect on the abundance of rhizobia, cellulolytic and denitrification bacteria. At combined fertilization (mineral plus organic) we observed higher abundance of bacterial spores, Azotobacter spp., denitrification, cellulolytic and nitrification bacteria in comparison with the variant without organic fertilization. The highest metabolic diversity and average utilization of carbon sources by microbial communities was recorded in soil samples collected from crop rotation system with 40 % contribution of cereals and combined fertilization with added organic fertilizer Veget.