Soil microorganisms play important roles in maintaining soil quality and plant production. The study of diversity, distribution, and behavior of microorganisms in soil habitats is essential for a broad understanding of soil health. Agricultural management practices, particularly inputs of manure and cover crops, can have large impact on the size and activity of soil microbial communities. The aim of this study was to evaluate changes in soil microbial community in response to soil depth throughout the melon, tomato, wheat and cotton growing season in a calcareous soil Uzbekistan semi arid region. The number of ammonifying, denitrifying, nitrifying, oligonitrophilic, oligotrophic bacteria and nitrogenase activity in serozem soil under different agricultural crops in Surhandarya region Uzbekistan were compared. Soil samples were collected from the soil under cotton, melon, tomato, wheat in spring, summer, autumn, and winter. We measured the microbial population at depth intervals of 0-10 cm, 10-20 cm, and 20-30 cm. Sites used in this study represent continuously cultivated (more than 50 years) fields located in Surhandarya province, southeastern part of Uzbekistan. Soil is calcareous serozem soil having a calcic horizon within 50 cm of the surface. The orchic horizon is low in organic matter. The climate is semi arid with mean annual air temperatures of 16 C and 18 C, and mean annual rainfalls of 200 mm. Plate dilution method was used for determination of numerous microorganisms using agar medium. Microbial density was expressed as colony forming units (CFU). Nitrogenase activity was measured using acetylene reduction assay. The results revealed that the number and enzymatic activity of microorganisms depended upon plant type, depth and date of sampling. The total number of ammonifying bacteria, and oligotrophic bacteria tended to be highest under tomato and wheat during summer and the lowest in winter. The total number of oligonitrophil bacteria decreased on soil planted to melon and wheat and increased in soil under cotton. These bacteria populations are distributing well, when soil has low N content. Uzbekistan soil is nitrogen deficient soil, and oligonitrophil bacterial strains are higher than other microbail populations. Bacterial density was the lowest in winter and increased gradually through spring and autumn. The number of ammonifying and oligotrophic bacteria were higher at the 10-20 cm soil depth of soil than at the 0-10 cm depth regardless of plant type. Seasonal changes in the numbers of soil microorganisms were marked in all agricultural crops, with the lower numbers in winter and higher numbers in spring and summer. The results of nitrogenase activity of soils revealed that tomato and cotton cultivated soil in the Surhandarya region contributed to the high nitrogenase activity. Soil without plant cover had a lower nitrogenase activity in comparison to soil with plant cover. This experiment indicated that different agricultural crop practice affected the microbial characteristics of soil and plant cover is important in increasing microbial population and soil enzyme in nutrient poor arid soils.