The conventional farming system, which predominates in most countries, is based on the use of agrochemical deep ploughing and other special methods. However, intensive farming has several negative impacts, including soil and water pollution and reduced biodiversity. The microbial community plays a crucial role in maintaining the health of agricultural ecosystems. In this context, we need to study how different agricultural practices affect the structural and functional characteristics of agricultural ecosystems. This study assessed the diversity, structure, and functional characteristics of the soil bacterial community in two different cropping systems. The subjects of the study were soil samples from Chernozem, which had been cultivated using the organic method for 11 years and the conventional method for 20 years. The fields are located in the southern part of the Russian Federation. Our results indicated minimal differences in the microbial diversity and soil community composition between the two systems studied. The profiling of the soil bacterial community revealed differences in the abundances of Proteobacteria, Bacteroidota, and Cyanobacteria, which were predominated in the conventional farming system (CFS), while Methylomirabilota and Fusobacteriota were more abundant in the organic farming system (OFS). Bacterial taxa and functional genes associated with nitrogen, phosphorus, and sulphur cycling were found to be more abundant in CFS soils than in OFS soils. The instrumental measurement of soil metabolic activity and microbial biomass content showed that CFS soils had higher microbiome activity than OFS soils. Overall, the study found that the agronomic practices used in conventional farming not only help to maintain the functional properties of the soil microbiome, but also significantly increase its microbiological activity and nutrient bioconversion, compared to organic farming practices.
