Bacteroidota structure in the face of varying agricultural practices as an important indicator of soil quality – a culture independent approach

The choice of appropriate agricultural practices has a major impact on soil quality, crop productivity, and bacterial community structure. The aim of our study was to gain insight into Bacteroidota structure, including the phylum, family, and genus in the context of the application of different agricultural practices (crop rotation, intercropping mixture, long-term maize monoculture) across changing seasons (spring, summer, autumn), which is undoubtedly novel among previous reports on different cropping systems. Additionally, the Spearman correlation test as well as ANOVA and RDA statistical analyses were conducted to expand the information on chemical factors directly affecting Bacteroidota abundance in the soil environment. Bacteroidota were shown to be present with varying abundance depending on the agricultural practice and the season. The highest abundance of Bacteroidota occurred when crop rotation was the main agricultural practice, where the highest average yield was also recorded. Thus, our study identified crop rotation as the best of the three agricultural practices compared. The reduction in the relative abundance of Bacteroidota, in particular Flavobacterium sp. in fields K20 (intercropping) and K21 (monoculture), and the achievement of almost twice the lower average yield in field K21 than in field K3, indicated the poorer quality of these soils. We therefore concluded that the increased abundance of Bacteroidota could indicate good quality agricultural soils. It was also proved that the genera Mucilaginibacter and Edaphobaculum are the most sensitive to soil chemistry over the changing seasons, while the genus Flavobacterium is sensitive to agricultural practices and its presence may indicate good quality of agricultural soils. Statistical analyses indicated that chemical properties have a strong influence on Bacteroidota structure formation in agricultural soils. Overall, our results have evidenced that the Bacteroidota community can be an important indicator of soil quality in studies of soil biological degradation processes, since a decrease in the abundance of these beneficial microorganisms potentially could be connected with reduction of the soil quality, fertility and ultimately affects crop yield. They have also shown that the community of this group of bacteria varies between seasons of the year.