Soil Microbiome Changes under Long-Term Rye and Maize Monocropping Systems, Crop Rotation and Bare Fallow under Different Fertilization Variants

Microbial communities are recognized as critical and essential factors in maintaining crop and soil health. However, our current understanding of soil microbial status, particularly in long-term monocropping systems, remains limited, especially concerning interactions and community structure. This study aims to provide information on soil microbial parameters in monoculture and bare fallow. The investigation was comprehensive and multifaceted, including determining the soil enzymatic activity, evaluating the community physiological profile (BIOLOG), and characterizing soil bacterial and fungal structure composition (NGS, t-RFLP, qPCR) within a field experiment involving 55 years of monocultures and fallow periods. We observed that the lowest levels of microbial parameters—including biochemical and enzymatic activity, prokaryotic community diversity, and functional gene abundance—occurred in the bare fallow treatment. However, the abundance of pathogenic microorganisms declines when fields are left fallow. Microbial taxonomy analyses based on sequencing showed that soil collected from fallow is more abundant in microorganisms, which are generally recognized as PGPR and are potential biocontrol agents (Bacillaceae, Streptomycetaceae, Azospirillales, Rhizobiales). Monocropping and long‑term bare fallow systems require minimal agrotechnical intervention. Nevertheless, given the growing challenges in agriculture and the need to protect soil health, replacing monoculture with sustainable farming practices remains essential.