Land-Use and Depth-Dependent Assembly of Soil Microbiomes Shapes Ecological Functions, Interaction Networks, and Phytopathogenic Communities Across Crop and Orchard Systems

Soil microorganisms are essential for nutrient cycling, plant productivity, and soil health, yet the relative importance of land-use and soil depth in shaping agricultural microbiomes remains poorly understood. This study investigated soil microbial communities across uncultivated land, alfalfa fields, crop systems (feed corn and sweet corn), and orchard systems (walnut and quince) in the Hajdúnánás region of Hungary using shotgun metagenomic sequencing and soil physicochemical analyses. Microbial alpha diversity showed limited variation among land-use systems but declined significantly with soil depth in both bacterial (Kruskal–Wallis, p = 0.00054) and fungal (p = 0.00051) communities. Beta diversity analyses identified soil depth as the primary driver of microbial community composition in both bacterial (R2 = 0.305, p = 0.001) and fungal (R2 = 0.277, p = 0.001) communities. In contrast, land-use significantly influenced only fungal community composition (R2 = 0.250, p = 0.005). Fungal alpha diversity showed significant negative relationships with soil pH and CaCO3, whereas bacterial diversity exhibited only weak correlations. Crop soils contained the highest numbers of unique bacterial and fungal taxa. Functional analyses revealed significant differences in nutrient cycling, plant-growth-related, decomposition, and environmental adaptation functions among land-use systems. In crop soils, topsoil communities were enriched in oxidative stress-related pathways involved in reactive oxygen species detoxification (ROS), redox homeostasis, and stress regulation, whereas subsoil communities showed a greater representation of antioxidant metabolite production functions. Co-occurrence network analyses indicated greater connectivity in perennial systems, particularly alfalfa soils. Analyses of bacterial and fungal species with reported phytopathogenic potential identified stable cores of phytopathogenic species across agricultural systems, with soil pH emerging as the strongest environmental factor associated with the abundance of phytopathogenic species. Overall, soil depth was the primary driver of bacterial and fungal community assembly, whereas land-use primarily shaped fungal community composition and influenced ecological functions, microbial interaction networks, and the distribution of phytopathogenic species.