Cover-Crop Types and Soil Depths Shape Soil Microbial Diversity and Enhance Network Complexity in an Apple Orchard

Cover crops are vital for sustainable orchard management, but their differential impacts on soil microbial communities and inter-domain networks across soil profiles remain unclear. To address this, we conducted a field experiment in a semi-arid apple orchard on China’s Loess Plateau, comparing three treatments—clear tillage (CT), natural grass (NG), and Medicago sativa (MS)—across two soil depths (0–10 cm and 10–20 cm). Soil physicochemical properties and microbial biomass were analyzed, and bacterial (16S rDNA) and fungal (ITS2) communities were characterized via high-throughput sequencing. Results showed that MS treatment significantly increased key soil nutrients, elevating soil organic carbon (SOC) by 25% and total nitrogen (TN) by 30% in the topsoil relative to CT. Microbial α-diversity was significantly enhanced under cover crops, with the Shannon index increasing by 8.5% for bacteria and 15.2% for fungi in MS topsoil. Co-occurrence network analysis revealed that MS fostered the most complex and stable microbial networks, marked by a 40% increase in nodes and a 55% increase in edges compared to CT, alongside strengthened fungal–fungal associations. These findings quantitatively demonstrate that legume cover crops like Medicago sativa are most effective in enhancing soil fertility and microbial network complexity in semi-arid orchards, with benefits extending into the subsurface soil.