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.

Background/Objectives: GDSL lipase is crucial for plant growth and the response to environmental stress. While GDSL gene families have been identified in some plants, a comprehensive genome-wide identification and analysis in M. domestica is lacking. Methods: In this study, we identified 131 MdGDSLs belonging to four subfamilies, distributed across 17 chromosomes in the M. domestica genome. Results: The molecular weights (MWs) of these MdGDSLs range from 14.44 to 83.26 kDa, with isoelectric points (PI) spanning from 4.32 to 10.09. Members within the same subgroup exhibit similar gene structures and conserved motifs. Furthermore, whole genome duplication (WGD) significantly contributes to the evolution of the MdGDSL gene family. The promoter regions of MdGDSL genes contain numerous cis-elements associated with abiotic stress and hormone responses. Additionally, RNA-seq data indicate that MdGDSL genes respond to high concentrations of CaCl₂ and cold stress treatments. Conclusions: This study provides a theoretical foundation for further investigation into the mechanisms underlying growth, development, and lipid metabolism in response to stress in M. domestica.