Species-Specific Cover Cropping Enhances Apple Quality Accompanied by Shifts in Soil Fungal Communities in Subtropical Red-Soil Orchards

Improving fruit quality is a core challenge in apple production in Southwest China, where long-term clean tillage has driven red soil acidification and fertility decline. However, how different cover crop species influence fruit quality through soil fungal pathways in this region remains unclear. Here, we compared five cover crop treatments—natural grass, alfalfa, perennial ryegrass, white clover, and orchardgrass—against clean tillage in a field experiment, integrating ITS sequencing with multivariate statistical analyses to evaluate their effects on soil properties, fungal communities, and apple fruit quality. Orchardgrass (DG) showed the most favorable performance, increasing sugar–acid ratio (+28.74%) and vitamin C content (+42.16%), followed by alfalfa and natural grass, while ryegrass had the weakest effects. Soil fertility improvement followed the same ranking, and soil pH, organic matter, and nitrogen were identified as key factors associated with fungal community shifts. Fungal community composition and diversity were closely linked to soil properties and fruit quality traits, with sugar–acid ratio co-regulated by nitrogen, pH, and fungal diversity, while vitamin C content was directly associated with cover crop treatment. These findings suggest that orchardgrass may be a promising cover crop for enhancing fruit flavor and nutritional quality under the subtropical red-soil conditions tested in this study, offering practical implications for cover crop selection, though the long-term stability of these effects requires further validation through multi-year trials.