Combined Controlled-Release and Common Fertilizer Application Increases Apple Productivity by Optimizing Soil Nutrient and Microbial Communities

Apples in China are planted mainly in nutrient-poor mountain soil, and a large amount of fertilizer input results in resource waste and a decrease in nutrient utilization efficiency. Controlled-release fertilizer (CRF) has been shown to be environmentally friendly and increase crop yield, but nutrient release cannot be precisely synchronized with apple demand. Here, a suitable secondary fertilization method was established by a two-year apple field experiment with CRF and common compound fertilizer (CF) at various ratios under a 25% reduction in application. The application of CF and CRF changes the temporal and spatial distributions of soil NPK nutrients, decreasing NPK losses and NH3 emissions. The NH3 emissions under CF and CRF decreased by 17.98–44.86%, as N loss decreased by 11.59–29.81% and by 4.45–8.19%, with respect to those under CF alone, while the soil pH and electrical conductivity increased by 8.28–17.12% and 10.73–18.29%, compared with those under CF alone. The increase in soil P and K also decreased losses by 8.28–17.12% and 10.73–18.29%. The combined application of CF and CRF can increase soil microbial diversity and functional taxa and nutrient cycling genes, resulting in efficient nutrient transformation and supply for apple trees. The regulation of nutrients and microbes by the secondary application of CF and CRF drives an increase in apple yield of 23.71–54.32%, resulting in high economic benefits. In total, the application ratio of CF and CRF at 3:7 in March and July was an effective way to balance apple productivity and the soil ecological environment, providing a sustainable solution for mountainous orchard ecosystems globally.