Understanding the stoichiometry of extracellular enzymes in soil, particularly in relation to nutrient acquisition (e.g., carbon, nitrogen, phosphorus), provides valuable insights into microorganisms’ resource requirements. This study investigates the metabolic constraints of soil microorganisms in response to different growth stages of apple trees under various soil management practices. A 14-year long-term experiment with a split-plot design was conducted, where the main plots received different cover crop treatments (bare vs. cover crop), and subplots were subjected to four fertilizer treatments (CK, M, NPK, MNPK). The significant main and interactive effects of cover crops, fertilizer treatment, and growth period on soil nutrients were observed (p < 0.001). Both cover crop and fertilizer treatments significantly increased the soil organic matter content, with implications for orchard resilience to drought. However, the cover factor alone did not notably influence soil carbon–nitrogen ratios or microbial communities. Microbial carbon limitations were driven by soil water dynamics and microbial biomass, while microbial phosphorus limitations were closely linked to total nitrogen levels. The results underscore the combination of cover crops and MNPK fertilizer-enhanced soil nutrient levels and enzyme activities, mitigating microbial carbon and phosphorus limitations. These findings suggest practical strategies for optimizing fertilization practices to improve soil fertility and address nutrient constraints in orchard ecosystems.
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