Effect of Nitrogen on Interaction Between Carbon, Nitrogen and Phosphorus Cycles in High-Altitude Apple Orchards

To elucidate the effects of nitrogen (N) addition on soil carbon (C), N, and phosphorus (P) cycling in high-altitude orchards on the Qinghai–Tibet Plateau, a three-year field experiment was conducted at an altitude of 3000 m with four N application rates (0, 150, 300, and 450 kg N ha−1, designated as CK, N150, N300, and N450, respectively). We determined soil physicochemical properties, 12 soil enzyme activities, and metagenomic characteristics, and further adopted partial least squares path modeling (PLS-PM) for data analysis and mechanism exploration. The results were as follows: (1) The N300 treatment yielded the maximum C-hydrolase activities and soil organic carbon content, with a 40.6% increase in soil organic carbon compared with the CK group. (2) The N450 treatment resulted in a 365.4% increase in soil nitrate content and significantly reduced the soil pH (from 6.32 to 5.86). Such environmental filtering significantly decreased the relative abundance of Nitrospirota and its core denitrification genes, including nosZ and narI. (3) Continuous N input induced secondary soil P limitation, leading to a more than 90% increase in phosphatase activities under the N450 treatment. Pseudomonadota activated soil P sources by enriching the functional potential of the phn gene cluster. Furthermore, the PLS-PM analysis revealed a significant negative statistical association between P-cycling enzymes and N-cycling functional potential (p < 0.01). This statistical linkage supports the observation of divergent metabolic responses among different element cycles. In conclusion, under the specific experimental conditions tested, an optimal N application rate of 300 kg N ha−1 is recommended to balance agricultural productivity and soil ecological health. The microbiome of alpine apple orchards responds to elevated N input through metabolic trade-offs, namely reducing the functional potential for denitrification and enhancing the P recycling system. These findings provide vital molecular evidence to guide fertilizer reduction, optimize nutrient management, and promote the sustainable development of high-altitude agroecosystems.