Long-Term Cropping Systems and Fertilization Interactively Drive Deep Soil Nitrate Accumulation and Vertical Transport in Highland Agroecosystems

How cropping systems and fertilization interactively affect deep nitrate accumulation and vertical distribution in highland agroecosystems remains poorly understood. We evaluated soil nitrate nitrogen (NO3−-N), dissolved organic carbon (DOC), and dissolved organic nitrogen (DON) in 0–300 cm soil profiles sampled in 2006 and 2019 from a 35-year long-term experiment established in 1984 on the Chinese Loess Plateau. Mineral N, DOC, and DON were measured in air-dried samples from both years. The experiment included unfertilized fallow (FW) and three cropping systems with different fertilizer treatments. Continuous winter wheat (WC) and grain–legume rotation (GLR) included unfertilized control (CK), phosphorus (P), chemical NP, and NP combined with manure (NPM), whereas continuous alfalfa (AC) included CK, P, and NPM. When averaged across the two sampling years, NO3−-N stocks across the 0–300 cm profile were significantly lower in the three cropping systems than in fallow, with reductions of 102.3–110.0 kg N ha−1. In the GLR and WC systems, both NP and NPM increased subsoil NO3−-N accumulation, with a greater increase under NPM. Under NPM, NO3−-N stocks across the 0–300 cm profile increased by 1426.9 kg N ha−1 in the GLR system and 908.9 kg N ha−1 in the WC system, but by only 93.9 kg N ha−1 in the AC system. NO3−-N accumulated mainly in deep soil in the GLR and WC systems, whereas the AC system maintained concentrations below 3.0 mg kg−1 at depths below 60 cm. The annualized changes in the NO3−-N profile center of mass under NPM were 4.2, 0.8, and −0.2 cm yr−1 in AC, GLR, and WC, respectively, indicating contrasting changes in nitrate vertical distribution within the sampled profile. The effects of NPM on subsoil NO3−-N differed among cropping systems and were associated with soil moisture, DOC, and the DOC/DON ratio. Overall, continuous alfalfa limited deep NO3−-N accumulation even under NPM, highlighting the potential of deep-rooted perennial cropping systems and improved coordination of N and C inputs to limit nitrate accumulation in deep soil.