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Understanding how conservation agricultural management improves soil nitrogen (N) stability in the face of climate change can help increase agroecosystem productivity and mitigate runoff, leaching and downstream water quality issues. We conducted a 2-year field study in a 36-year-old rain-fed cotton production system to evaluate the impacts of changing climatic factors (temperature and precipitation) on soil N under conservation management, including moderate inorganic N fertilizer application (0 and 67 kg N ha−1 ), winter cover crops (fallow; winter wheat, Triticum aestivum L.; hairy vetch, Vicia villosa Roth), and reduced tillage (no-till; disk tillage). Structural equation modeling (SEM) was used to quantify and compare the effects of conservation management and climatic factors on soil N concentrations. Fertilizer and vetch cover crops increased soil total N concentration by 16% and 18%, respectively, and also increased microbial N transformation rate by 41% and 168%. In addition, vetch cover crops also increased soil labile N concentrations by 57%, 21%, and 79%, i.e., extractable organic N, ammonium, and nitrate, respectively. The highest soil δ15N value (6.4 ± 0.3‰) was observed under the 67 kg N ha−1 fertilizer-wheat-disk tillage treatment, and the lowest value (4.8 ± 0.3‰) under the zero-fertilizer-wheat-no-till treatment, indicating fertilizer and tillage might accelerate microbial N transformation. The SEM showed positive effects of temperature and precipitation on labile N concentrations, suggesting destabilization of soil N and the potential for soil N loss under increased temperature and intensified precipitation. Fertilizer and vetch use might mitigate some of the effects of temperature by accelerating microbial N transformations, with vetch having a larger effect than fertilizer (0.35 vs. 0.15, Table 1). No-till can reduce some of the effects of precipitation on soil labile N by maintaining soil structure. Our study suggests that fertilizer, vetch cover crop, and no-till might help improve function and resilience of agroecosystems in relation to soil N cycling. Soil N stabilization in cropping systems can be enhanced by adjusting agricultural management.