The ground cover rice production system (GCRPS) has considerable potential for securing rice production in hilly mountainous areas. However, its impact on yields and N fates remains uncertain under varying rainfall conditions. A two-year field experiment (2021–2022) was carried out in Ziyang, Sichuan Province, located in the hilly mountains of southwest China. The experiment included two cultivation methods: conventional flooding paddy (Paddy, W1) and GCRPS (W2). These methods were combined with three N management practices: N1, no-N fertilizer; N2, 135 kg urea N per hm2 as a base fertilizer; and N3, 135 kg urea N per hm2 with split application for W1 and 67.5 kg N per hm2 of urea and chicken manure separately for W2. The WHCNS (soil water heat carbon nitrogen simulator) model was calibrated and validated to simulate ponding water depth, soil water storage, soil mineral N content, leaf area index, aboveground dry matter, crop N uptake, and rice yield. Subsequently, this model was used to simulate the responses of rice yield and N fates to GCRPS under different precipitation year types using meteorological data from 1980 to 2018. The results indicated that the WHCNS model performed well in simulating crop growth and N fates for both Paddy and GCRPS. Compared with Paddy, GCRPS reduced N leaching (35.1%–54.9%), ammonia volatilization (0.7%–13.6%), N runoff (71.1%–83.5%), denitrification (3.8%–6.7%), and total N loss (33.8%–56.9%) for all precipitation year types. However, GCRPS reduced crop N uptake and yield during wet years, while increasing crop N uptake and yield during dry and normal years. Fertilizer application reduced the stability and sustainability of rice yield in wet years, but increased the stability and sustainability of rice yield in dry and normal years. In conclusion, GCRPS is more suitable for normal and dry years in the study region with increasing rice yield and reducing N loss.
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