Analysis of Soil Nutrients and Microbial Community Characteristics in Rainfed Rice–Potato Cropping Systems

Background: Rainfed rice–potato cropping systems represent an emerging agricultural pattern in Yunnan Province. This study investigates the dynamics of soil nutrient release and microbial community structure under rainfed rice–potato cropping systems. Methods: Four experimental treatments were established using two rice cultivation methods (flooded and rainfed cultivation) as the preceding crop, followed by two distinct potato cultivars: rainfed rice–potato Dianshu 23 (DR), rainfed rice–potato Dianshu 1418 (DY), flooded rice–potato Dianshu 23 (WR), and flooded rice–potato Dianshu 1418 (WY). Soil samples were collected before rice planting and at harvest, as well as before potato planting and at 40-, 80-, and 120-days post-planting. Soil nutrient release dynamics and microbial community composition were analyzed across all treatments. Results: Flooded rice cultivation as the preceding crop exhibited higher soil nutrient depletion compared to rainfed systems, accompanied by more pronounced increases in soil urease and invertase activities. Following potato establishment, rainfed rice–potato systems demonstrated an accelerated release of available nitrogen and potassium during the initial growth period relative to flooded rice–potato systems. At potato harvest, soil urease and invertase activities increased in rainfed rice–potato systems compared to pre-planting levels, while decreasing in flooded rice–potato systems. Proteobacteria constituted the dominant bacterial phylum across all treatments. Rainfed rice cultivation significantly enhanced Cyanobacteria relative abundance, whereas flooded rice cultivation promoted increased Thermodesulfobacteria abundance. Ascomycota dominated fungal communities, with flooded rice showing significantly greater reductions in Ascomycota relative abundance compared to rainfed systems. Rainfed rice–potato systems exhibited superior soil microbial community richness, diversity, and species abundance relative to flooded rice–potato systems. Bacterial genera associated with nitrogen metabolism showed higher relative abundance in rainfed rice–potato systems, as did pathogenic fungal genera. Conclusions: Soil nutrient characteristics and microbial community profiles in rainfed rice–potato cropping systems differ markedly from traditional flooded rice–potato rotation practices. These findings provide valuable insights for optimizing water and nutrient management strategies in rainfed rice–potato cropping systems.