Co-application of alternate wetting and drying irrigation and Bacillus subtilis increases yield and reduces N₂O emissions in paddy ecosystems

Alternate wetting and drying (WD) irrigation is an effective water-saving practice for rice production but often increases nitrous oxide (N₂O) emissions. Plant growth-promoting bacteria such as Bacillus subtilis (BS) can enhance crop growth; however, the combined effects of WD and BS on rice yield and N₂O emissions remain unclear. A 3-year field experiment using two japonica rice cultivars was conducted to evaluate the effects of two irrigation regimes (continuous flooding (CF) and WD) and BS application (without BS, –BS; and with BS, +BS) on rice yield and N₂O emissions. The results showed that BS application significantly increased the rice yields under both irrigation regimes. Compared with CF–BS, CF+BS and WD+BS increased the yields by 3.9–9.0% and 5.8–12.6%, respectively, mainly due to a higher total spikelet number. CF+BS had no significant effect on N₂O emissions, whereas WD–BS markedly increased cumulative N₂O emissions, while WD+BS reduced emissions by 34.8–45.9% compared with WD–BS. The WD+BS treatment enhanced root oxidation activity and increased root surface area and volume density in the 20–40 cm soil layer. It also reduced the soil NO₃⁻-N content, raised the NH₄⁺/NO₃⁻ ratio, and enhanced urease and sucrase activities, thereby promoting the accumulation of dissolved organic carbon (DOC) and microbial biomass nitrogen (MBN), along with a higher abundance of the nitrous oxide reductase gene (nosZ) associated with N₂O reduction. Overall, integrating WD with BS increased rice yield while mitigating N₂O emissions. The enhanced root function and aboveground agronomic traits, improved soil enzyme activity, and optimized nitrogen transformation and microbial processes were the key mechanisms for achieving a high yield with reduced environmental impacts.