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.

Root morphology and physiology influence aboveground growth and yield formation in rice. However, root morphological and physiological differences among rice varieties with differing nitrogen (N) sensitivities and their relationship with grain yield are still unclear. In this study, rice varieties differing in N sensitivity over many years of experiments were used. A field experiment with multiple N rates (0, 90, 180, 270, and 360 kg ha⁻¹) was conducted to elucidate the effects of N application on root morphology, root physiology, and grain yield. A pot experiment with root excision and exogenous application of 6-benzyladenine (6-BA) at heading stage was used to further verify the above effects. The findings revealed that (1) under the same N application rate, N-insensitive varieties (NIV) had relatively large root biomass (root dry weight, length, and number). Grain yield was associated with root biomass in NIV. The oxidation activity and zeatin (Z) + zeatin riboside (ZR) contents in roots obviously and positively correlated with grain yield in N-sensitive varieties (NSV), and accounted for its higher grain yield than that of NIV at lower N application rates (90 and 180 kg ha⁻¹). (2) The root dry weight required for equal grain yield of NIV was greater than that of NSV. Excision of 1/10 and 1/8 of roots at heading stage had no discernible effect on the yield of Liangyoupeijiu (NIV), and it significantly reduced yield by 11.5% and 21.3% in Tianyouhuazhan (NSV), respectively, compared to the treatment without root excision. The decrease of filled kernels and grain weight after root excision was the primary cause for the yield reduction. Root excision and exogenous 6-BA application after root excision had little influence on the root activity of NIV. The oxidation activity and Z + ZR contents in roots of NSV decreased under root excision, and the increase in the proportion of excised roots aggravated these effects. The application of exogenous 6-BA increased the root activity of NSV and increased filled kernels and grain weight, thereby reducing yield loss after root excision. Thus, the root biomass of NIV was large, and there may be a phenomenon of "root growth redundancy." Vigorous root activity was an essential feature of NSV. Selecting rice varieties with high root activity or increasing root activity by cultivation measures could lead to higher grain yield under lower N application rates.