Returning low C/N crop straw to the paddy field can achieve the dual benefits of reduced methane emissions and enhanced yield stability

The combination of upland-paddy rotation and straw returning is a common practice in China's subtropical regions. However, the effect and mechanisms of returning the upland crop residues to the paddy field on methane (CH₄) emissions during the rice (Oryza sativa L.) season under different upland-paddy rotation systems remain scarce. To this end, a two-year field experiment (2023–2024) compared five of the most popular rotation systems: wheat-rice, rapeseed-rice, green vegetable-rice, Vicia villosa var.-rice, and fallow-rice in the Sichuan Basin. CH₄ emissions, rice yields, greenhouse gas intensity, and soil methanogenic and methanotrophic gene abundances were measured. Dry-season crops received distinct fertilizer inputs, while rice-season management remained uniform. The results showed that: wheat-rice had the highest abundance of the methanogenic gene (5.00 × 10⁷ and 2.27 × 10⁷ copies g⁻¹ soil in 2023 and 2024, respectively) during the rice growth period, resulting from high carbon-to-nitrogen ratio straw inputs (43.91), which enhanced methanogen activity, leading to the largest cumulative CH₄ emissions (683.41 and 238.65 kg hm⁻²) and higher rice yields (7741.83 and 8231.04 kg hm⁻²). Therefore, the greenhouse gas intensity of wheat-rice (2.22 and 0.74 kg CO₂-eq kg⁻¹ grain yield) was significantly higher than that of other systems. In contrast, the Vicia villosa var.-rice (147.56 and 39.55 kg hm⁻²) rotation with low carbon-to-nitrogen ratio straw (11.28) reduced cumulative CH₄ emissions compared to wheat-rice through balancing methanogenic and methanotrophic gene abundances (ratio 0.61–1.19), while maintaining stable yields (7668.22–8614.37 kg hm⁻²). The yield of the Vicia villosa var.-rice rotation system was not significantly different from green vegetable-rice (8117.98 and 9203.85 kg hm⁻²) and was higher than that of the other systems. Notably, Vicia villosa var.-rice achieved the lowest greenhouse gas intensity (0.48–0.12 kg CO₂-eq kg⁻¹) by synergistically optimizing carbon-nitrogen dynamics and soil organic carbon sequestration. The above results indicate that the Vicia villosa var.-rice rotation system exhibits superior performance in terms of stable yield and emission reduction. This study highlights that the straw carbon-to-nitrogen ratio plays a pivotal role in regulating methane metabolism and maintaining carbon-nitrogen balance, thereby presenting a climate-smart strategy for rice cultivation. It provides a robust scientific foundation for optimizing crop rotation systems and contributes to mitigating agricultural greenhouse gas emissions.