Impact of Organic Material Return on Greenhouse Gas Emission Flux and Soil Microorganisms in Paddy Soil

The incorporation of Chinese milk vetch (CMV, Astragalus sinicus L.) and rice straw is a common strategy to reduce chemical fertilizer in Chinese southern paddy fields. However, the effect of replacing part of the chemical fertilizer with organic material on greenhouse emissions is still a subject of controversy. Therefore, a field experiment initiated in 2009 was conducted to investigate the effects of different organic material return on greenhouse emissions, soil microbial community and soil fertility. There were five treatments, including CK (no chemical fertilizer, no CMV, no straw); NPK (chemical fertilizer alone); MF40 (CMV plus 40% of NPK); MS (CMV plus rice straw return); and MSF40 (CMV plus straw return plus 40% of NPK). The results showed that, compared with CK, all fertilization treatments significantly increased rice yield, with MSF40 treatment achieving a yield 19.98% ± 1.57% higher than that of NPK. Relative to NPK, the application of organic material significantly increased soil organic matter (SOM), total nitrogen (TN), and available phosphorous (AP) contents, and the available potassium (AK) content under MSF40 increased by 25.87% ± 2.15%. Compared with NPK, although MSF40 significantly increased cumulative CH4 emissions and global warming potential (GWP), it exhibited a comparable yield-scaled GWP with that of NPK. The cumulative N2O emissions were negative across all treatments with −8.54 ± 0.67 to −3.61 ± 0.27 kg ha−1, indicating that the paddy field acted as a sink for N2O, with MSF40 treatment showing the strongest absorption capacity. Organic material return enriched microbial taxa involved in soil element cycling which may result in improved soil fertility and rice yield, e.g., MS enriched Zavarzinella, Polyangia, Apiosordaria, and Lecythophora; MSF40 enriched Bacteroidales, Clonostachys and Junghuhnia. Redundancy analysis showed that soil OM, TN and AP were significantly positively correlated with rice yield and CH4 emission. In conclusion, MSF40 represents a suitable fertilization strategy for balancing high rice yield, soil fertility improvement, and GHG per unit yield equivalent to NPK in the Fuzhou rice region. However, these findings are based on a single-season field experiment, and therefore require validation across multiple growing seasons.