Roles of Microbial Community and Keystone Taxa in Rice Productivity under Green Manuring in South China

Green manure (GM)–rice–rice rotation is an important management practice for improving soil fertility and rice productivity. The microbiological mechanisms for the increase in grain yield in GM–rice–rice rotation remain unclear. The responses of soil biodiversity, bacterial and fungal communities, and their interactions in the GM–rice–rice rotation were investigated based on two long-term field experiments in Gaoqiao (GQ) and Nanxian (NX) in Hunan Province, south China. Results showed that rice yields were raised by 11.79% and 15.03% under GM in GQ and NX, respectively. GM promoted Shannon diversity and Pielou’s evenness and changed the community structures of bacteria and fungi. The co-occurrence network analysis found that the percentages of negative edges were higher in GM (40.79% and 44.32% in GQ and NX, respectively) than those in the corresponding winter fallow (34.86% and 29.13% in GQ and NX, respectively) in the combined bacterial–fungal networks, suggesting more stable microbial community under GM. Moreover, GM had higher percentages of bacterial–fungal and fungal–fungal edges than winter fallow, indicating that GM increased the interaction between bacteria and fungi and fungi play more essential roles in affecting soil processes under GM. The keystone taxa in GM were positively linked with C metabolism-related enzymes and soil multifunctionality, and were important in improving soil fertility and rice productivity. We concluded that the fungal community was more sensitive to GM application than the bacterial community and that keystone taxa had important influences on soil properties and rice productivity in the GM–double-rice cropping system, which can effectively support the sustainable development of the paddy field ecosystem in southern China.