Microbe-mediated reduction of methane emission in rice-frog crop ecosystem

Rice-frog crop ecosystem (RFCE) can significantly reduce CH4 emission from paddy soils to mitigate global warming. However, information on the correlation of soil microbial communities with paddy soil CH4 emission in RFCEs remains limited. This study evaluated the influence of frogs on CH4 flux, paddy soil/water properties, and abundance/community composition of methanogens and methanotrophs in an RFCE between 2018 and 2019. The study parameters were compared between "with frogs " (RFCE; 15,000 frogs ha(-1)) and "without frogs " (control check [CK]) conditions. Frogs in paddies significantly decreased the CH4 flux during the rice-growing seasons (p < 0.05) but increased the paddy water/soil dissolved oxygen (DO) concentration, redox potential (Eh), and soil organic carbon (SOC) content. Compared with the CK, the RFCE significantly decreased the relative abundance of the soil methanogen species Candidatus Methanoperedens nitroreducens and Methanocella arvoryzae, genera Candidatus Methanoperedens and Methanocella, and families Methanoperedenaceae and Methanocellaceae (p < 0.05); however, it significantly increased the abundance of the soil methanotroph species Methylosinus sp. LW2, Methylocystis sp. KS3, and Methylocystis sp. KS30; genera Methylosinus and Methylocystis; and family Methylocystaceae (p < 0.05). Furthermore, variation partitioning analysis revealed that oxygen (DO and Eh) explained 41.2% of the variation in the abundance of soil methanogens, which was greater than the effects of C/ N (38.2%) and SOC content (38.1%). For soil methanotrophs, oxygen (DO and Eh) explained 45.6% of the variation, which was more than the effects of C/N or pH. Oxygen concentration in the paddy soil/water was the driving factor for the change in the composition of soil methanogenic and methanotrophic microbial communities. Bioturbation due to the frogs increased oxygen availability in the paddy soil, decreased CH4 production by soil methanogens, and increased CH4 oxidation by type II methanotrophs, all of which reduced CH4 emission. Thus, this study provides strong evidence for the microbial mechanisms underlying the reduction of CH4 emission from RFCE.