Combined metabolomic and microbial community analyses reveal that biochar and organic manure alter soil C-N metabolism and greenhouse gas emissions.

The use of biochar to reduce the gas emissions from paddy soils is a promising approach. However, the manner in which biochar and soil microbial communities interact to affect CO 2 , CH 4 , and N 2 O emissions is not clearly understood, particularly when compared with other amendments. In this study, high-throughput sequencing, soil metabolomics, and quantitative real-time PCR were utilized to compare the effects of biochar (BC) and organic manure (OM) on soil microbial community structure, metabolomic profiles and functional genes, and ultimately CO 2 , CH 4 , and N 2 O emissions. Results indicated that BC and OM had opposite effects on soil CO 2 and N 2 O emissions, with BC resulting in lower emissions and OM resulting in higher emissions, whereas BC, OM, and their combined amendments increased cumulative CH 4 emissions by 19.5 %, 31.6 %, and 49.1 %, respectively. BC amendment increased the abundance of methanogens (Methanobacterium and Methanocella) and denitrifying bacteria (Anaerolinea and Gemmatimonas), resulting in an increase in the abundance of mcrA, amoA, amoB, and nosZ genes and the secretion of a flavonoid (chrysosplenetin), which caused the generation of CH 4 and the reduction of N 2 O to N 2 , thereby accelerating CH 4 emissions while reducing N 2 O emissions. Simultaneously, OM amendment increased the abundance of the methanogen Caldicoprobacter and denitrifying Acinetobacter, resulting in increased abundance of mcrA, amoA, amoB, nirK, and nirS genes and the catabolism of carbohydrates [maltotriose, D-(+)-melezitose, D-(+)-cellobiose, and maltotetraose], thereby enhancing CH 4 and N 2 O emissions. Moreover, puerarin produced by Bacillus metabolism may contribute to the reduction in CO 2 emissions by BC amendment, but increase in CO 2 emissions by OM amendment. These findings reveal how BC and OM affect greenhouse gas emissions by modulating soil microbial communities, functional genes, and metabolomic profiles.