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 CO₂, CH₄, and N₂O 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 CO₂, CH₄, and N₂O emissions. Results indicated that BC and OM had opposite effects on soil CO₂ and N₂O emissions, with BC resulting in lower emissions and OM resulting in higher emissions, whereas BC, OM, and their combined amendments increased cumulative CH₄ 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 CH₄ and the reduction of N₂O to N₂, thereby accelerating CH₄ emissions while reducing N₂O 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 CH₄ and N₂O emissions. Moreover, puerarin produced by Bacillus metabolism may contribute to the reduction in CO₂ emissions by BC amendment, but increase in CO₂ 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.