Low N2O emissions from wheat in a wheat-rice double cropping system due to manure substitution are associated with changes in the abundance of functional microbes

•Soil N2O emissions have been rarely linked to N-related functional genes in wheat cropland.•Manure N substitution of chemical N fertilizer reduced N2O emissions from wheat cropland.•Manure N combination decreased the abundance of AOB while increased that of nosZ.•The abundance of AOB was significantly increased, relative to that of AOA unaltered by N input.