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 N 2 O emissions have been rarely linked to N-related functional genes in wheat cropland. • Manure N substitution of chemical N fertilizer reduced N 2 O 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. Fertilization has been shown to affect nitrogen (N) cycling and its related functional microbes in agricultural soils. However, the linkage between soil N 2 O emissions and N-related functional genes under different fertilization strategies from wheat in a wheat-rice double cropping system is rarely examined. Here, we carried out a two-year field study to examine the response of soil N 2 O emissions driven by N cycling functional genes [archaeal and bacterial amoA (AOA + AOB), nirS , nirK and nosZ to different fertilization strategies in a wheat cropland of subtropical China. Three fertilizer treatments were established consisting of chemical phosphorus (P) and potassium (K) fertilizer application (PK), chemical N (urea) and PK fertilizer application (NPK), and chemical NPK fertilizer application with chemical N partially replaced with manure (composted pig manure) (NPKM). Over the two wheat seasons, seasonal total N 2 O emissions averaged 0.66, 3.60 and 3.11 kg N ha−1 for PK, NPK and NPKM plots, respectively. Relative to the NPK treatment, the NPKM treatment significantly decreased N 2 O emissions by 14 % without compromising grain yield, with a lowered combined fertilizer-induced emission factor (EF) of 1.02 %. Compared with the PK treatment, N fertilization consistently and significantly increased the abundance of ammonium-oxidation bacteria (AOB), nirS , nirK and nosZ genes. The nosZ gene, which drives N 2 O reduction during denitrification, showed a greater extent under NPKM with manure N combination. The AOB had a more sensitive response than ammonium-oxidation archaea (AOA) to chemical N fertilization. Seasonal N 2 O emissions showed significant positive correlations with AOB gene abundance and the ratio of (nirK + nirS)/ nosZ , while had a negative correlation with nosZ gene abundance across N fertilized treatments. The N 2 O-related microbial composition of functional genes was significantly changed by N fertilizer application and also showed contrasting patterns between treatments of chemical N fertilizer with and without manure N substitution. Together, partially replacing chemical N fertilizer with manure reduced N 2 O emissions from wheat in a wheat-rice double cropping system, mainly through decreasing AOB associated-nitrifying potential, and particularly stimulating N 2 O reduction. [ABSTRACT FROM AUTHOR]