Nitrosospira cluster 3 lineage of AOB and nirK of Rhizobiales respectively dominated N2O emissions from nitrification and denitrification in organic and chemical N fertilizer treated soils

Agricultural soils are known as nitrous oxide (N2O) sources due to the input of nitrogen (N) fertilizer and livestock faecal excretion. However, few studies have explored the responses of N2O microbial emission pathways and their related functional guilds to long-term soil fertilization regimes. This study examined the effects of four 38-year long-term fertilization treatments (control with no-fertilizer (CK); inorganic N fertilizer (N); manure (M); inorganic N fertilizer with manure (MN)) on the N2O levels generated from nitrification and denitrification, as well as on the nitrifiers and heterotrophic denitrifiers. The acetylene inhibition method was used to determine the microbial pathways of the N2O emissions and molecular biological techniques (cloning, high-throughput sequencing and quantitative PCR) were performed to investigate the nitrifier and denitrifier responses. The organic fertilization demonstrably increased the N2O emissions from nitrification and the abundance of canonical ammonia oxidizers and complete ammonia oxidizers (clade B), but distinctly decreased the abundance of clade A. Combined with the results that strong and positive relationships were detected between the abundance of bacterial amoA genes and N2O content produced from nitrification. We proposed that organic fertilizer applications stimulated the generation of N2O from nitrification dominated by the Nitrosospira cluster 3 lineage of AOB. In contrast, the amount of N2O produced by denitrification was appreciably stimulated by chemical N fertilization, compared to organic fertilization. Strong and positive relationships were detected between the nirK-type denitrifying gene abundances and the N2O emissions generated from denitrification. This suggested that single N fertilizer additions appreciably stimulated N2O production from denitrification dominated by the nirK lineage of the Rhizobiales. These results indicated that chemical N and organic fertilizers stimulated N2O emissions from denitrification and nitrification, respectively, which were dominated by the Nitrosospira cluster 3 lineage of AOB and the nirK lineage of Rhizobiales, respectively.