LAUSR

Abstract Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) influence the nitrate (NO3−) reduction and its final fate in the environment. However, it is unclear how denitrifying and DNRA bacterial communities respond to different environment conditions. Here, we investigated the effects of fertilization and sampling time (April, July and November) on the abundances of nitrogen (N) cycling genes in processes of denitrification and DNRA at different soil depths (0–20, 20–40 and 40–60 cm) based on a long-term fertilization experiment station (initiated in 1987). The abundances of genes involved in NO3− reduction process were determined using quantitative PCR (qPCR) analysis method. Sampling time showed a stronger effect on the abundances of denitrifying and DNRA genes than fertilization. And the effect of fertilization on the abundances of genes involved in NO3− reduction process was decreased with soil depths. Compared with no fertilizer (CK), the application of mineral N fertilizer (N2 and N4) reduced the abundances of denitrification and DNRA genes at 0–20 cm soil depth, regardless of sampling time. However, the application of organic manure combined with mineral N fertilizer (M2N2) clearly increased the abundance of specific denitrifying genes, including napA (NO3− to NO2−) and nosZ (N2O to N2) genes compared with N2 and N4 treatments at 0–20 and 20–40 cm soil depths. Although the abundance of nrfA gene was the highest, the abundance of norB gene was the most sensitive to environmental variation among all the tested N cycling genes. Ratio of NO3− to ammonium (NO3−/NH4+) was significantly correlated with all the denitrifying and DNRA genes. In general, long-term application of organic manure combined with mineral N fertilizer has a potential to mitigate the NO3− leaching and N2O production, and NO3−/NH4+ ratio is an important factor driving the dynamics of bacterial communities involved in the NO3− reduction process.