LAUSR

Abstract Ammonia oxidation, the rate-limiting step of autotrophic nitrification, is carried out by ammonia-oxidizing archaea (AOA) and bacteria (AOB) that differ in their physiology and metabolic pathways. However, there has been little field investigations on the dynamic responses of ammonia oxidizers to different fertilizer inputs in intensive crop rotations. Here, we examine the soil potential nitrification rates (PNR), abundance and communities of AOB and AOA across different growth stages of wheat and maize at two soil depths (0–20 and 20–40 cm) under three fertilization regimes, namely zero fertilization (CK), chemical fertilizer (NPK) and partial replacement of the chemical fertilizer nutrients with organic manure (NPKM). Soil PNR was higher in the surface soil than in the subsoil in the wheat season, but no significant difference was observed in the maize season. Fertilization especially NPK treatment increased soil PNR, and the effect was more pronounced in the surface soil in the wheat season. The influence of soil depth on the abundance and communities of AOA and AOB was greater than that of fertilizer regime or plant growth stage across wheat and maize growth stages. The differences of ammonia oxidizers communities were mainly attributable to soil total nitrogen, organic carbon and soil moisture contents in the two depths. The abundance of AOB decreased more sharply than that of AOA with increasing soil depth. In general, application of NPK only increased AOB abundance in both wheat and maize seasons, whereas NPKM treatment increased AOB abundance only in the maize season (except in the subsoil at harvest). Generally, soil PNR was correlated with AOB and AOA abundances except for AOB in the subsoil in the wheat season and AOA in the surface soil during maize growth. Fertilization regime did not increase AOA abundance or alter AOA communities across all soil depths and plant growth stages. Our results indicate that the ammonia oxidizers differ greatly in responses to fertilization regimes and the changes are associated with soil depth and crop growth stage. The dynamics of soil microorganisms should be integrated into fertilizer and crop management to achieve sustainable agricultural systems.