Objectives Long-term fertilization significantly altered the soil nitrogen cycle and the community structure of ammonia oxidizers. However, the different fertilization treatments, especially organic manure, had the significant effect on the soil pH of acid soils. Systematical studies are needed to clarify the change in abundance and composition of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB).

Methods An acidic upland soil, sited under long-term (27-year) fertilization, was chose for the investigation with maize as tested materials. Soil samples were collected from the four treatments of mineral N fertilizer (N), mineral NPK fertilizer (NPK), organic manure (OM) and an unfertilized control (CK). The abundance and composition of AOA and AOB were determined using real-time polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE)．

Results 1) Long term fertilization resulted in significant changes in soil pH values. The lowest soil pH was in treatment N, only 4.03, that in treatment NPK and CK were slightly higher, and that in treatment OM was the highest, which was 6.40, close to neutral. 2) Long-term fertilization improved the content of soil organic matter, total nitrogen, ammonium nitrogen and nitrate nitrogen. 3) The OM treatment significantly increased the soil NH₃ concentration, the others did not. 4) Fertilization significantly increased the abundance of AOA, with the maximum amplitude in OM treatment. The AOA abundance was extremely significantly correlated with the contents of soil organic matter, carbon and total nitrogen (P < 0.01), and significantly correlated with NH₄⁺-N and soil NH₃ concentrations (P < 0.05), not significantly correlated with soil pH and NO₃^–-N (P > 0.05). The community structure of AOA was changed, but that only in OM treatment was obvious. Phylogenetic analyses showed that most of the AOA sequences from the fertilization treatments were affiliated with group 1.1b thaumarchaea and a few with the group 1.1a-associated thaumarchaea. The RDA analysis showed that soil pH, organic matter, total nitrogen, ammonium nitrogen and NH₃ concentrations in soil were the main environmental factors leading to the change of AOA community. 5) Only OM treatment showed significant effect on the abundance and composition of AOB. The AOB sequences from OM treatment soil were affiliated with Nitrosospira Cluster 3 and some with and Nitrosospira Cluster 9. The AOB abundance was positively correlated with soil NH₃ concentration (P < 0.01), and positively correlated with organic matter, carbon and total nitrogen (P < 0.05).

Conclusions Long-term different fertilizations have caused different variation of soil physical and chemical properties, as well as the abundance and community structure of AOA and AOB in acid soil, especially the application of organic manure. Most of the AOA in all the treatments are affiliated with group 1.1b thaumarchaea and a few with the group 1.1a-associated thaumarchaea. Only the AOB group was detected in the OM treatment, most of which were affiliated with Nitrosospira Cluster 3, and a few were affiliated with Nitrosospira Cluster 9.