Variable responses of ammonia oxidizers across soil particle-size fractions affect nitrification in a long-term fertilizer experiment

•Fertilization and soil particle-size fraction significantly influenced soil potential nitrification activities and ammonia oxidizers communities.•AOA abundance outnumbered AOB abundance even hundreds of times.•AOB responded more sensitively to ambient changes than AOA did.

We used soils from a 33-year fertilizer experiment and performed high-throughput pyrosequencing analyses targeting the ammonia monooxygenase alpha subunit (amoA) gene (also qPCR and terminal restricted fragment length polymorphism (T-RFLP)) to determine whether and how the composition and structure of ammonia-oxidizing microbes in different particle-size fractions (>2000, 2000-200, 200-63, 63-2 and 2-0.1 μm) have changed in response to chronic inorganic (NPK) and organic (NPKM) fertilizer additions under a rice-wheat rotation. We found fertilization and particle-size fractions had strong effects on abundance and structure of ammonia-oxidizers and potential nitrification activity (PNA) (P < 0.05) which was significantly enhanced under NPKM across all soil fractions. PNA was higher in clay fraction and lowest in silt fraction which was largely correlated to total N and C:N ratio. Aggregated boosted tree emphasized the role that total N and C:N ratio play on ammonia oxidizer abundance. Pyrosequencing data revealed that the Nitrososphaera and Nitrosospira were the dominant clusters of ammonia-oxidizing archaea (AOA) and bacteria (AOB), respectively. Even though AOA population was hundreds of times greater than AOB, it seemed AOB responded more sensitively to ambient shifts which was convinced by NMDS analyses based on Bray-Curtis distance of TRFs and also of OTUs from 454 pyrosequencing.