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Purpose: The study aimed to improve understanding of the transformation of N in the Ili River Valley by investigating the abundance and community composition of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under different land uses at bulk soil and aggregate levels. Materials and methods: Soil samples were collected from plots of three types of land use, i.e., native pasture (NP), conventional farming (CF), and organic farming (OF). Soil aggregates were separated using wet-sieving method. The abundance and structure of AOB and AOA communities were assessed by qPCR and DGGE, respectively. Results and discussion: Compared with CF, OF and NP both increased soil TN and SOC stock but via contrasting mechanisms. The abundance of AOB under cropland uses (CF and OF) was higher than those of NP. The AOB sequences, belonging to Nitrosospira cluster 1, which is adaptable to high mineral N content in cold region, increased in CF than in other land uses. Conversion of NP to cropland did not affect the abundance, but the community structure of AOA. The abundance of AOB and AOA in large macroaggregate and silt and clay aggregate were significantly lower than those in small macroaggregate under cropland uses. In cropland, the small macroaggregate provided the microenvironment for the growth of AOB and AOA, thereby serving as a potential hotspot for ammonia oxidation. Conclusions: Reclamation of grassland to cropland significantly increased the AOB abundance, and shifted the community structure and spatial distribution variation of AOB and AOA at the soil aggregates. The results indicated that soil N cycle could be substantially altered and this should be well integrated in the improvement of regional land utilization. [ABSTRACT FROM AUTHOR]