Long-term agricultural fertilization significantly affects nitrogen cycling in soils. However, there is little
information about the response of different functional genes involved in the nitrogen cycle to chemical
and organic fertilization, and the key factor influencing the community abundance. We investigated the
influence of long-term application of chemical fertilizer (NPK) and combined with wheat straw or livestock
manures on the abundance of six nitrogen cycle genes (nifH, archaeal and bacterial amoA, nirS, nirK
and nosZ) by quantitative PCR. Compared with non-fertilization treatment, long-term application of NPK
fertilizers significantly increased the abundance of nirK, nosZ and bacterial amoA genes but decreased
archaeal amoA gene abundance, with no significant effect on the abundance of nifH and nirS genes. Compared
with NPK treatment, the application of NPK+ organic manure increased the abundance of all the
nitrogen-cycling genes while the application of NPK+ wheat straw had little effect. The abundance of
amoA genes contributed the most to the variations in the abundance of the nitrogen cycling community
between different fertilization strategies. Soil available P and total N were the most important factors
influencing the abundance of microbial communities involved in the nitrogen cycle. These results indicated
that, under the application of chemical fertilizers, the addition of livestock manures had much
stronger effects on the abundance of nitrogen cycle genes than the addition of wheat straw, and bacterial
and archaeal amoA genes were more sensitive to fertilization than other functional genes.