Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle

•Livestock manure had stronger impact on N-cycling gene abundances than wheat straw.•AmoA genes were more sensitive to fertilization than other N-cycling genes.•Available P was the most important factor affecting the abundance of N-cycling communities.

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.