Abstract:Polymerase Chain Reaction (PCR) and DNA sequencing techniques were applied to explore the effects of long-term fertilization on the community of bacteria and diversity of nitrifying and denitrifying bacteria in paddy soil. The analyses were based on the sequence libraries of 16S rDNA, amoA and nosZ genes. The Shannon Indices indicated that the diversity of soil bacteria and amoA gene of N treatment was lower than that of CK and NPK treatments, whereas the diversity of nosZ gene was opposite while the highest diversity occurred in N treatment. The LUBSHUFF statistical analyses demonstrated that both bacterial 16S rDNA and amoA gene libraries of CK, N and NPK treatments were significantly different from each other. As to the nosZ gene libraries, N and NPK treatments were remarkably different from CK, however, no significant difference was found between N and NPK treatments. It inferred that the application of chemical fertilizers influenced the community structure of bacteria and the functional genes of amoA and nosZ.