Objectives Nitrifying and denitrifying bacteria play important roles in nitrogen cycle in paddy soil. We studied the variation of nitrifying and denitrifying bacterial communities and abundance of functional genes after long-term organic material return, to provide a reference for efficient utilization and management of nitrogen in paddy soil in red soil area.

Methods Soil samples were taken from four treatment plots in a long-term positioning experiments that had lasted for 40 years, they were: no fertilizer input control (CK), only chemical fertilizer application (NPK), returning Astragalus smicus to early rice (M1), and returning Astragalus smicus to early rice field and return straw to late rice field (M2). Metagenomic sequencing and fluorescent quantitative PCR technology through marker genes (amoA, nirK, nirS and hao) were used to analyze the community structure and diversity of nitrification and denitrification bacteria.

Results Most nirK, nirS denitrifying bacteria and AOB (amoA), hao bacteria belong to Proteobacteria. In all the tested treatments, the dominant genera of nirK-type denitrifying bacteria were Ardenticatena, Nitrospira and Rhodanobacter, and the relative abundance of Rhodanobacter was significantly higher in M2 than in other treatments (P<0.05). Steroidobacter and Bradyrhizobium accounted for 33% and 29% of the total nirS-type denitrifying bacteria in M2 and NPK treatments, respectively. Among AOB (amoA) bacteria, Bradyrhizobium had the highest proportion in CK and M1 treatments, accounting for 30% and 32%, respectively. Methylomonas in Proteobacteria had the largest proportion in M2 treatment. The proportion of Nitrospira was significantly higher in CK than in the other treatments. Geobacter was recorded the highest relative abundance among hao bacteria in all the treatments. The redundancy analysis showed that soil available N (P=0.002), available P (P=0.006) and organic carbon (P=0.002) were the main factors driving the changes in community composition of nirK-type and nirS-type denitrifying bacteria. Soil organic carbon (P=0.008) and available K (P=0.008) were the key factors for the community structure changes of hao bacteria, and vailable N (P=0.004), available P (P=0.004) and total P (P=0.002) were the key factors for the community structure changes of AOB (amoA) bacteria. The Spearman correlation analysis showed that soil organic carbon, total N and ammonium nitrogen had a negative (P<0.01) correlation with the abundance of functional genes of amoA, hao, nirK and nirS.

Conclusions Long-term fertilization significantly affects the community composition of nitrifying and denitrifying bacteria, reduces the abundance of functional genes and slows down the nitrogen cycling in red soil paddy field, due to the increased available P, available N and organic carbon under long-term fertilization and orgnic material return.