Objectives  Paddy field is regarded as one of the important terrestrial nitrogen (N) reservoirs. Microorganism community and quantity play an essential role in N biogeochemical cycle and are regarded as indicators of soil fertility. Thus, we studied the effects of different fertilizer treatments on the structure and function of soil microbial communities in a paddy field.

Methods  This study was conducted in a long-term paddy field experiment in Jinhua City, Jiangsu Province. The treatments on the field include: no fertilizer application (control, CK), pure chemical fertilizer (CF), chemical fertilizer plus crop straw (CSF), and chemical fertilizer plus pig manure (CMF). Soil samples were taken in the sixth year of the experiment, while the microbial community structure and the population of N cycle-related functional microorganisms were measured using quantitative PCR and high-throughput sequencing.

Results  The CMF and CSF treatments significantly increased the total carbon (TC) and soluble organic carbon (DOC) contents more than CF did, whereas total nitrogen (TN), NH₄⁺-N and NO₃⁻-N increased in similar pattern under the three fertilization treatments. Cluster analysis showed there were differences in soil bacterial community structure between CK and fertilization treatments while soil pH and NH₄⁺-N and NO₃^–-N content were the dominant factors. The bacterial community clusters of CK and CMF treatments were close, while the bacterial community structure of CF and CSF treatments were also close. Compared with CK, the abundance of ammonia oxidizing bacteria (AOB) and iron ammonia oxidizing microorganism (Feammox A6) significantly increased in CF, CMF and CSF treatments. Feammox A6 increased by 87.6%, 158% and 157%, respectively.

Conclusions  Long-term fertilization affected soil chemical properties, and the NH₄⁺, NO₃^– contents and soil pH were dominantly responsible for the soil microbial community succession and composition. The cluster of microorganism community under combined application of chemical fertilizer and pig manure was close to that of control, while the clusters of soil microorganism community structure under both pure chemical fertilization and combined application of chemical and crop straw were close. Abundance of AOA did not change with long-term fertilization, but abundance of AOB and Feammox A6 increased. Chemical fertilizer plus pig manure or straw increased Feammox A6 population more than pure chemical fertilizer. The gene copies of denitrification functional groups ( nirK , nosZ ) were significantly higher under pure chemical fertilization compared to other treatments.