Objective  The evolution of soil fertility and the shift in soil microbial diversity under a long-term fertilizer experiment (1981–2016) were explored on a yellow brown soil in Wuhan. This aimed to provide a scientific basis for soil fertilization and sustainable development of agriculture.

Methods  Five fertilization treatments no fertilization (CK), nitrogen, phosphorous and potassium fertilizers (NPK), constant organic manure (OM), NPK fertilizers and constant organic manure (NPK+OM), NPK fertilizers and high amount organic manure (NPK+OMM) were involved in the study. The soil physical and chemical properties were analyzed using standard procedures, and the bacterial diversity was analyzed using Illumina MiSeq high-throughput sequencing technique, and the relationships of tested indexes with yield were determined using partial least square path model (PLS-PM).

Results  1) Compared with CK, the organic fertilization significantly increased the contents of available nutrient and organic carbon (SOC), while NPK treatment only increased organic C content in soil. The available P and K contents in NPK+OMM treatment were significantly higher than those in OM and NPK+OM, the available N and organic C contents were similar among the three organic-amended treatments. Fertilization significantly increased rice yield, however there was no significant difference among the four treatments. 2) The bacterial diversity in OM treatment was the highest and that in NPK+OMM was the lowest, even though, the differences were not significant among fertilization treatments. 3) Long-term fertilization affected soil bacterial community structure. OM treatment increased the relative abundances of Proteobacteria and Actinomycetes, but decreased those of Chloroflexi and Nitrosporium. NPK treatment decreased the relative abundances of Actinomycetes and Nitrosporium whereas it increased that of Acidobacteria. Compared with NPK+OM, NPK+OMM treatment decreased the relative abundances of Actinomycetes and α-Proteobacteria, increased those of Anaerolineae, Chloroflexi and Nitrosporium. 4) PLS-PM showed that SOC, available N, available P and readily available K were positively correlated with bacterial community structure (path coefficients = 0.36), while it was negatively correlated with pH (path coefficients = –0.48); although they had little effect on bacterial diversity. The main soil chemical properties that affected rice yield were SOC, available N, and available P. Soil bacterial diversity had a positive regulation on rice yield (Path coefficients = 0.42).

Conclusions  Soil organic carbon and available nutrient content have positive impact while soil pH has negative impact on the diversity of bacteria. Long-term application of organic manure with chemical fertilizer could increase available P and K content. Application of manure only enhances the soil bacterial diversity on the long run when applied at an annual ordinary rate.