Objectives  Bacteria is the largest microorganism species in soil, its diversity is an important indicator of soil quality and soil health. Different fertilization modes provide mineral nutrients and different carbon sources for bacteria. Investigation of the diversity and function of bacteria community in soils under different long-term fertilization modes will help further understanding of the microbial driving process of soil nutrient transformation and the optimization of fertilization management measures.

  Methods  In a 37-years long fertilization experiment at Laiyang, China, soil samples were collected from four treatments of non-fertilization (CK), chemical nitrogen fertilizer (N), manure only (M) and M plus N (MN). Miseq pro-sequencing technology was used to detect the differences in soil bacterial abundance (16S rRNA gene copy number), α diversity and β diversity in the treatments. FAPROTAX method was used to identify the differences in the abundance of main functional populations among treatments, and Mantel test was used to analyze the correlation between bacterial diversity and yield and soil nutrient content.

  Results  Long-term application of manure significantly increased soil bacterial abundance, and the copy number of 16S rRNA gene in MN and M treatments were 11.8 and 10.7 times of those in CK and N treatments, respectively (P < 0.05). Manure (M) treatment had the highest bacterial diversity (Shannon index) and richness (Chao1 index). Proteobacteria, Acidobacteria and Actinobacteria were the dominant phyla in fluvo-aquic soils. Compared with CK, the relative abundances of Bacteroidetes and Verrucomicrobia were significantly increased by the three fertilization treatments. Compared with N treatment, MN treatment significantly increased the abundance of Proteobacteria, Firmicutes and Bacteroidetes, but decreased the abundance of Acidobacteria. Chemoheterotrophy, aerobic chemoheterotrophy, fermentation, nitrification and nitrate reduction were the main ecological functions in fluvo-aquic soils. The abundance of bacterial species with chemoheterotroph function in MN treatment was 2.2%–4.2% significantly higher than those of other treatments. The relative abundance of bacterial species with fermentation function in MN and M treatments were more than 3 times of those in other treatments. Compared with CK, the three fertilization treatments significantly increased the relative abundance of bacterial species with phototrophy and photoheterotrophy functions. There were significant (P < 0.05) or extremely significant (P < 0.01) correlations between the β diversity and function of bacterial and the contents of soil organic matter (SOM), total nitrogen (TN), nitrate (NO₃⁻-N) and crop yield.

  Conclusions  Long-term application of organic fertilizer increases the number and diversity of bacteria, increases the abundance of Proteobacteria, Firmicutes and Bacteroidetes in the soil, and decreases the abundance of Acidobacteria. The abundance of bacterial species with chemoheterotrophy is significantly higher under the combined application of organic fertilizer and chemical fertilizer, which may be the main bacterial population for optimizing soil nutrient cycling and improving crop yield after the application of organic fertilizer. It is necessary to further study the composition and functional regulation of soil bacterial population.