Objectives Good soil micro-ecological environment is important for biological transformation of soil nutrients and quality of flue-cured tobacco. Long-term monocropping tends to reduce biodiversity of soil bacteria community. This study was to clarify the variation in soil bacterial community diversity and structure composition by analyzing the 16S rRNA gene hypervariable regions of soil bacteria in soils after different years of monocropping using high-throughput sequencing technology.

Methods We selected fields that had been planted tobacco for 1, 3, 5, 8, 10 and 12 years in Chongqing City. The soil was yellow soil, soil samples were taken from the top 0–20 cm tillage layers of the tobacco fields and a field without planting tobacco as the control. The soil physical and chemical properties were measured. Using the high-throughput sequencing technology, bacterial primordial sequences were divided into different OTUs according to 97% similarity threshold. The sequence was used to analyze the composition of bacterial communities (key species difference comparison histogram). A series of statistical and visual analysis, including sample comparison analysis (beta diversity analysis), correlation and model prediction analysis (correlation heatmap chart), were carried out.

Results 1) Soil pH was decreased with continuous monocropping years. The pH, organic matter and microbial biomass C contents in the 8–12 years’ fields were significantly lower than those in the 1–5 years fields, while those of the 12 years were significantly lower than those of the 8–10 years. Soil available N and K contents were increased significantly with cropping years, and the available N content was in order of 1 a < 3–5 a < 8 a < 10–12 a (P < 0.05), the readily available K content in 1–5 years fields was significantly lower than that in the 8 years, and that of the 8 years fields was significantly lower than that of the 10–12 years (P < 0.05). The available P content, by contrast, kept decreasing with cropping years, especially the 12 year field, which was significantly lower than that in all the fields except the 8 year field. 2) The diversity of community and composition of soil bacteria in tobacco fields were the highest in the 5 years’ field, and reached 6.23 and 1686, respectively. After five years of monocropping, the diversity of community and composition of bacteria began to decline, and reached the lowest level in the 12 year’ fields, when the content of Acidobacteria decreased sharply to 13.9%, one of the main genera of Acidobacteria disappeared, and the content of Anaerobic bacteria increased significantly to 2.42%. Among the 13 main soil bacteria (relative abundance > 1%), Bacteroides (P < 0.01), Phytophthora (P < 0.01), Armorella(P < 0.01) and Cyanobacteria (P < 0.01) were significantly different in tobacco fields of different years. 3) Long-term continuous cropping significantly impacted bacterial community composition in tobacco fields. Soil bacterial diversity and composition were closely related to soil pH and soil nutrients. The Actinomycetes, Proteus, Curvularia and Acidobacteria were positively affected by pH, and Curvularia was positively correlated with soil pH, organic matter, total C and available N contents.

Conclusions Continuous cropping of tobacco impacts the soil physical and chemical properties, especially in the fields growing tobacco for more than five years where soil pH, organic matter, active organic carbon and available P were significantly decreased. The variation leads to significant decrease in the community and diversity of bacteria. Therefore, rotation of tobacco with other crops is strongly suggested in the replanting fields of more than 5 years, in order to improve the soil micro-environment and promote the healthy and sustainable utilization of tobacco field.