Purpose Microbial communities and physicochemical properties of the soil on tobacco-rice farming fields were analyzed to reduce obstacles for continuous cropping.

Method Soil at the sites encountering severe problems in continuous cropping tobacco and rice were sampled for high-throughput sequencing on microbial community and agrochemical analysis on physicochemical properties.

Result The richness and diversity of the microbial communities in the soil declined significantly as the cultivation practice continued. The ACE and Chao1 indices decreased by 10.2% and 9.2%, respectively, and the Shannon index by 5%, while the fungal Shannon and Simpson indices rose by 26.65% and 8.0%, respectively. The relative abundance of microbes with the functions of urea decomposition, nitrification, and denitrification decreased significantly by 83.78%, 166.67% and 30.43%, respectively. That of dominant genera, Bradyrhizobium and Bryobacter, also decreased significantly by 17.0% and 23.1%, respectively. On the other hand, the soil-borne pathogenic Fusarium multiplied significantly with a relative abundance increase of 199.2%. The contents of organic matter, total nitrogen, available phosphorus, and available potassium in the soil declined by 41.38%, 17.31%, 39.15%, and 34.7%, respectively, becoming significantly lower than those in non-continuous cropping, problem-free counterparts.

Conclusion The microbial diversity, community structure, and dominant genus abundance in the soil of sampled tobacco and rice continuously cropping fields underwent significant changes due to the farming practice. The soil experienced impeded organic matter degradation, total nitrogen deficiency, retarded conversion of total phosphorus and potassium into available forms, and significantly weakened supply of available nutrients.