Effects of mushroom-tobacco rotation on microbial community structure in continuous cropping tobacco soil

Abstract Aims Rotation is an effective strategy for controlling crop diseases and improving plant health. However, the effect of a mushroom-tobacco rotation on the composition and structure of microbial communities in continuous cropping soil is unclear. Methods and results This study analysed the structure and function of soil bacterial and fungal communities using Illumina MiSeq high-throughput 16S rRNA gene sequencing. The results showed that the physicochemical properties (organic matter, available nitrogen, available phosphorus, and available potassium) and enzymatic activity (phosphatase, catalase, urease and invertase activity) in the rotation treatments (Y1, M1, Y2 and M2) were significantly higher than those in the control (continuous cropping) treatment (CK) and reached peak values in the M2 treatment. PCA showed that the soil microbial community structure in each rotation treatment was different from that in the control. The dominant bacterial phyla of the different soil treatments were Proteobacteria and Actinobacteriota, and the dominant fungal phyla of the different soil treatments were Ascomycota and Basidiomycota. The M2 rotation significantly reduced the relative abundance of harmful fungi (Penicillium and Gibberella) compared to the other treatments. RDA showed that the most abundant bacterial taxa were negatively correlated with pH and positively correlated with physicochemical properties. However, the most abundant fungal taxa were positively correlated with pH and negatively correlated with physicochemical properties. Conclusions The mushroom-tobacco rotation can effectively maintain the ecological balance of the substrate microbial environment, and provide a more effective way to prevent the continuous cropping of tobacco.