Effects of a novel bio-organic fertilizer on the composition of rhizobacterial communities and bacterial wilt outbreak in a continuously mono-cropped tomato field

Continuous cropping practice in tomato leads to an outbreak of the destructive soilborne disease bacterial wilt (BW). In this study, an integrated microbiome agent (IMA) was produced as organic fertilizer to improve successive crop soil and suppress tomato BW. Three treatments were established: IMA, organic fertilizer (OF), and control (CK, without the application of IMA or OF). Compared to CK and OF, the treatment of IMA significantly improved the growth of tomato plants and reduced the disease severity index (DSI) of tomato BW (P < 0.05, Tukey test). The contents of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), and exchangeable calcium were significantly higher in the IMA treatment than in the CK treatment (P < 0.05, Tukey test). The Illumina sequencing-based community analysis revealed that IMA increased rhizobacterial richness and diversity. Actinobacteria and Bacteroidetes were more abundant and Acidobacteria was less abundant in the IMA treatment than in the CK or OF treatments. Linear discriminant analysis effect size (LEfSe) analyses showed that the application of IMA significantly enriched the rhizosphere soil with Terrabacter, Acidovorax, Truepera, Mycobacterium, and Oxalicibacterium (P < 0.05, Tukey test). The redundancy analysis (RDA) revealed a negative relationship between the tested soil properties and DSI. Moreover, the abundances of bacterial phyla, including Bacteroidetes, Actinobacteria, and Firmicutes, were negatively correlated with DSI, while others, including Planctomycetes, Gemmatimonadetes, and Proteobacteria, were positively correlated with DSI. Overall, these results suggested that the application of IMA could effectively control tomato BW by improving soil physiochemical properties and affecting the composition of the rhizobacterial community.