Vermicompost can suppress Fusarium oxysporum f. sp. lycopersici via generation of beneficial bacteria in a long-term tomato monoculture soil

Background and aims Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) has severely decreased global tomato production. Organic amendments are widely applied to suppress Fol all over the world. However, the ways in which different amendments alter soil bulk microflora and thereby induce the suppression of Fol remain unclear. Methods In this study, the effects of three organic amendments on the suppression of Fol in soil and the underlying mechanisms of those effects were studied. The organic amendments included in this study are rice straw, chicken manure compost, and vermicompost. High-throughput HiSeq sequencing and Real-Time PCR were used to determine the effect of the soil microbiota on the abundance of Fol. Results The abundance of Fol increased significantly with the duration of tomato cultivation. Vermicompost was the most effective organic fertilizer to suppress Fol in long-term continuous tomato cropping soil. Partial Least Squares Path Modeling revealed a strong positive relationship between the relative abundance of bacterial groups (including the genera Nocardioides, Ilumatobacter and Gaiella) and Fol inhibition. Soil chemical properties (pH, NH4+-N, soil organic matter and dissolved organic carbon) were positively associated with the genera Nocardioides, Ilumatobacter and Gaiella. Compared with chemical fertilizer and rice straw, vermicompost addition significantly increased soil pH, NH4+-N, soil organic matter and dissolved organic carbon concentrations in the soil with 20 years of tomato cultivation. Most importantly, the genera Nocardioides, Ilumatobacter and Gaiella were enriched in vermicompost, which may contribute to the propagation of these bacteria in the soil when vermicompost is added. Conclusions This study provides a mechanistic framework that permits the exploration of specific functions at lower taxonomic levels. This may represent a novel approach in the management of crop pathogens via promotion of beneficial organisms.