De-coupling of root–microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness

It was hypothesized that disruption of the root–microbiome association creates empty rhizosphere niches that could be filled by both soilborne pathogens and beneficial microbes. The effect of de-coupling root–microbiome associations related to improve soil suppressiveness was investigated in cucumber using the pathogen Fusarium oxysporum f. sp. Cucumerinum (FOC) and its antagonist Bacillus amyloliquefaciens SQR9 (SQR9) system. The root–soil microbiome association of cucumber was disrupted by applying the fungicide carbendazim to the soil, and then FOC or/and its antagonist SQR9 were inoculated in the rhizosphere. In the fungicide treatment, the FOC wilt disease incidence was significantly increased by 13.3 % on average compared to the FOC treatment without fungicide. However, when the fungicide treatment was applied to the soil with SQR9 and FOC, the SQR9 effectively reduced the disease incidence, and improved cucumber plant growth compared to a no fungicide control. These results indicate that de-coupling of root–microbiome associations followed by antagonist inoculation can improve rhizosphere soil suppressiveness, which may help to develop strategies for efficient application of rhizosphere beneficial microbes in agriculture.