Pathogen suppression assay: a strategic tool for managing soilborne diseases in cotton

Abstract

Verticillium dahliae Kleb. is a soilborne fungal pathogen causing verticillium wilt and significant yield losses in Australian cotton making it agronomically important. Effective control of soilborne diseases involves managing pathogen at different microsites in soil and different time periods (pre-season or in-crop). Interactions between pathogen and microbial communities affect pathogen survival and growth during non-crop periods and in the rhizosphere influencing infection. Biological disease suppression mediated by soil microbiomes can influence pathogen for its survival and growth. A short-term soil-based laboratory assay using quantitative PCR has been standardised to quantify V. dahliae (ND and defoliating strains) suppression capacity of Australian cotton soils. Surface soils (0-10 cm) soils collected from established field experiments at ACRI, Narrabri, NorthStar in NSW and farmer fields in NSW and Qld were used. Assay efficacy was compared with one using a GFP-transformed nondefoliating (ND) strain. The assay successfully quantified the impact of rotation crops and fallow on pathogen suppression potential (PSP) in crop rotation and cover crop experiments. Results from the assay also demonstrated the seasonal variation and the effects of amendments such as crop residues, C sources and fertiliser N on biological suppression against V. dahliae. The PSP assay protocol is potentially adaptable for other soilborne pathogens of cotton.