Quantification of Fusarium oxysporum disease potential from soil DNA

Authors: Matson, Michael; CROUCH, UMA - Former ARS Employee; Kane, Saben; Henry, Peter; Goldman, Polly; Martin, Frank

Submitted to: Methyl Bromide Alternatives and Emissions Research Conference Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 9/4/2020
Publication Date: 11/3/2020
Citation: Matson, M.E., Crouch, U., Kane, S.M., Henry, P.M., Goldman, P.H., Martin, F.N. 2020. Quantification of Fusarium oxysporum disease potential from soil DNA. Methyl Bromide Alternatives Outreach (MBAO) Conference, November 3-5, 2020 (virtual).

Interpretive Summary: Techniques were developed for quantification of several important soilborne plant pathogens of strawberry. However, the sensitivity of detection of the pathogen responsible for Fusarium wilt was not enough to accurately predict risk to the grower. A new technique was developed to extract DNA from larger volumes of soil that provides the sensitivity needed for accurate quantification of the pathogen in production fields.

Technical Abstract: Some of the more common soil borne diseases affecting the strawberry industry in California include Verticillium wilt due to Verticillium dahliae (Vd), charcoal root rot due to Macrophomina phaseolina (Mps), and Fusarium wilt due to Fusarium oxysporum f.sp. frageriae (Fof). In an effort to better manage diseases while efficiently utilizing available fumigants following the phase-out of methyl bromide, a USDA-ARS areawide project is investigating the practicality of site-specific zone fumigation. This project involves investigating fields scheduled to be fumigated prior to strawberry production, obtaining soil samples across the field, predicting pathogen pressure, and prescribing high or low fumigant applications to field sectors showing high and low disease potential. Quantification down to 1-2 or 3 propagules/g soil of Vd and Mps in soil samples, respectively, have used kit-based soil DNA extraction and subsequent qPCR quantification methods to determine pathogen pressure. However, the biology of Fof resting spores prevents reliable quantification using the same kit-based DNA extraction. Reasons for this include the single-nucleate chlamydospore resting structures in F. oxysporum and the presence of humic acids and other PCR inhibitors from soil DNA extractions. Given these challenges, and in spite of an assay specific to Fof (Burkhardt et al., 2019), quantification of Fof pressure approaching the theorized limits of pathogenicity on strawberry was not reliable for soil samples. An improved method for DNA extraction from 15 g of soil that increases sensitivity of detection was developed.