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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Research Project #442413

Research Project: Investigating Soil Microbiomes that Increase Suppression of Verticillium Dahliae and Potato Early Dying Disease

Location: Vegetable Crops Research

Project Number: 5090-21220-006-036-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2022
End Date: Jul 31, 2024

We propose to: (1) develop a reproducible and scalable bioassay of V. dahliae infectiveness in a live soil context, then use this assay to (2) investigate the soil microbiomes that can increase Verticillium suppression with a greenhouse experiment, and (3) evaluate microbiomes’ performance of Verticillium suppression in the field setting.

Objective 1: Our first objective is to establish a feasible protocol for growing potato seedlings in soils inoculated by V. dahliae. We will test V. dahliae dosage, timing of inoculation, and growing conditions in a controlled greenhouse environment until we find an approach that results in reproducible wilting symptoms on susceptible potato varieties in sterilized soil backgrounds. We will test seedling populations derived from two tolerant varieties and two susceptible varieties. Objective 2: We will use soils from our previous soil microbiome study of Wisconsin potato farms to investigate the aspects of the soil microbiome that can increase Verticillium suppression. We will inoculate pots of collected soils with selected Verticillium dosage for each potato variety based on the results from Objective 1, transplant newly germinated potato seedlings, and measure symptoms of Verticillium wilt. A control without any soil microbiome effect (sterilized soil) will also be included. We will characterize soil bacterial and fungal communities via metabarcode sequencing of 16S and ITS gene markers, respectively. We will use qPCR to quantify total bacterial, fungal, and the native V. dahliae population size. We will use a variety of statistical and machine learning approaches to determine the aspects of soil microbiome structure that predict high or low suppressive ability. Objective 3. Based on our understanding of the aspects of soil microbiomes that influence Verticillium suppression obtained from Objective 2, we will develop a predictive model to determine whether a soil is Verticillium suppressive or conducive based on the microbial community structure. We will test this prediction by carefully monitoring Verticillium wilt/plant early dying disease (PED) symptoms in a select number of unfumigated fields (or unfumigated sections of fields) from both Wisconsin commercial potato farms and the Hancock research station. We will also test whether our seedling assay can be used as a proxy for field PED symptoms, by collecting soils from those fields at three time points (pre-planting, 30 days post-planting, and 60 days post-planting) to set up pot assays with no additional V. dahliae inoculation. This will test whether the seedlings are sensitive enough to display symptoms based on the indigenous V. dahliae population in field soil, and if these symptoms closely match the severity of symptoms observed in the field.