Source: OREGON STATE UNIVERSITY submitted to NRP
CHARACTERIZING SOIL MICROBIAL COMMUNITIES THAT SUPPRESS POWDERY SCAB OF POTATOES: A COMPREHENSIVE APPROACH TOWARDS DISEASE MANAGEMENT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1032645
Grant No.
2024-67011-43008
Cumulative Award Amt.
$180,000.00
Proposal No.
2023-11574
Multistate No.
(N/A)
Project Start Date
Aug 15, 2024
Project End Date
Aug 14, 2027
Grant Year
2024
Program Code
[A7101]- AFRI Predoctoral Fellowships
Recipient Organization
OREGON STATE UNIVERSITY
(N/A)
CORVALLIS,OR 97331
Performing Department
(N/A)
Non Technical Summary
Potatoes are a staple food crop globally, critical to food security and economies. However, the potato tuber blemish disease known as powdery scab, caused by Spongospora subterranea f. sp. subterranea (Sss), poses a significant threat. This disease causes blemishes on the tubers, making them unmarketable. Moreover, Sss is the only known vector for the virus, potato mop-top virus (PMTV), which can cause tuber necrosis and result in end-of-season losses for potato growers. Currently, there are no effective management strategies or chemical treatments to suppress either pathogen. To address these challenges, we are investigating how soil microbial communities might suppress powdery scab. We aim to identify of beneficial microbial communities that are associated with suppression of powdery scab by conducting greenhouse experiments with field soils that have been shown to either reduce or support disease.We anticipate that our research will provide the groundwork to develop new tools to help farmers assess the risk of powdery scab and PMTV in their fields. Additionally, we aim to identify agricultural practices linked to disease suppressive activity, allowing growers to adopt practices that promote soil health. In total, results of this project will contribute to the development of disease management strategies that are both effective and economically viable to prevent end-of-season losses caused by Sss and PMTV. We will be sharing our progress and findings with the agricultural community and the public through an established LinkedIn profile and peer-reviewed publications. This initiative is a crucial step towards securing the health and productivity of potato crops, benefiting both growers and consumers.
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
21213101160100%
Knowledge Area
212 - Pathogens and Nematodes Affecting Plants;

Subject Of Investigation
1310 - Potato;

Field Of Science
1160 - Pathology;
Goals / Objectives
Our goal is to improve management of potato powdery scab, caused by Spongospora subterraneaf. sp.subterranea(Sss), and potato mop-top virus (PMTV). To do this, we developed an approach that focuses on Sss, the vector of PMTV. Specifically, we plan to gain deeper insight into the biotic and abiotic factors in soil that contribute to powdery scab incidence and severity, and identify agricultural practices that may enhance disease suppression. Our primary hypotheses are that 1) soil microbial communities contribute to disease suppressive activity in soils and 2) disease suppressive activity of soil is affected by soil salinity. To test these hypotheses, we proposed the following objectives:Objective 1. Characterize the specific soil microbial taxa linked to the suppression of powdery scab and identify indicator species associated with powdery scab suppression.Objective 2. Identify the soil physical and chemical properties that correlate with shifts in microbial communities associated with disease suppression and examine if salinity affects the soil microbial community and powdery scab incidence or severity.
Project Methods
We will conduct two greenhouse experiments to identify soils with powdery scab suppressive and characterize the microbiomes of soils with suppressive activity associated with biotic soil characteristics and determine if differences in disease expression or suppressive activity is associated with soil salinity.To do this, we will collect potato soils from multiple fields in the Columbia River Basin and Klamath Falls region of Oregon for their powdery scab suppressive activity. Field soils will be selected due to their diverse physical properties and planting histories. Soil characteristics will be measured, including soil moisture and temperature at sampling, soil texture, soil pH, organic matter, soluble salts, cation exchange capacity, and a routine nutrient analysis. Sss inoculum present in the soil will be quantified. A greenhouse bioassay will be performed to assess powdery scab suppressive activity. Briefly, potato plants planted in the field soils will be inoculated with sporosori collected from S. subterranea-infected tubers using published methods. Powdery scab incidence and severity will be evaluated for each plant by counting the number of galls on the root system and estimating the percent of the tuber surface that is covered by lesions for all tubers. The potato rhizosphere and bulk soil will be sampled, and DNA will be extracted after a four-month growing period. Bacterial and fungal community composition will be assessed using amplicon sequencing and the open-source platform QIIME will be used to optimize sequence data and to assign taxonomy. The UNITE and SILVA databases will be used to assign taxonomy for fungi and bacteria, respectively. Sampling depth will be normalized, to account for the difference in sequencing depth, and data may be transformed prior to statistical analysis.For both greenhouse experiments, analysis of variance will be used to determine how powdery scab incidence and severity and potato phenotypes vary as a function of experimental treatment. Similarly, regression analysis will be used to examine links between plant health and field-level physical and chemical soil characteristics. Univariate and multivariate analyses will be used to identify correlations between soil microbial communities, disease incidence or severity, potato productivity, and soil physical, chemical, or biological characteristics. Analysis of bulk and rhizosphere microbiomes will help identify if core microbial communities recruited by potatoes result in community structures and taxa that are more similar across treatments when compared to those of bulk soils. In total, our analyses will help elucidate links between microbial community structure and disease suppressive activity and/or soil salinity. Finally, we will use indicator species analysis to identify OTUs associated with disease suppressive activity or salinity response.Information and results from this project will be disseminated to farmers in the Pacific Northwest region through talks at grower education events and field days, through stakeholder networks, and through informal conversation at grower education events (e.g., meetings, field days, etc.)Short-, medium-, and long-term metrics and evaluation of progress metrics.Short3-4 Experiments/surveys completedAnalyses completed2-3 Presentations at scientific meetings2-3 of extension publications and/or media produced100+ clientele reached at field days and grower education eventsMedium2-3 Journal articles/publications generatedDissertation writtenDegree completionGrower understanding of key soil health building practicesLongIndustry/processor adoption of our assessment recommendationsFarmers testing their soils and assessing soil physical and biological quality in ways that are relevant to potato productionExpectations for achievement of evaluation metrics will be discussed and defined at the start of the project. Each year, we will collect data on each evaluation metric and report on annual progress. Evaluation metrics may be adjusted in subsequent years depending on our achievement and new knowledge that is gained. Evaluation metrics will be summarized at the end of the project to document overall accomplishments. We expect long-term metrics may be challenging to evaluate before the project is completed.

Progress 08/15/24 to 08/14/25

Outputs
Target Audience:Farmers and crop managers: The project aims to provide farmers with improved management strategies and diagnostic tools to reduce losses due to powdery scab. Currently, no commercially accepted potato varieties have complete resistance to powdery scab, and existing cultural or chemical management tactics are ineffective. This research seeks to fill these critical gaps by offering growers alternatives for disease management. During the reporting period, we held a field day and presented on the basic biology of this pathogen and what disease suppressive soils are. Scientific community: The project contributes to characterizing microbiomes in conferring disease suppressive activity, which is a significant area of study. Spongospora subterranea f. sp. subterranea is an understudied pathogen, and the preliminary results of this study were shared at the American Phytopathological Society national meeting, Plant Health 2025, with others within the scientific community. Changes/Problems:No major changes or problems have been encountered. What opportunities for training and professional development has the project provided?To further support her professional development, Daniella Echeverria is currently enrolled in Oregon State University's Graduate Certificate in College and University Teaching, a credential that demonstrates her effectiveness as an instructor and facilitator. Throughout this reporting period, she met regularly with her primary mentor, Dr. Ken Frost, to discuss research progress, writing objectives, and career development strategies. Many of these meetings also included her co-advisor, Dr. Hannah Rivedal. From February to July 2025, she participated in a microbiome sequencing workshop led by Dr. Michelle Odoi, a postdoctoral scholar in the Frost Lab, which enhanced her technical skills in microbial data analysis. On June 3, 2025, she met with her thesis committee to review her academic progress, clarify her timeline for graduation, and outline the structure of her thesis chapters. How have the results been disseminated to communities of interest?At the 2025 Potato Field Day at the Hermiston Agricultural Research and Extension Center, I presented our study on soil microbial communities and their possible suppressive activity to powdery scab to both growers and stakeholders, and sharing basic information about the biology and possible outcomes of this work. Potato Field Day is attended by approximately 125 participants which included growers, stakeholders, and crop advisors. The preliminary results of this study were shared at the American Phytopathological Society national meeting, Plant Health 2025, where I discussed this project with other scientific professionals and students. What do you plan to do during the next reporting period to accomplish the goals? Complete analysis of 2024 data: comparing disease incidence and severity to treatments, identifying possible specific taxa responsible for a reduction in disease, and comparing soil microbial communities Complete the 2025 greenhouse study and proceed with analysis Write and publish peer-reviewed, scientific, educational, and extension publications Increased knowledge of the effects of soil salinity on powdery scab and powdery scab suppression in the scientific community Growers are educated and able to consider long-term management to increase soil health through soil microbial communities

Impacts
What was accomplished under these goals? A primary concern for potato growers in the Pacific Northwest (PNW) is the introduction and spread of Spongospora subterranea f. sp. subterranea (Sss), the causal pathogen of powdery scab (PS) of potato. Infection by Sss results in blemishes on the tuber, distortion or galling of root and stolon tissue, and reduced tuber quality and value. Sss is the vector of potato mop-top virus (PMTV), which causes tuber necrosis resulting in buyer rejection of potatoes produced for processing, seed, and fresh markets. Potatoes grown in the PNW are irrigated, and the region is predicted to become more arid due to more variable and extreme weather patterns, resulting in increased soil salinity. Currently, management options are limited, therefore, studies of soil microbial communities that contribute to disease suppressive activity in soils are necessary to identify agricultural practices linked to disease suppressive activity, allowing growers to adopt practices that promote suppressive activity. Results of this project will contribute to the development of disease management strategies that are effective in preventing end-of-season losses caused by Sss and PMTV. In the first year of our study, we conducted two greenhouse studies, one in 2024 and another currently in progress in 2025. In 2024, soil samples were collected from the bulk and rhizosphere soil of our inoculated potato plants to characterize the soil microbial community members, identify species associated with PS suppression, and identify the soil physical and chemical properties that correlate with shifts in microbial communities responsible for disease suppression, including soil salinity. We have sequenced the soil microbial communities using metabarcoding, and the analysis of data collected in 2024 is in progress. Data collection for 2025 has started and will be completed in the Fall. By the next reporting period, we anticipate that both 2024 and 2025 data will be analyzed and results available.

Publications