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Research Project: Integrated Disease Management of Exotic and Emerging Plant Diseases of Horticultural Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

2022 Annual Report

Objective 1: Describe the pathogen biology and disease epidemiology of exotic and emerging plant pathogens affecting horticultural crops. Sub-objective 1A: Comparative genomics of Phytophthora pathogens. Sub-objective 1B: Population genomics and evolution of Phytophthora pathogens. Sub-objective 1C: Characterize the fungal, oomycete and bacterial microbiome associated with horticultural crops. Sub-objective 1D: Disease surveys of small fruits in the Pacific Northwest. Objective 2: Develop improved integrated disease management of pathogens of horticultural crops. Sub-objective 2A: Integrate disease risk forecasters with models for air turbulence to predict pathogen dispersal and spatially explicit disease risk. Sub-objective 2B: Develop methods to monitor presence of fungicide resistance in pathogen inoculum. Sub-objective 2C: Optimize fungicide selection and application timing to manage powdery mildew on grape berries. Sub-objective 2D: Identify inoculum sources of Botrytis cinerea in caneberry fields and evaluate methods to reduce overwintering populations. Sub-objective 2E: Develop and evaluate alternative control measures for management of diseases that reduce fruit yield or quality.

The long-term goal of this project is to develop the knowledge and tools needed to respond to plant disease epidemics using approaches that are economically and environmentally sustainable, with emphasis on increasing our ability to respond to exotic, emerging, and re-emerging pathogens. This will be accomplished through trans-disciplinary approaches that increase our knowledge of pathogen genetics, biology, and disease epidemiology and incorporates this information into decision support aids for horticultural crops. The biology of exotic, emerging, and re-emerging plant pathogens is either poorly understood or inadequate to enable economic and environmentally sustainable management. We will develop and test methods for monitoring pathogen dispersion and describe the genomes, evolutionary history, population structure, genetics, epidemiology, and ecology of these pathogens. This knowledge will then be used in Objective 2 to develop decision support tools for producers of horticultural crops. Once there is a more detailed understanding of pathogen ecology, this knowledge will be translated into disease management strategies that are continually optimized and/or improved to address changing climate, market and regulatory pressures. We will develop and improve disease management strategies for select pathogens affecting horticultural crops. The development and improvement of integrated disease management strategies for endemic pathogens will also improve our ability to respond to changing climatic conditions while enhancing the economic and sustainable production of horticultural crops.

Progress Report
This is the final report for project 2072-22000-041-000D, which expired in May 2022 and has been replaced by new project, 2072-22000-045-000D, “Knowledge Based Tools for Exotic and Emerging Diseases of Small Fruit and Nursery Crops.” In support of Sub-objective 1A, ARS researchers at Corvallis, Oregon, sequenced and studied whole genomes of six Phytophthora ramorum strains using Pacific Biosciences and nanopore long-read technology and these reads were assembled into whole genomes. These genomes are much improved compared to previously available genomes and provide a novel resource for future comparative genomics and transcriptome analysis. We compared genomes of the plant pathogen, Phytophthora infestans, and documented that populations at the center of origin in Mexico are predominantly diploid, whereas clonal lineages that are dominant around the world are predominantly triploid. An expansion and divergence of Argonaute genes in the Oomycete genus Phytophthora were documented. This work has important implications for understanding emergence of plant pathogens in agriculture. In support of Sub-objective 1B, we monitored populations of the sudden oak death pathogen in the United States and worldwide using various genotyping approaches, including whole genome sequencing. We characterized several invasions of clonal lineages NA1, EU1 and NA2 into Oregon forests and new invasions of the sudden oak death pathogen into U.S. forests, including the EU1 and NA2 clonal lineages. These results document that we are seeing continued migration of the sudden oak death pathogen in the nursery industry. We demonstrated that a sexual hybrid of the sudden oak death pathogen emerged in a nursery in Canada based on whole genome sequencing. This is the first report of sexual reproduction in a nursery and provides evidence of a distinct risk for emergence of sexual lineages in Oregon forests, given that both mating types A1 and A2 are now established in natural forests. A population genetic analysis on a new emergence of the sudden oak death pathogen in the Midwest was shown to be caused by the NA2 clonal lineage that was previously only detected on the West Coast. Previously, only the NA1 linage was detected from P. ramorum-infected plants in the Eastern United States. This result documents that we are seeing continued migration of the sudden oak death pathogen in the nursery industry. In support of Sub-objective 1C, we studied the composition of the fungal and oomycete microbiome of rhododendron roots under varying growth conditions, nurseries, and cultivars. Few oomycetes were found, and fungal communities were dominated by saprobes and mutualists. Nurseries that grew plants in containers and in the field had a significantly higher diversity of fungi than those that only grew plants in containers. Microbiome composition differed significantly among growth conditions and nurseries, but not among cultivars. This suggests that, among these cultivars of rhododendron, environment is important in structuring the root microbiome, but cultivar is not. Additionally, we characterized the fungal, oomycete and bacterial microbiome associated with raspberry flowers and fruit over two years from five commercial fields. We optimized processes to generate microbiome data and reduced interference of plant DNA to improve detection of bacteria and fungi in raspberries. These methods will be useful to other studies of the microbiome of plant tissues. The microbiome data for the red raspberry is complete and being analyzed. A new technique for visualizing microbiomes was developed and implemented in the R package (statistics software) metacoder. The technique provides a tree-based visualization that is color coded based on significant differences among taxons and communities characterized using metabarcoding. This Heat-Tree tool provides much deeper insights into microbiome data than previously available with stacked bar charts or pie charts. An unknown Phytophthora species was discovered in the central Peruvian Andes on blighted foliage of the native South American plant species, Urera lacineata. Urera is a genus of native flowering shrubs in the nettle family, Urticaceae. This new taxon Phytophthora urerae sp. nov. was formally described based on extensive morphological analysis and phylogenetic analysis. This pathogen is a close relative of the potato late blight pathogen and provides novel insights into host adaptation and evolution of the potato late blight pathogen. In support of Sub-objective 1D, disease surveys of small fruits in the Pacific Northwest (PNW) were conducted in blackberry, blueberry, cranberry, and red raspberry fields. We studied two uncommon diseases that reduce berry yields, aerial stem gall (bacterial) of blueberry and blackberry collapse, and a fungal cane disease killing 15% of plants in fields. We isolated, identified and are studying the disease cycle of these emerging pathogens. The cranberry fruit rot complex reduced marketable yield of cranberries by 15 to 40% in the PNW. The gray mold pathogen, Botrytis, was isolated from 5 to 40% of blueberries, blackberries, and raspberries sampled. Sixty percent of Botrytis isolates were resistant to fungicides used for disease control. A third of those isolates were resistant to three or more types of fungicides. Emergence of multi-fungicide resistance in Botrytis leaves growers with fewer options for effective gray mold control. In support of Sub-objective 2A a series of experiments were designed to understand how canopy geometry (shape and row structure) and topology influence the creation of air turbulence that carries pathogens. Surrogate spores (fluorescent microspheres) were released in vineyard canopies and traced up to 180 meters from the source. In addition, the air turbulence over vineyards was characterized by instrumenting vineyards with extensive weather monitoring equipment, including several eddy covariance towers with multiple sonic anenometers, carbon dioxide and water vapor sensors, and a two-beam Scintillometer. These data were used to create biophysical models for turbulence formation and vapor and particle transport. These models are now used to test various sampling strategies for monitoring disease development and predicting pathogen spread. Extensive progress was made towards Sub-objective 2B. Quantitative polymerase chain reaction assays for rapidly detecting resistance to quinolone outside inhibitors and demethylase inhibitors in Erysiphe necator were developed and validated for monitoring. A novel method (swabbing worker gloves or other materials moved through the canopy and using a rapid DNA extraction procedure) for sample collection was developed and shown to be superior to visual disease scouting and equivalent, but significantly cheaper, to airborne inoculum sampling. In addition, DNA from these samples is suitable for deep sequencing to assess the presence of other genetic markers for resistance to fungicides and monitoring population diversity to estimate immigration and selection. An improved methodology was developed to characterize fungicide resistance more rapidly and accurately in E. necator. These methods have allowed the grape industry to rapidly assess fungicide resistance risk and avoid the catastrophic losses of 2016. These protocols have now been implemented by numerous commercial labs across the Western United States. In support of Sub-objective 2C, laboratory studies demonstrated that many chemistries are mobile through two or more mechanisms. Small plot experiments demonstrated that timing mobile fungicides from berry set to early lag phase resulted in superior powdery mildew control with significantly less disease development. Several chemistries considered immobile on grape were shown to be mobile by at least one mechanism. Demonstration trials in commercial vineyards demonstrated that growers could reduce their use of synthetic fungicide by targeting application to set and early berry development, improving disease management compared to their conventual practices. This work also improves mitigation and management of fungicide resistance by reducing the use of synthetic pesticides by targeting their use to periods with the most impact. In support of Sub-objective 2D, we completed sampling over the dormant season through harvest in eleven raspberry fields in northern Washington and this research will continue with our new project 2072-22000-045-000D. In support of Sub-objective 2E, we found that low concentrations of aluminum salts are lethal to Botrytis in culture. In blackberry field trials, solutions of aluminum sulfate or aluminum potassium sulfate reduced yellow rust incidence on fruits by 30% and gray mold by 50% compared to water-treated controls. We tested yeasts (commercial biocontrol and our collection of yeasts) in field trials and observed significant, 50% reduction, in gray mold. None of the treatments reduced yield or berry weight compared to water controls. The experiment was repeated in 2021, but unusually high temperatures (the heat dome) killed the berries. The experiment will be repeated. In the long term, integration of materials, such as aluminum ions or yeast, into conventional disease management programs may provide growers additional tools for sustainable management of diseases that affect fruit quality or yield.

1. A novel highly specific method of characterizing communities of water molds using metabarcoding. Oomycetes, commonly referred to as water molds, include some of the costliest plant pathogens. ARS researchers at Corvallis, Oregon, developed a novel barcode method suitable for detecting all oomycetes in environmental samples using a mitochondrial gene (Rops10). This method relies on high throughput sequencing and is more specific DNA sensitive than previously available methods. This will allow scientists to more efficiently monitor water molds in terrestrial and aquatic environments.

2. Improved methods to detect presence of grape powdery mildew and markers for fungicide resistance. Fungicide resistant grape powdery mildew is threatening grape production. ARS researchers at Corvallis, Oregon, developed and tested novel techniques for monitoring resistance. Over three years of trials at a commercial scale, it was demonstrated that swabbing gloves moved through grape canopies can be used for detecting pathogen inoculum levels and risk of resistance to fungicides. These methods are allowing growers to more effective deploy the limited management tools for grape powdery mildew.

3. Identification of Gnomoniopsis idaeicola as the pathogen associated with blackberry collapse. Blackberry collapse is a recently emerging disease in blackberry in Oregon of unknown origin. It is causing 10-17% plant death in infected thornless, training blackberry fields. ARS researchers at Corvallis, Oregon, isolated the fungal pathogen, Gnomoniopsis idaeicola, from lesions and showed that it caused a cane disease on blackberry. The isolation and identification of the causal agent is the first step towards developing management practices for this emerging and damaging disease of blackberry.

4. Reclassification of the causal agent of dry berry of raspberry and blackberry as Monilinia rubi. Historically, dry berry disease of raspberry and blackberry periodically caused crop losses of 40 to 80% in British Columbia. The causal agent was misidentified in the 1950’s and named Rhizoctonia rubi. ARS researchers at Corvallis, Oregon, showed that the causal agent is Monolinia rubi, based upon genetic and detailed morphological analysis of the type culture and an extensive collection of raspberries with dry berry symptoms in northern Washington. The correct identification will allow for improved management recommendations, based on similar diseases caused by other Monolinia species, while researchers study the pathogen ecology and disease epidemiology to further improve disease management recommendations.

Review Publications
Stockwell, V.O., Shaffer, B.T., McGhee, G., Hardigan, M.A. 2022. First report of Gnomoniopsis idaeicola causing cane wilt and canker in commercial blackberry fields in Oregon. Plant Disease. 106(7):1980.
Webber, B.J., Wada, S., Stockwell, V.O., Wiman, N.G. 2021. Susceptibility of some Corylus avellana L. cultivars to Xanthomonas arboricola pv. corylina. Frontiers in Plant Science. 12. Article 800339.
Foster, Z.S., Albornoz, F.E., Fieland, V.J., Larsen, M.M., Jones, F.A., Tyler, B.M., Nguyen, H.D., Burgess, T., Riddell, C., Voglmayr, H., Martin, F.N., Grunwald, N.J. 2022. A new oomycete metabarcoding method using the rps10 gene. Phytobiomes Journal. 6(3):214-226.
Weldon, W., McGhee, G., Jones, L.A., Stockwell, V.O. 2022. Taxonomic reclassification of the fungal pathogen causing dry berry disease of caneberries into the division Ascomycota as Monilinia rubi. Plant Disease.
Peterson, E.K., Sondreli, K.L., Reeser, P., Navarro, S., Nichols, C., Wiese, R., Fieland, V.J., Grunwald, N.J., LeBoldus, J.M. 2022. First report of the NA2 clonal lineage of the sudden oak death pathogen, Phytophthora ramorum, infecting tanoak in Oregon forests. Plant Disease Notes. 106(9):2537.
Hamelin, R.C., Bilodeau, G., Heinzelmann, R., Hrywkiw, K., Capron, A., Dort, E., Dale, A., Giroux, E., Kus, S., Carleson, N., Grunwald, N.J., Feau, N. 2022. Genomic biosurveillance detects a sexual hybrid in the sudden oak death pathogen. Communications Biology. 5. Article 477.
Peterson, E.K., Grunwald, N.J., Parke, J.L. 2022. Risk of epidemic development in nurseries from soil inoculum of Phytophthora ramorum. Phytopathology. 112(5):1046-1054.