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Research Project: Improved Strategies for Management of Soilborne Diseases of Horticultural Crops

Location: Horticultural Crops Research

2015 Annual Report

Objective 1: Identify and characterize key pathogens to pinpoint critical pathogen vulnerabilities and develop targeted disease management strategies. Objective 2: Identify plant germplasm and cultivars of small fruits resistant to economically-important soilborne diseases. Objective 3: Expand knowledge of genomic features and regulatory mechanisms in biological control strains of Pseudomonas spp. to develop more consistent and effective tools for biologically-based disease management.

Determine the prevalence and characterize the population diversity of important soilborne pathogens affecting horticultural crops. Results from this research will identify specific pathogen populations that constrain production of horticultural crops. These populations can be targeted in the future to develop more effective, economical, and environmentally-acceptable disease management systems. Evaluate germplasm of black raspberry (Rubus occidentalis) for resistance to Verticillium wilt, caused by V. dahliae, and germplasm of red raspberry (Rubus ideaus) for resistance to the root lesion nematode, P. penetrans. Our research will identify Rubus genotypes and raspberry cultivars that are resistant to these soilborne diseases, and can be deployed in horticultural production systems in the future. Develop improved knowledge of the mechanisms by which the biological control agent Pseudomonas fluorescens Pf-5 suppresses disease. Results from this research will enable pathologists, horticulturists, and growers to develop more effective and reliable biological controls for soilborne diseases of horticultural crops.

Progress Report
Towards our first objective to identify key pathogens limiting the production of small fruit or nursery crops, we completed diversity analyses of 10 isolates of Verticillium dahliae from commercial nurseries by vegetative compatibility group (VCG) typing. Six isolates were in VCG 4B, a group frequently associated with potato. Results will establish whether there is host preference of Verticillium isolates for woody plant hosts in the Pacific Northwest. Genetic diversity and mefenoxam sensitivity analyses of 115 Pythium irregulare, P. sylvaticum, and P. ultimum from commercial nurseries were completed and showed that fungicide resistant isolates have been moved among forest nurseries. Results are critical for developing disease management strategies to minimize the spread of pathogens. Pathogens isolated from Rhododendron and Ribes plants in several commercial nurseries were identified as part of an agreement aimed at improving plant health for nursery production. One greenhouse and four field trials were initiated to evaluate pathogenicity, effects of irrigation and pathogen population size on disease development, and disease management with fungicides. To continue to explore the genetic diversity of the virus transmitting plant-parasitic nematode Xiphinema americanum, the genome of a population was sequenced using Mi-Seq. A preliminary analysis of the data revealed a total coverage of 310 Mbp and the presence of several potential endosymbionts. This data will be used to continue to explore the molecular mechanisms of virus vectoring, the role of endosymbionts in nematode health, and the development of diagnostic tools. In collaborative research with Oregon State University, we collected 266 isolates of Pseudomonas syringae from infected blueberries grown in commercial fields in the major blueberry production areas of Oregon and Washington. Phylogenetic analysis demonstrated that strains of P. syringae associated with bacterial canker are diverse, falling into six of thirteen described phylogroups making up the P. syringae complex. Current efforts are focused on developing a reliable disease assay on blueberry to complete Koch’s postulates on bacteria representing each of the six phylogroups. Almost all of the 266 isolates were sensitive to streptomycin and oxytetracycline, suggesting that these antibiotics could be effective in managing the disease until resistance develops in the pathogen population. 87% of isolates from Washington and 14% of strains in Oregon are resistant to kasumin, a newly-registered antibiotic for plant agriculture; these data suggest that kasumin will not be effective for management of bacterial canker of blueberry. 60% of Oregon isolates and 81% of Washington isolates were resistant to copper; although copper is commonly used for management of the disease in commercial plantings, our data indicate that it is not likely to be effective. These data have been communicated to growers to aid in design of their disease management strategies. Towards our second objective to identify small fruit germplasm with resistance to soilborne pathogens, we continued evaluations of 54 Rubus genotypes in a greenhouse trial and a field trial. Two black raspberry genotypes continue to look promising for possible resistance to V. dahliae. Information will be used to develop breeding material for the development of resistant Rubus genotypes. We have also evaluated 18 blueberry cultivars for resistance to Phytophthora cinnamomi. Results will be used to develop recommendations for growers with fields contaminated by the pathogen. The field trial evaluating the response of 8 raspberry varieties to Pratylenchus penetrans was completed. All of the data has been compiled and analyzed and a manuscript completed. The USDA National Institute of Food and Agriculture (NIFA) funded project was completed. We discovered that bed fumigation performed as well as broadcast fumigation for the control of soilborne pathogens and nematodes. We also discovered that all of the commonly planted raspberry varieties in Washington are extremely susceptible to damage by P. penetrans, demonstrating the necessity to manage this production-limiting pest. In ARS and the Animal and Plant Health Inspection Service (APHIS) funded research on a new cyst nematode species, three years of pathogenicity trials were completed and summarized. Globodera ellingtonae caused a reduction in yield only at high initial inoculation densities (80 eggs/g soil) in the one field location evaluated. The search for a source of resistance in potato to all potato cyst nematode species continues with collaborators in Idaho and New York. In addition to available germplasm, wild Solanum species are being evaluated. From a molecular perspective, the genome of G. ellingtonae was sequenced and has been assembled with collaborators. In addition, the transcriptome generated from multiple life stages of G. ellingtonae was also sequenced. Towards our third objective of developing knowledge of mechanisms of biological control of plant diseases, we discovered that the biological control bacterium Pseudomonas protegens Pf-5, which produces 7 known antibiotics, produces another antibiotic that is toxic to many bacteria and fungi. We identified the antibiotic's chemical structure and toxicity against plant-pathogenic bacteria, and discovered that production of the antibiotic is suppressed by oxygen. This discovery is important because antibiotic production is key to biological control by Pseudomonas and, with this compound identified, we now have the opportunity to evaluate its role in biological control.

1. Pathogen movement among forest nurseries. Pythium species are important soilborne pathogens causing damping-off and root rot of tree seedlings in forest nurseries. ARS scientists at Corvallis, Oregon, with collaborators from Oklahoma State University, used simple sequence repeat microsatellites and amplified fragment length polymorphism analyses to determine the genetic diversity of three common Pythium species (P. irregulare, P. sylvaticum, and P. ultimum) from three commercial forest nurseries. The results established that certain lineages and genotypes of all three pathogens, including two fungicide resistant P. ultimum isolates, are shared among nurseries. This research indicates that pathogen movement is occurring among forest nurseries and therefore is a risk for unintentionally introducing new pathogen species and fungicide resistant isolates into new locations. This information is being used to develop management strategies for minimizing the spread of pathogens from incoming nursery stock purchased from other nurseries.

2. Root lesion nematode management in raspberry varieties. Commonly planted raspberry varieties suffer extensive damage from root lesion nematode. The root lesion nematode is a production-limiting pest of red raspberry. ARS scientists at Corvallis, Oregon, with collaborators at Washington State University, evaluated the impact of root lesion nematode on the establishment and productivity of eight raspberry varieties over a three year period in a field trial. They discovered that all of the raspberry varieties were extremely susceptible to damage caused by the root lesion nematode. By the end of the experiment, yield loss across varieties was at least 63%. These results are significant because raspberry growers now know that they cannot use variety selection to manage this nematode.

Review Publications
Stewart, J.E., Kroese, D.R., Tabima, J.F., Larsen, M.M., Fieland, V.J., Press, C.M., Zasada, I.A., Grunwald, N.J. 2014. Pathogenicity, fungicide resistance, and genetic variability of Phytophthora rubi isolates from raspberry (Rubus idaeus) in the Western United States. Plant Disease. 98:1702-1708.
Han, Z., Walters, T.W., Zasada, I.A. 2014. Impact of Pratylenchus penetrans on established red raspberry productivity. Plant Disease. 98:1514-1520.
Song, C., Van Der Voort, M., Van De Mortel, J., Hassan, K.A., Elbourne, L.D., Paulsen, I.T., Loper, J.E., Raaijmakers, J.M. 2014. The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis. Microbial Biotechnology. 8(2):296-310.
Philmus, B.J., Shaffer, B.T., Kidarsa, T.A., Yan, Q., Raaijmakers, J.M., Begley, T.P., Loper, J.E. 2015. Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5. ChemBioChem. doi: 10.1002/cbic.201500247.
Mano, E.T., Minami, S.N., Loper, J.E., Araujo, W.L. 2015. First description of necrosis in leaves and pseudo-bulbs of Oncidium orchids caused by Burkholderia gladioli in São Paulo State, Brazil. Plant Disease. doi: 10.1094/PDIS-03-15-0297-PDN.
Zasada, I.A., Weiland, G.E., Han, Z., Walters, T.W., Moore, P.P. 2015. Impact of Pratylenchus penetrans on establishment of red raspberry. Plant Disease. 99(7):939-946.
Ersahin, Y.S., Weiland, G.E., Zasada, I.A., Reed, R.L., Stevens, J.F. 2014. Identifying rates of meadowfoam (Limnanthes alba) seed meal needed for suppression of Meloidogyne hapla and Pythium irregulare in soil. Plant Disease. 98(9):1253-1260.
Howland, A.D., Schreiner, R.P., Zasada, I.A. 2014. Spatial distribution of plant-parasitic nematodes in semi-arid Vitis vinifera vineyards in Washington. Journal of Nematology. 46:321-330.
Ingham, R.E., Kroese, D.R., Zasada, I.A. 2015. Effect of storage environment on hatching of Globodera ellingtonae. Journal of Nematology. 47:45-51.
Zasada, I.A., Peetz, A.B., Wade, N., Navarre, D.A., Ingham, R.E. 2013. Host status of different potato (Solanum tuberosum) varieties and hatching in root diffusate of Globodera ellingtonae. Journal of Nematology. 45:195-201.
Zasada, I.A., Moore, P.P. 2014. Host status of Rubus species and hybrids for the root lesion nematode, Pratylenchus penetrans. HortScience. 49:1128-1131.
Weiland, G.E., Garrido, P., Kamvar, Z.N., Marek, S.M., Grunwald, N.J., Garzon, C.D. 2015. Population structure of Pythium irregulare, P. sylvaticum, and P. ultimum in forest nursery soils of Oregon and Washington. Phytopathology. 105(5):684-694.
Weiland, G.E. 2015. First report of Phytophthora cactorum and P. citrophthora causing root rot of Ribes lobbii (Gray) in Oregon. Plant Disease. 99(1):157.
Weiland, G.E., Santamaria, L. 2015. Greenhouse plants, ornamental – Pythium seed rot, damping-off, and root rot. Pacific Northwest Plant Disease Control Handbook. p. 4G-47-4G-48.
Vargas, O., Bryla, D.R., Weiland, G.E., Strik, B.C., Sun, L. 2015. Irrigation and fertigation with drip and alternative micro irrigation systems in northern highbush blueberry. HortScience. 50(6):897-903.
Grunwald, N.J., Press, C.M., Rolfe, K.J., Weiland, G.E., Davis, E.A. 2013. Efficacy of management tools for control of Pythium root rot of Douglas fir seedlings, 2010. Plant Disease Management Reports. 7:OT010.
Grunwald, N.J., Press, C.M., Rolfe, K.J., Weiland, G.E., Davis, E.A. 2015. Efficacy of management tools for control of Pythium root rot of Douglas-fir seedlings, 2013. Plant Disease Management Reports. 9:OT004.