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

Location: Horticultural Crops Research

2017 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
This is the final report for project 2072-12220-004-00D, which has been replaced by a new project 2072-22000-043-00D "Development of Knowledge-based Approaches for Disease Management in Small Fruit and Nursery Crops" in May 2017. Substantial results were realized over the five years of the project advancing knowledge of key pathogens and sustainable management practices to improve the management of soilborne pathogens in small fruit and ornamental crops. Forest nursery growers should rotate fungicide use among different chemistries to prevent establishment of resistance. Fungicide resistance can be a significant problem in managing soilborne diseases, particularly when there are multiple pathogen species in the nursery system. These species differ in sensitivity to commonly applied fungicides and genetic analyses showed that fungicide resistant isolates were moved among nurseries. A mitochondrial marker was developed that distinguishes three populations of Xiphinema americanum, a group of plant-parasitic nematodes that vector plant viruses. When the genome of X. americanum was sequenced, a bacterial mutualist in the gut and ovaries of the nematode was found. This bacterium is likely a nutritional mutualist, which might be manipulated as part of a novel management strategy to limit the nutrient pathway in the nematode. Plant resistance is key to reducing reliance on chemicals for the management of soilborne pathogens. Many raspberry species and cultivars were evaluated for resistance plant-parasitic nematode Pratylenchus penetrans and fungal pathogen Verticillium dahliae. Some raspberry material was identified as resistant to Verticillium, but not P. penetrans. Therefore, the use of plant resistance is currently not an option for the management of P. penetrans in raspberry. Yield of several commercially available raspberry cultivars was reduced by at least 50% by the nematode. On the biological control research front, new genes and their roles in the biological control of plant disease were discovered. Genomic techniques identified approximately 900 genes expressed by the biological control bacterium Psudomonas fluorescens Pf-5 on seeds, where interactions between a biological control agent and seed-infecting pathogens occur. It was also discovered that Pf-5, which produces 7 known antibiotics, produces another antibiotic that is toxic to many bacteria and fungi. This discovery is important because antibiotic production is key to biological control by Pf-5. For the first time it was demonstrated that an intermediate in the biosynthesis of antibiotics, phloroglucionol, is important in the biosynthetic pathway of a biological control agent. The overall impact of this project is that growers of ornamental and small fruit crops have new information on pathogen diversity, plant resistance sources, fungicide management, and biological control to make decisions to maximize profits and sustainably manage production-limiting soilborne pathogens while sustaining yield.

1. Six plant-parasitic nematode genomes were sequenced. The lack of genomic resources for plant-parasitic nematodes severely limits the ability to make gene comparisons among species and facilitate genomic discoveries in a group of agriculturally important pests that are responsible for $100 billion in crop loss annually in the United States. ARS scientists at Corvallis, Oregon, with collaborators at Oregon State University, were the first to sequence the genomes, the complete set of genes in an organism, of six economically-important plant-parasitic nematodes. They provided a rapid and affordable avenue for biological inquiry and hypothesis generation from genomic data. This method led to the discovery of novel bacterial endosymbionts, Wolbachia and Cardinium, both first reports in the root lesion nematode Pratylenchus penetrans. These results provide a road map for the rapid processing of genomic data and will ultimately lead to additional genomic resources within this important group of agricultural pests.

2. Root lesion nematode is characterized to improve the efficacy of soil fumigation. One of the major constraints on the production of red raspberries is the presence of the root lesion nematode Pratylenchus penetrans. Current management of this nematode relies on soil fumigation, the injection of biocidal gas into the soil, a method which is expensive and variable in efficacy. ARS scientists at Corvallis, Oregon characterized the distribution and longevity of P. penetrans in the raspberry production system to help growers improve the efficacy of soil fumigation. They demonstrated how and where nematodes are escaping soil fumigation and discovered that P. penetrans can survive in old root material for up to eight months after the previous raspberry crop is terminated. Knowing more about how P. penetrans is distributed may allow growers to more effectively target management practices to when and where the nematode is most vulnerable.

3. Irrigation line placement, mulch type, and gypsum treatment found to affect root rot. Phytophthora cinnamomi is an important pathogen of blueberry worldwide, where it causes root rot and limits establishment of new blueberry fields. Fungicides cannot be used in organic blueberry production; therefore, cultural methods of disease control are needed for blueberry. ARS scientists at Corvallis, Oregon, with collaborators at Oregon State University, evaluated whether irrigation line placement (narrow or wide), mulch type (sawdust or plastic weedmat), and gypsum treatment (amended in soil or not) were effective at reducing root rot. They discovered that the combination of wide irrigation line placement, sawdust mulch, and soil amendment with gypsum initially reduced root infection by P. cinnamomi. Narrow irrigation line placement and plastic weedmat promoted root rot by causing wetter soil and higher soil temperatures, respectively, which stimulated P. cinnamomi infection. These results are important to organic blueberry growers because they provide cultural disease control methods that provide root rot protection in new blueberry plantings.

4. A new canker pathogen was disovered. Calocedrus decurrens, or incense-cedar, is a native tree species used to produce exterior lumber products and is planted in low-input landscapes as windbreaks and as an ornamental. ARS scientists at Corvallis, Oregon, with collaborators at Oregon State University and the United States Forest Service, found a new canker pathogen, Phaeobotryon cupressi, which kills branches throughout the crown of the tree. Landowners with native stands of incense-cedar or specimen trees consider the pathogen to be responsible for tree death. This is the first time this pathogen, originally described from Iran, has been found causing canker disease in the United States.

Review Publications
Peetz, A.B., Zasada, I.A. 2016. Species-specific diagnostics using a B-1,4-endoglucanase gene for Pratylenchus spp. occurring in the Pacific Northwest of North America. Nematology. 18(10):1219-1229. doi: 10.1163/15685411-00003026.
Zasada, I.A., Walters, T.W. 2016. Effect of application timing of oxamyl in nonbearing raspberry for Pratylenchus penetrans management. Journal of Nematology. 48:177-182.
Brown, A.M., Wasala, S.K., Howe, D.K., Peetz, A.B., Zasada, I.A., Denver, D. 2016. Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts. Scientific Reports. 6(34955). doi:10.1038/srep34955.
Kroese, D.R., Weiland, G.E., Zasada, I.A. 2016. Distribution and longevity of Pratylenchus penetrans in the red raspberry production system. Journal of Nematology. 48(4):241–247.
Yeo, J.R., Weiland, G.E., Sullivan, D.M., Bryla, D.R. 2017. Nonchemical, cultural management strategies to suppress phytophthora root rot in northern highbush blueberry. HortScience. 52(5):725-731. doi: 10.21273/HORTSCI11437-16.
Zasada, I.A., Ferris, H. 2017. Nematode parasites of grapevines. In: Wilcox, W.F., Gubler, W.D., Uyemoto, J.K., editors. Compendium of Grape Diseases, Disorders, and Pests. 2nd edition. Minneapolis, MN: APS Press. p. 240.
Walters, T., Bolda, M., Zasada, I.A. 2017. Alternatives to current fumigation practices in western states raspberry. Plant Health Progress. 18:104-111. doi: 10.1094/PHP-RS-16-0068.
Denver, D., Brown, A.M., Howe, D.K., Peetz, A.B., Phillips, W.S., Zasada, I.A. 2016. Genome skimming: A rapid approach to gaining diverse biological insights into multicellular pathogens. PLoS Pathogens. 12(8):e1005713. doi: 10.1371/journal.ppat.1005713.
Howland, A., Skinkis, P.A., Wilson, J.H., Riga, E., Pinkerton, J.N., Schreiner, R.P., Zasada, I.A. 2015. Host status of own-rooted Vitis vinifera varieties to Meloidogyne hapla. Journal of Nematology. 47:141-147.
Macfarlane, S.A., Zasada, I.A., Lemaire, O., Demangeat, G. 2016. Nematode-borne plant viruses. In: Brown, J.K., editor. Vector-Mediated Transmission of Plant Pathogens. St. Paul, MN: APS Press. p. 365-378.
Phillips, W.S., Brown, A.M., Howe, D.K., Peetz, A.B., Blok, V., Denver, D., Zasada, I.A. 2016. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. Biomed Central (BMC) Genomics. 17:706-719. doi: 10.1186/s12864-016-3047-x.
Brown, A.M., Howe, D.K., Wasala, S.K., Peetz, A.B., Zasada, I.A., Denver, D.R. 2015. Comparative genomics of a plant-parasitic nematode endosymbiont suggest a role in nutritional symbiosis. Genome Biology and Evolution. 7(9):2727-2746. doi: 10.1093/gbe/evv176.
Phillips, W.S., Kitner, M.L., Zasada, I.A. 2017. Developmental dynamics of Globodera ellingtonae in field-grown potato. Plant Disease. 101(7):1182-1187. doi: 10.1094/PDIS-10-16-1439-RE.
Rangel, L.I., Henkels, M.D., Shaffer, B.T., Walker, F.L., Davis Ii, E.W., Stockwell, V.O., Bruck, D.J., Taylor, B.J., Loper, J.E. 2016. Characterization of toxin complex gene clusters and insect toxicity of bacteria representing four subgroups of Pseudomonas fluorescens. PLoS One. 11(8):e0161120. doi: 10.1371/journal.pone.0161120.