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United States Department of Agriculture

Agricultural Research Service


Location: Horticultural Crops Research

2011 Annual Report

1a. Objectives (from AD-416)
Evaluate the etiology and epidemiology of soilborne diseases of small fruit and nursery crops and the biology of causal pathogens. Develop, evaluate, and enhance strategies for the management of soilborne diseases of horticultural crops. Develop knowledge of mechanisms contributing to biological control of soilborne plant diseases.

1b. Approach (from AD-416)
Dose-response relationships between propagule density in irrigation water and disease. Identification of factors influencing pathogen dispersal and disease spread among containers in a nursery. A systematic survey of blueberry fields throughout the PNW will be conducted to identify nematode pathogens. Greenhouse and microplot experiments will be employed to determine the effects of a range of population densities of nematode species found in the survey on the health of a widely planted blueberry cultivar. Test the Electrocatalytic Oxidation/precipitation (EO) method. Identify factors influencing the efficacy of the EO method. Test the EO method in an experimental nursery setting. Use the recently-described genomisotopic approach to purify the two cryptic metabolites from cultures of Pf-5. Derive mutants of Pf-5. Assess the role of novel metabolites in biological control. Test toxicity of the purified metabolites. Evaluate gene expression by Pf-5 on seed surfaces using RNA isolation, labeling and hybridization. Characterize the nutritional composition of seed exudates. Generate derivatives of Pf-5 with mutations in selected genes. Test mutants for spermosphere colonization and biological control of Pythium damping off.

3. Progress Report
The first objective of our project focuses on the biology of pathogens of horticultural crops. 1) We identified 19 Pythium species associated with forest nursery soils and inoculated tree seedlings with isolates of the most common species to identify those causing seedling mortality. Identification of the predominant pathogenic species is essential for developing non-fumigant disease management strategies in the future. 2) We developed an effective method for inoculating woody nursery crops with Verticillium dahliae, one of the most important pathogens limiting nursery crop and small fruit production in the Pacific Northwest. This inoculation method will be used to test raspberry germplasm for resistance to the pathogen in the coming years. 3) Populations of Pseudomonas syringae and symptoms of bacterial canker and leaf spot on blueberry were monitored monthly in two field trials. Observations and quantitative data are being integrated with 2009 data to develop knowledge of the population dynamics and life cycle of this important pathogen. Our second objective is to develop improved plant disease management strategies. 1) We identified four reduced-rate fumigant treatments that were as effective as a full-rate methyl bromide application in controlling diseases of Douglas fir seedlings caused by Pythium spp. Adoption of the tested treatments will decrease the amount of fumigant applied, result in lower fumigant emissions, and provide alternatives to methyl bromide, a known ozone-depleting agent, for disease control. 2) A microplot field trial was planted to evaluate eight grape rootstocks and self-rooted ‘Chardonnay’ or ‘Cabernet Sauvignon’ for susceptibility to the northern root knot nematode, Meloidogyne hapla. In coming years, we will evaluate nematode population densities in soil and roots, vine establishment, pruning weights, yield, and vine nutrient status of all treatments to identify differences in nematode susceptibility of these grape varieties. 3) We evaluated eleven Rubus spp. in greenhouse trials, and identified three species that exhibited some resistance to the root lesion nematode Pratylenchus penetrans, which is a production-limiting pest in red raspberry. 4) We developed a disease assay for P. syringae, used it to screen blueberry cultivars for sensitivity to bacterial canker, and observed differential sensitivities of cultivars to the disease. This information, when confirmed, will be useful to growers selecting cultivars for commercial production. Our third objective focuses on mechanisms of biological control. We completed a project generating and analyzing the genomic sequences of seven strains of Pseudomonas spp. that suppress plant disease. Many gene clusters with potential roles in biological control were identified, providing avenues for the future discovery of natural products useful in disease management. We identified a chemical signal responsible for the co-regulation of two antibiotics in the biocontrol bacterium Pseudomonas fluorescens Pf-5, which provides new insight into factors controlling the expression of biocontrol traits.

4. Accomplishments
1. Reduced-rate fumigant alternatives to methyl bromide for Pacific Northwest Forest Nurseries. The $350 million Pacific Northwest forest nursery has experienced tree seedling losses in excess of 50% in nonfumigated fields due to the presence of soilborne diseases. The fumigant methyl bromide has traditionally been applied to control soilborne diseases, but its use is increasingly limited by state and federal regulations for ozone-depleting agents. ARS researchers at Corvallis, Oregon, evaluated reduced-rate alternative fumigant treatments to methyl bromide for their ability to control soilborne diseases in forest nurseries and found four formulations that were as effective as methyl bromide in reducing disease damage. The results are significant because the alternative fumigant treatments allow growers to continue to manage soilborne diseases as methyl bromide use is phased out, and the ability to use reduced-rates will decrease chemical inputs and result in lower fumigant emissions.

2. Genomic sequences of seven plant-associated strains of Pseudomonas spp. reveal potential new determinants of biological control. Biological control is a promising approach for management of plant diseases, but knowledge of biocontrol mechanisms is needed to improve its reliability for US agriculture. Towards this end, ARS scientists in Corvallis, OR, Pullman, WA, Davis, CA, and Charleston, SC, with colleagues at Macquarie University and the J. Craig Venter Institute sequenced the genomes of seven well-characterized biological control strains of Pseudomonas spp. (P. fluorescens, P. chlororaphis and P. synxantha). Through comparative genomic analyses, they identified approximately 2800 genes that are shared by all strains and 300 to 900 genes that are unique to each strain. In the unique regions of each genome, they discovered new gene clusters with potential roles in biological control, including those coding for insect toxins and new secondary metabolites. These gene clusters provide avenues for the future discovery of novel natural products, including those contributing to biological control of plant disease.

3. Host status of grapevines to the northern root-knot nematode. The northern root-knot nematode (Meloidogyne hapla) was detected at moderate to high population densities in 75% of the eastern Washington vineyards surveyed. The impact of this nematode on vine establishment and productivity is unknown. Two years after inoculation of self-rooted Chardonnay and Cabernet Sauvignon with the northern root-knot nematode, ARS and Washington State University scientists showed that Chardonnay was a better host for this nematode; populations of root-knot nematode were ten times higher on Chardonnay compared to Cabernet Sauvignon. There was no difference in pruning weights between nematode-inoculated and control vines. However, there was a trend for lower pruning weight of Chardonnay vines that were infected with the nematode compared to the control. These findings are important to Washington grape growers and may direct planting material selection in replant sites that have high northern root-knot nematode populations.

Review Publications
Weiland, G.E. 2011. Influence of isolation method on recovery of Pythium species from forest nursery soils in Oregon and Washington. Plant Disease. 95:547-553.

Zasada, I.A., Walters, T.W., Hanson, B.D. 2010. Challenges in producing nematode and pathogen free fruit and nut nursery crops in the United States. Outlooks on Pest Management. 21:246-250.

Stockwell, V., Johnson, K.J., Sugar, D., Loper, J.E. 2010. Control of fire blight by Pseudomonas fluorescens A506 and Pantoea vagans C9-1 applied as single strains and mixed inocula. Phytopathology. 100(12):1330-1339.

Stockwell, V., Johnson, K.J., Sugar, D., Loper, J.E. 2011. Mechanistically compatible mixtures of bacterial antagonists improve biological control of fire blight of pear. Phytopathology. 101(1):113-123.

Hartney, S., Mazurier, S., Kidarsa, T.A., Quecine, M., Lemanceau, P., Loper, J.E. 2011. TonB-Dependent outer-membrane proteins and siderophore utilization in Pseudomonas fluorescens Pf-5. Biometals. 24(2):193.

Mavrodi, D.V., Joe, A., Mavrodi, O., Hassan, K.A., Weller, D.M., Paulsen, I.T., Loper, J.E., Alfano, J.R., Thomashow, L.S. 2011. Structural and functional analysis of the type III secretion system from Pseudomonas fluorescens Q8r1-96. Journal of Bacteriology. 193(1):177-189.

Olcott, M.H., Henkels, M.D., Rosen, K., Walker, F., Sneh, B., Loper, J.E., Taylor, B. 2010. Lethality and developmental delay of Drosophila melanogaster following ingestion of selected Pseudomonas fluorescens strains. PLoS One. 5(9):e12504.

Treonis, A.M., Austin, E.A., Buyer, J.S., Maul, J.E., Spicer, L., Zasada, I.A. 2010. Effects of organic amendments and tillage on soil microorganisms and microfauna. Applied Soil Ecology. 46(1):103-110.

Masler, E.P., Zasada, I.A., Sardanelli, S., Rogers, S.T., Halbrendt, J.M. 2010. Effects of benzyl isothiocyanate on the reproduction of Meloidogyne incognita on Glycine max and Capsicum annuum. Nematology. 12(5):693-699.

Skantar, A.M., Handoo, Z.A., Carta, L.K., Zasada, I. A., Ingham, R.E., Chitwood, D.J. 2011. Morphological and molecular characterization of Globodera populations from Oregon and Idaho. Phytopathology. 101:(4)480-491.

Last Modified: 2/23/2016
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