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United States Department of Agriculture

Agricultural Research Service


Location: Horticultural Crops Research

2012 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:
Results from the five-year project 5358-12220-003-00D, which terminated on May 8, 2012 and was replaced with project 5358-12220-004-00D, include the following. Forest nurseries of the Pacific Northwest USA were surveyed for the presence of soilborne pathogens and eight Pythium spp. pathogenic to Douglas-fir seedlings were found. Reduced-rate alternative fumigant treatments were identified that were as effective as methyl bromide at disease and weed control in forest nursery field studies. Aerated steam, irrigation management, and certain fungicides were also effective for the control of soilborne pathogens. These findings are significant because they provide economically viable alternatives to methyl bromide for disease control and their implementation can reduce emissions through lower rates of applied fumigants. The host status of blueberry varieties to plant-parasitic nematodes and the impact of stubby root nematode (Paratricodorus renifer) on blueberry were determined. Blueberry varieties with genetic backgrounds including Vaccinium corymbosum and V. angustifolium were excellent hosts for stubby root nematode, but V. ashei was a poor host for this nematode. In field microplots, berry yield was reduced by at least 25% by stubby root nematode. Knowledge of a resistance mechanism to plant-parasitic nematodes can lead to the development of nematode resistant blueberry cultivars. On grape, another plant-parasitic nematode, ring nematode (Mesocriconema xenoplax), initially caused decreased root growth, but its above-ground impact on plant productivity was not apparent until the third year of a four-year study. The apparent ring nematode resistance of the rootstock 101-14 broke down in year three, with only the rootstock 420A remaining highly resistant to the nematode. Growers will use this information to select rootstocks for planting and to direct the timing of management practices to minimize the impact of ring nematode on vine establishment and productivity. We devised an inoculation assay and used it to assess susceptibility of blueberry varieties to Pseudomonas syringae. We also confirmed that growing ornamentals such as lilac in plastic shelters provided excellent control of bacterial blight caused by P. syringae and demonstrated that this control is due primarily to reduced leaf wetness, not frost protection as previously thought. Towards our objective of developing knowledge of mechanisms of biological control of plant diseases, we completed a project comparing genomic sequences of ten biological control strains of Pseudomonas spp., and identified genes for the biosynthesis of novel antibiotics and insect toxins. Using genomic mining, we discovered two new natural products and demonstrated the anti-fungal activities of these compounds. We developed a microarray for the biological control organism (Pseudomonas protegens strain Pf-5) and used it to identify genes expressed by the bacterium on plants as well as factors controlling the expression of genes required for biological control. This information is allowing us to use directed strategies to improve the reliability of biological control for agriculture.

4. Accomplishments
1. Genomic sequences of seven biological control strains in the Pseudomonas fluorescens group completed. Biological control is a promising approach for management of plant diseases and pests, but knowledge of biocontrol mechanisms is needed to improve the reliability of bicontrol for U.S. agriculture. Towards this end, ARS researchers at Corvallis, Oregon, Pullman, Washington, Davis, California, and Charleston, South Carolina, with colleagues at Macquarie University and the J. Craig Venter Institute; completed and published the genomic sequences of seven well-characterized biological control strains. They mapped genes encoding biological control traits on the genome of each strain and linked the gene inventories to certain traits, including insect toxicity, the production of antibiotics and enzymes, and the utilization of specific nutrients. The genomic sequences, which are now available to the public and the scientific community, provide new directions for the future discovery of new traits, including those contributing to biological control of plant disease or insect pests.

2. Meadowfoam seed meal controls soilborne pathogens of ornamentals and small fruits. Growers of ornamental and nursery crops lack safe and effective methods for controlling soilborne pathogen-induced crop losses, making the discovery of environmentally- and economically-sound control strategies critical. One potential control strategy is soil amendment with meadowfoam seed meal, a byproduct obtained after extracting of oil from seed of meadowfoam, which contains compounds that are potentially toxic to soilborne pathogens. ARS researchers at Corvallis, Oregon, with collaborators from Oregon State University, tested five naturally-occurring compounds in meadowfoam seed meal for toxicity against three soilborne pathogens and identified three compounds that were toxic. Each pathogen differed in its sensitivity to these compounds. These results are significant because they identify specific compounds that are responsible for the toxicity of meadowfoam seed meal to soilborne pathogens and will guide the application of meadowfoam seed meal in ornamental and small fruit production systems.

Review Publications
Zasada, I.A., Walters, T.W., Pinkerton, J. 2011. Post-Plant nematicides for the control of root lesion nematode in red raspberry. HortTechnology. 20:856-862.

Zasada, I.A., Weiland, G.E., Reed, R.L., Stevens, J.F. 2011. Activity of meadowfoam (Limnanthes alba) seed meal glucolimnanthin degradation products against soilborne pathogens. Journal of Agricultural and Food Chemistry. 60:339-345.

Meyer, S.L., Zasada, I.A., Orisajo, S.B., Morra, M.J. 2011. Mustard seed meal mixtures: management of Meloidogyne incognita on pepper and potential phytotoxicity. Journal of Nematology. 43(1):7-15.

Kroese, D., Zasada, I.A., Ingham, R.E. 2011. Comparison of Meldola’s Blue staining and hatching assay with potato root diffusate for assessment of Globodera sp. egg viability. Journal of Nematology. 43(3/4):182-186.

Weiland, G.E., Leon, A.L., Edmonds, R.L., Littke, W.R., Browning, J.E., Rose, R., Cherry, M., Davis, E.A., Beck, B.R., Miller, T. 2011. The effects of methyl bromide alternatives on soil and seedling microbial populations, weeds, and seedling morphology in Oregon and Washington forest tree nurseries. Canadian Journal of Forest Research. 41(8):1885-1896.

Subramoni, S., Gonzalez, J.F., Johnson, A., Pechy-Tarr, M., Rochat, L., Paulsen, I., Loper, J.E., Keel, C., Venturi, V. 2011. Bacterial subfamily of LuxR regulators that respond to plant compounds. Applied and Environmental Microbiology. 77(13):4579-4588.

Lim, C., Hassan, K.H., Tetu, S., Loper, J.E., Paulsen, I. 2012. The effect of iron limitation on the transcriptome and proteome of Pseudomonas fluorescens Pf-5. PLoS One. 7(6):e39139.

Kidarsa, T.A., Goebel, N.C., Zabriskie, T., Loper, J.E. 2011. Phloroglucinol mediates crosstalk between the pyoluteorin and 2,4-diacetylphloroglucinol biosynthetic pathways in Pseudomonas fluorescens Pf-5. Molecular Microbiology. 81(2):395-414.

Loper, J.E., Hassan, K.A., Mavrodi, D., Davis, E.W., Lim, C., Shaffer, B.T., Elbourne, L.H., Stockwell, V.O., Hartney, S.L., Breakwell, K., Henkels, M.D., Tetu, S.G., Rangel, L.I., Kidarsa, T.A., Wilson, N.L., Van Mortel, J., Song, C., Blumhagen, R., Radune, D., Hostetler, J.B., Brinkac, L.M., Durkin, A., Kluepfel, D.A., Wechter, W.P., Anderson, A.J., Kim, Y., Pierson Iii, L.S., Pierson, E.A., Lindow, S.E., Raaijmakers, J.M., Weller, D.M., Thomashow, L.S., Allen, A.E., Paulsen, I.I. 2012. Comparative genomics of plant-associated Pseudomonas spp.: Insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genetics. 8(7):e1002784.

Walters, T.A., Zasada, I.A., Pinkerton, J.N., Koch, C. 2012. Host status and damage potential of Paratrichodorus renifer and Pratylenchus penetrans (Nematoda) to blueberry (Vaccinium spp.). Canadian Journal of Plant Pathology. 34(2):277-282.

Last Modified: 2/23/2016
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