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United States Department of Agriculture

Agricultural Research Service


Location: Horticultural Crops Research

2009 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. Replaced 5358-12220-001-00D (3/03). FY03 $73,538 Program Increase. FY06 $133,650 Program Increase (memo #44). Replacing 5358-12220-002-00D (3/07). FY09 perm F/T from 5358-21000-037-00D (6/08).

3. Progress Report
We completed high quality draft genomic sequences of seven biological control strains of Pseudomonas spp., with the complete genomes of each strain represented on only 7 to 15 scaffolds. We manually updated the existing annotation of approximately 70% of the genome of the biocontrol agent Pseudomonas fluorescens Pf-5, which serves as an important resource for the scientific community. We completed microarray experiments identifying genes expressed by Pf-5 on surfaces of pea seed under the control of two global regulators, GacA and RpoS. Using a collection of mutants of Pf-5 with stacked mutations in 10 antibiotic biosynthesis pathways, we identified the antibiotics responsible for Pf-5’s suppression of Fusarium spp. and Pseudomonas syringae, and its phytotoxicity to rice and wheat. We completed field experiments demonstrating that plastic shelters provide an excellent cultural control method for suppression of bacterial blight of lilac caused by Pseudomonas syringae. A plant-parasitic nematode survey of blueberries was continued in Washington and expanded to include Oregon. During a survey conducted in 2008, it was discovered that Pratylenchus spp. was present in > 50% of the fields surveyed. However, in a greenhouse pathogenicity study where six blueberry genotypes were exposed to P. penetrans, very little or no reproduction of this nematode occurred on these genotypes. To determine where and when Pratylenchus spp. are associated with blueberry plants, a more in-depth sampling was undertaken to include blueberry roots and rhizosphere soil as well as weed roots. Field microplots (a pot-in-pot system) were established to study the effects of the ring nematode, Mesocriconema xenoplax, on physiology and growth ‘Pinot noir’ grapevines. The first impact of M. xenoplax on grape production that we detected was fewer fine roots but higher root-soil respiration in self-rooted vines and vines on ‘3309C’ rootstock than in tolerant or resistant rootstocks in 2007. By 2008, M. xenoplax no longer altered root-soil respiration, but affected aboveground performance of the vines. A greenhouse study was conducted and is being repeated to study the pathogenicity of plant-parasitic nematodes on a range of blueberry genotypes. All genotypes except for rabbit-eye blueberry were excellent hosts for Paratrichodorus renifer. Surveys of Verticillium dahliae in woody ornamental nurseries in Oregon are continuing. Evaluation of methods for isolation of pure cultures of V. dahliae are in progress. Greenhouse studies to evaluate suitable inoculation methods are in progress. Efficacy of low doses of four alternative fumigants in reducing Pythium populations was compared to populations from nonfumigated plots and plots treated with methyl bromide. Three methods for isolation of Pythium species from soils were selected and have been used throughout the study. Quantification of prefumigation and 2 postfumigation Pythium populations have been completed from 3 forest nurseries. Isolates have been put into a culture collection and are currently being identified to species. Pathogenicity studies on Dougfir have been initiated.

4. Accomplishments
1. Nematode (Paratrichodorus renifer) resistance in blueberry. The stubby root nematode, Paratrichodorus renifer, has been shown to be widespread in established blueberry plantings in the Pacific Northwest. Very little is known about the biology and pathogenicity of this nematode in blueberry. A greenhouse experiment was conducted by ARS scientists in the Horticultural Crops Research Unit in Corvallis, OR to determine the host status of different blueberry genotypes to the plant-parasitic nematode P. renifer. Blueberry genotypes with genetic backgrounds including Vaccinium corymbosum and V. angustifolim were excellent hosts for this nematode, but rabbit-eye blueberry (V. ashei) was a very poor host for P. renifer with fewer nematodes being recovered than were added to plants. Research is ongoing to continue to understand this potential source of resistance which exists in Vaccinium. Knowledge of a resistance mechanism to plant-parasitic nematodes in Vaccinium can lead to the development of nematode resistant blueberry varieties.

2. Pythium species associated with forest nurseries. Pythium species associated with damage to conifer seedlings were traditionally identified on the basis of morphology, but morphological features may not adequately distinguish between Pythium species. Current methods using DNA sequences allow more accurate identification. A survey of Pythium species associated with damage to conifer seedlings in forest nurseries was conducted, and fifteen species have been isolated and identified on the basis of DNA sequence. ARS scientists in Corvallis, OR have tested twelve Pythium species for pathogenicity to Dougfir and all cause at least 25% mortality. This research identifies Pythium species not previously associated with damage to conifer seedlings. Knowledge of Pythium species that cause disease in conifer seedlings is essential in developing effective disease management.

Review Publications
Loper, J.E., Bruck, D.J., Pechy-Tarr, M., Maurhofer, M., Keel, C., Gross, H. 2008. Genomic Analysis of Secondary Metabolite Production by Pseudomonas fluorescens Pf-5. In: Lorito, M., Woo, S.L., Scala, F., editors. Biology of Molecular Plant-Microbe Interactions. Volume 6. [CD-ROM]. St. Paul, MN. International Society for Molecular Plant-Microbe Interactions. Chapter 101.

Mavrodi, D.V., Loper, J.E., Paulsen, I.T., Thomashow, L.S. 2009. Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiology. 9:8.

Stockwell, V., Hockett, K., Loper, J.E. 2009. Role of RpoS in stress tolerance and environmental fitness of the phyllosphere bacterium Pseudomonas fluorescens 122. Phytopathology. 99:689-695.

Zasada, I.A., Masler, E.P., Rogers, S.T., Halbrendt, J.M. 2009. Behavioral response of Meloidogyne incognita to benzyl isothiocyanate. Nematology. 11:603-610.

Meyer, S.L., Rice, C., Zasada, I.A. 2009. DIBOA: Fate in Soil and Effects on Root-knot Nematode Egg Numbers. Soil Biology and Biochemistry. 41:1555-1560.

Hagen, M., Stockwell, V., Whistler, C., Johnson, K.B., Loper, J.E. 2009. Stress tolerance and environmental fitness of Pseudomonas fluorescens A506, which has a mutation in rpoS. Phytopathology. 99:689-695.

Last Modified: 2/23/2016
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