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United States Department of Agriculture

Agricultural Research Service

Research Project: CONTROL OF PATHOGENS IN STRAWBERRY AND VEGETABLE PRODUCTION SYSTEMS
2010 Annual Report


1a.Objectives (from AD-416)
Objective 1: Optimize delivery and evaluate performance of chemical, cultural, biological, and genetic alternatives to methyl bromide for crops/pathogen combinations currently benefiting from the use of methyl bromide. a. Evaluate alternative fumigants. b. Identify genes associated with pathogenicity of Verticillium dahliae based on a Verticillium comparative genomics study to support the development of alternative control procedures. c. Identify emerging diseases and their etiology and evaluate resistant germplasm for diseases of strawberry, lettuce, and vegetables. d. Evaluate the influence of crop rotation on pathogen populations and beneficial microbial community dynamics in the soil and severity of Verticillium wilt and other diseases. Develop tools to evaluate and understand the role of myxobacteria in agricultural and natural ecosystems in an effort to elucidate their potential for pathogen control. Objective 2: Develop molecular diagnostic tools for the identification of emerging diseases of vegetables and strawberries, and use these tools in the development of management strategies as alternatives to methyl bromide.


1b.Approach (from AD-416)
Develop integrated management approaches including crop rotation, biological control, selection of disease resistant varities, organic production, other biological practices, and combinations of biological practices with reduced concentrations of chemical fumigants to control diseases. Identifying useful commercial biological agents as well as new agents from the strawberry rhizosphere that will help to improve plant growth and disease management. Molecular tools will be developed for evaluation of the fficacy of pathogen management and modeling population dynamics of beneficial microbes. Replaces 5305-22000-009-00D(11/07).


3.Progress Report
Comparative analyses of the predicted protein sets from the genomes of fungal vascular wilt pathogens V. dahliae, Fusarium oxysporum, and V. albo-atrum, revealed a conserved set of proteins that may be important for niche adaptation and pathogenesis in these fungi. Further analyses of these genes were initiated in a collaborative effort with other researchers.

Research was initiated to quantify the fungus V. dahliae in commercial spinach seeds and to examine the localization of the fungus in spinach seeds. Analyses of a method to distinguish between two races of V. dahliae, was conducted, and nearly completed, in collaboration with the UC Davis.

We continued with the analyses of genes that may have a role in plant resistance to fungi. Analyses of a publicly available plant gene database revealed a lettuce gene that shares homology with a gene that confers race 1 resistance to Verticillium wilt disease of tomato and potato.

Additional insertional mutants of the fungus V. dahliae were generated and analyses of the mutants are ongoing using pathogenicity tests.

We described six novel diseases from the Western US and made tentative identifications of the pathogens from four of the diseases. We completed Koch’s postulates on three pathogens causing bacterial leaf spot on parsley, identified two of the pathogens and demonstrated the usefulness of MLST/MLSA for allocating strains to pathovars of Pseudomonas syringae.

We completed the evaluation of rifampicin resistant variants of bacterial plant pathogens for virulence and growth characters and began to use them in population experiments.

We began data analysis of FAME results from an experiment measuring the impact of 1 – 5 years vegetable rotation on organic strawberry production in collaboration with UCSC.

We transferred P. syringae pv. alisalensis to P. cannabina, resulting in a proposal for a novel species and an additional pathovar, P. cannabina pv. cannabina.

We characterized phage pBS1 to which P. cannabina pv. alisalensis is specifically sensitive.

Dose response studies are in progress to evaluate the efficacy of alternative fumigants and what concentrations are needed to manage specific soilborne pathogens (Pythium ultimum and Rhizoctonia solani)

A comprehensive multigene phylogenetic analysis of 4 Phytophthora species and species complexes has been completed in collaboration with 3 other labs and the results are currently being written up. A comprehensive mitochondrial multigene phylogeny of the genus Phytophthora has been concluded, the data analysis is in the final stages and the manuscript will be written up shortly.

A new diagnostic marker system for Phytophthora has been developed and is currently being validated with field samples from the USDA-FS P. ramorum national survey (this work will support the mission of the USDA-FS).


4.Accomplishments
1. Gene sets in two fungal pathogens that enable infection of lettuce. ARS researchers in Salinas, California along with a team of international researchers analyzed the genomes of two soilborne, fungal plant pathogens, Verticillium dahliae and V. albo-atrum. These two fungi cause vascular wilt diseases on over 200 plant species worldwide, and costly soil fumigants are sometimes deployed to kill these fungal pathogens in the soil. The research discovered gene sets that enable the two fungi to infect their host crops and permit their ecological adaptation. Identification of the genetic basis for pathogenicity or host range expansion may lead to alternative strategies for their control in high value crops such as lettuce.

2. International movement of the Verticilium wilt plant pathogen on spinach seed. ARS researchers in Salinas, California collaborated with a team of university researchers to assess the possibility that Verticillium dahliae, the soilborne fungus that incites Verticillium wilt disease of lettuce and a wide range of other crop species, can be transmitted over long distances on spinach seed. Verticillium wilt is a relatively new and devastating disease of lettuce, and the pathogen can persist in the soil for many years. The results indicate that there has likely been intra- and intercontinental dissemination of the fungus on spinach seeds from domestic and foreign seed production areas to the major vegetable production area of central, coastal California. Movement of V. dahliae on seed from a seed production area into a vegetable production area has troubling implications for Verticillium wilt disease control and mitigation, especially with potentially decreased use of expensive soil fumigants to control this pathogen in U.S. agriculture.

3. Development of the 2010 List of names of Bacterial Plant Pathogens. The nomenclature of bacterial plant pathogens changes as our understanding of relationships among bacteria is advanced. Confusion arises when there are two or more proposals for classification, each with a different nomenclature, for the same organism. A clarified nomenclature is essential to the identification of plant pathogens and other bacteria. An ARS researcher at Salinas, CA convened the International Society of Plant Pathology, Committee on the Taxonomy of Plant Pathogenic Bacteria to develop an official list of names to be used by researchers, regulators, quarantine officials world-wide.

4. Genetic analysis of an important soilborne pathogen of lettuce and other important crops. Verticillium wilt, incited by the soilborne fungus Verticillium dahliae, is a serious disease of lettuce and many other important crop species. Current techniques for identifying sub-populations, such as different pathogenic races, of the pathogen are slow, and as a result may adversely affect management and cropping decisions by farmers. ARS researchers at Salinas, CA sequenced parts of the mitochondrial DNA from diverse isolates of the pathogen. They also developed an analytical technique for (haplotype) analysis of mitochondrial DNA that complements current techniques for identification of sub-population groups using vegetative compatibility groupings and nuclear DNA analysis. The mitochondrial technique is currently under evaluation using a much larger number of field isolates of the pathogen that have been fully characterized by nuclear DNA analysis to evaluate the utility of mitochondrial haplotype analysis for population studies of this important pathogen.

5. Web site to support Phytophthora research. The fungal genus Phytophthora is responsible for many diseases of crop plants worldwide and consists of approximately 106 species, which are difficult to identify. ARS researchers at Salinas, CA and other ARS and university researchers with support of NRI Plant Biosecurity grants developed a web-based database for Phytophthora research to enhance the understanding of the genus, simplify species identification and stimulate further research on the genus. The database includes complete morphological descriptions, information on host range and geographical distribution, a comprehensive molecular phylogeny using seven nuclear genes (four mitochondrial genes will soon be added), and a section on molecular identification and detection. This database will serve as a resource for researchers working on the genus as well as a repository for future work. Expansion of the database web portal to include the related pathogens Pythium, downy mildews and Albugo was initiated.


5.Significant Activities that Support Special Target Populations
• Mentored five students (4 women and one minority) from Hartnell College and CSUMB (both minority serving institutions) through a grant funded internship program. • Organized and participated in 5 field trips or outreach activities by the USDA for Hartnell College or CSUMB classes or students. • Initiated a project in which our research station is “adopting” with four 5th grade classes at a local minority serving elementary school to provide science programming and field trips. • Organized USDA participation and participated in a Teacher Externship Day Thirty teachers from the Salinas valley attended. • Participated in WISE Women In Science Exploration of Hartnell Community College as a mentor and sponsor. • Serves on the Committee for Equality and Diversity for American Pathological Society. • Mentored one minority intern student • Worked with administrators and teachers at Spreckels Union School District on their science curriculum. Gave classroom presentations in two 5th grade and two 7th grade classes. • Contributed to two classroom presentations (lead responsibility on one) in four 5th grade classes at a local minority serving elementary school the has been “adopted” by our research station to provide science programming and field trips.


Review Publications
Almeida, N., Yan, S., Cai, R., Morris, C.E., Schaad, N.W., Schuenzel, E., Lacy, G.H., Sun, X., Jones, J.B., Castillo, J.A., Bull, C.T., Leman, S., Gutman, D.S., Setubal, J.C., Vinatzer, B.A. PAMDB, 2010. A Multilocus Sequence Typing & Analysis Database and Website for Plant-Associated Microbes. Phytopathology. 100:208-215.

Bull, C.T., Lesaux, M., Manceau, C., Lydon, J., Kong, H.N., Vinatzer, B.A. 2010. Pseudomonas cannabina pv.cannabina pv. nov., and Pseudomonas cannabina pv. alisalensis(Cintas Koike and Bull 2000)comb. nov., are members of the emended species Pseudomonas cannabina(ex Šutic & Dowson 1959)Gardan et al., 1999. Systematic and Applied Microbiology. doi:10.1016/j.syapm.2010.02.001.

Last Modified: 10/20/2014
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