Food Safety Research Information Office
Title:Control of Pathogens in Strawberry and Vegetable Production Systems
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.
    1. Evaluate alternative fumigants.
    2. Identify genes associated with pathogenicity of Verticillium dahliae based on a Verticillium comparative genomics study to support the development of alternative control procedures.
    3. Identify emerging diseases and their etiology and evaluate resistant germplasm for diseases of strawberry, lettuce, and vegetables.
    4. 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.
    5. 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.
  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.
More Info:
APPROACH: 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).
Funding Source:United States Department of Agriculture (USDA), Agricultural Research Service (ARS)
Type:USDA Inhouse
Start Date:2007
End Date:2012
Project Number:5305-22000-012-00D
Accession Number:0412723
Institutions:USDA/ARS - Pacific West Area
Investigators:Martin, Frank
Published Journal
Articles USDA
ARS (NP 108):
RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae
Duressa D, Anchieta A, Chen D, Klimes A, Garcia-Pedrajas MD, Dobinson KF, Klosterman SJ.
BMC Genomics. 2013 Sep 9;14(607):1-18.
Analyses of the population structure in a global collection of Phytophthora nicotianae isolates inferred from mitochondrial and nuclear DNA sequences
Mammella MA, Martin FN, Cacciola SO, Coffey MD, Faedda R, Schena L.
Phytopathology. 2013 Jun;103(6):610-22.
Colonization of spinach by Verticillium dahliae and effects of pathogen localization on the efficacy of seed treatments
Maruthachalam K, Klosterman SJ, Anchieta A, Mou B, Subbarao KV.
Phytopathology. 2013 Mar;103(3):268-80.
Membrane-based oligonucleotide array developed from multiple markers for the detection of many phytophthora species
Chen W, Djama ZR, Coffey MD, Martin FN, Bilodeau GJ, Radmer L, Denton G, Lévesque CA.
Phytopathology. 2013 Jan;103(1):43-54.
"Light-tagged" bacteriophage as a diagnostic tool for the detection of phytopathogens
Schofield D, Bull CT, Rubio I, Wechter WP, Westwater C, Molineux IJ.
Bioengineered. 2013 Jan;4(1):50-4.
Molecular detection and quantification of Pythium species: Evolving taxonomy, new tools and challenges
Schroder K, Martin F, De Cock A, Levesque A, Spies C, Okubara P, Paulitz T.
Plant Disease. 2013 Jan;97(1):4-20.
Comparative genomics of multiple strains of Pseudomonas cannabina pv. alisalensis, a potential model pathogen of both monocots and dicots
Sarris PF, Trantas EA, Baltrus DA, Bull CT, Wechter WP, Yan S, Ververidis F, Almeida NF, Jones CD, Dangl JL, Panopoulos NJ, Vinatzer BA, Goumas DE.
PLoS One. 2013;8(3):e59366.
Bacterial leaf spot of radicchio (Cichorium intybus) is caused by Xanthomonas hortorum
Zacaroni AB, Koike S, De Souza RM, Bull CT.
Plant Disease. 2012 Dec;96(12):1820.
Identification and detection of Phytophthora: Reviewing our progress, identifying our needs
Martin F, Abad GZ, Balci Y, Ivors K.
Plant Disease. 2012 Aug;96(8):1080-103.
Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification
Amyotte SG, Tan X, Pennerman K, Jimenez-Gasco Mdel M, Klosterman SJ, Ma LJ, Dobinson KF, Veronese P.
BMC Genomics. 2012 Jul 16;13:314.
First report of the crucifer pathogen Pseudomonas cannabina pv. alisalensis causing bacterial blight on radish (Raphanus sativus) in Germany
Rubio I, Hiddink G, Asma M, Bull C.
Plant Disease. 2012 Jun;96(6):904.
Development of an engineered bioluminescent reporter phage for detection of bacterial blight of crucifers
Schofield DA, Bull CT, Rubio I, Wechter WP, Westwater C, Molineux IJ.
Appl Environ Microbiol. 2012 May;78(10):3592-8.
A real-time PCR assay for detection and quantification of Verticillium dahliae in spinach seed
Duressa D, Rauscher G, Koike ST, Mou B, Hayes RJ, Maruthachalam K, Subbarao KV, Klosterman SJ.
Phytopathology. 2012 Apr;102(4):443-51.
Development of an assay for rapid detection and quantification of Verticillium dahliae in soil
Bilodeau GJ, Koike ST, Uribe P, Martin FN.
Phytopathology. 2012 Mar;102(3):331-43.
First report of bacterial streak of fennel (Foeniculum vulgare) in California caused by Pseudomonas syringae pv. apii
Jardini TM, Koike ST, Bull CT.
Plant Disease. 2012 Feb;96(2):285.
Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi
Martin FN, Coffey MD.
Phytopathology. 2012 Feb;102(2):229-39.
Species tree estimation for the late blight pathogen, Phytophthora infestans, and close relatives
Blair JE, Coffey MD, Martin FN.
PLoS One. 2012;7(5):e37003.
List of New Names of Plant Pathogenic Bacteria (2008-2010)
Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, Saddler GS, Scortichini M, Stead DE, Takikawa Y.
Plant Pathol. 2012;94(1):21-7.
Identification of pathogenicity-related genes in the vascular wilt fungus Verticillium dahliae by Agrobacterium tumefaciens-mediated T-DNA insertional mutagenesis
Maruthachalam K, Klosterman SJ, Kang S, Hayes RJ, Subbarao KV.
Mol Biotechnol. 2011 Nov;49(3):209-21.
Analysis of Verticillium dahliae suggests a lack of correlation between genotypic diversity and virulence phenotypes
Atallah ZK, Maruthachalam K, Vallad GE, Davis RM, Klosterman SJ, Subbarao KV.
Plant Disease. 2011 Oct;95(10):1224-32.
First report of bacterial blight of crucifers caused by Pseudomonas cannabina pv. alisalensis in Australia
Bull CT, Rubio I.
Plant Disease. 2011 Aug;95(8):1027.
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens
Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, Chen Z, Henrissat B, Lee YH, Park J, Garcia-Pedrajas MD, Barbara DJ, Anchieta A, de Jonge R, Santhanam P, Maruthachalam K, Atallah Z, Amyotte SG, Paz Z, Inderbitzin P, Hayes RJ, Heiman DI, Young S, Zeng Q, Engels R, Galagan J, Cuomo CA, Dobinson KF, Ma LJ.
PLoS Pathog. 2011 Jul;7(7):e1002137.
One step construction of Agrobacterium-Recombination-ready-plasmids (OSCAR), an efficient and robust tool for ATMT based gene deletion construction in fungi
Paz Z, García-Pedrajas MD, Andrews DL, Klosterman SJ, Baeza-Montañez L, Gold SE.
Fungal Genet Biol. 2011 Jul;48(7):677-84.
Multilocus sequence typing of Pseudomonas syringae sensu lato confirms previously described genomospecies and permits rapid identification of P. syringae pv. coriandricola and P. syringae pv. apii causing bacterial leaf spot on parsley
Bull CT, Clarke CR, Cai R, Vinatzer BA, Jardini TM, Koike ST.
Phytopathology. 2011 Jul;101(7):847-58.
SSH reveals a linkage between a senescence-associated protease and Verticillium wilt symptom development in lettuce (Lactuca sativa)
Klosterman SJ, Anchieta A, Garcia-Pedrajas MD, Maruthachalam K, Hayes RJ, Subbarao KV.
Physiol Mol Plant Pathol. 2011 Jun;76(1):48-58.
Genetic characterization of Phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial DNA
Mammella MA, Cacciola SO, Martin F, Schena L.
Fungal Biol. 2011 Apr;115(4):432-42.
First report of bacterial blight of cabbage (Brassica oleracea var. capitata L.) caused by Pseudomonas cannabina pv. alisalensis in California
Mauzey SJ, Koike ST, Bull CT.
Plant Disease. 2011 Jan;95(1):71.
First report of bacterial blight of brussels sprouts (Brassica oleracea var. gemmifera) caused by Pseudomonas cannabina pv. alisalensis in California
Bull CT, Mauzey SJ, Koike ST.
Plant Disease. 2010 Nov;94(11):1375.
Mitochondrial haplotype analysis as a tool for differentiating isolates of Verticillium dahliae
Martin FN.
Phytopathology. 2010 Nov;100(11):1231-9.
Molecular variation among isolates of Verticillium dahliae and polymerase chain reaction-based differentiation of races
Maruthachalam K, Atallah ZK, Vallad GE, Klosterman SJ, Hayes RJ, Davis RM, Subbarao KV.
Phytopathology. 2010 Nov;100(11):1222-30.
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 Sutic & Dowson 1959) Gardan et al., 1999
Bull CT, Manceau C, Lydon J, Kong H, Vinatzer BA, Fischer-Le Saux M.
Syst Appl Microbiol. 2010 Apr;33(3):105-15.
PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes
Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, Schuenzel EL, Lacy GH, Sun X, Jones JB, Castillo JA, Bull CT, Leman S, Guttman DS, Setubal JC, Vinatzer BA.
Phytopathology. 2010 Mar;100(3):208-15.
First report of Phytophthora root rot, caused by Phytophthora cryptogea, on spinach in California
Koike ST, Martin FN.
Plant Disease. 2010 Jan;94(1):131.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR.
Genome Biol. 2010;11(7):R73.
Comprehensive list of names of plant pathogenic bacteria, 1980-2007
Bull CT, De Boer SH, Denny TP, Firrao G, Saux FL, Saddler GS, Scortichini M, Stead DE, Takikawa Y.
J Plant Pathol. 2010;92(3):551-92.
First report of blossom blight of strawberry (Fragaria × Ananassa) caused by Pseudomonas marginalis
Bull CT, Huerta AI, Koike ST.
Plant Disease. 2009 Dec;93(12):1350.
Production of polyclonal antibodies against Pelargonium zonate spot virus coat protein expressed in Escherichia coli and application for immunodiagnosis
Gulati-Sakhuja A, Sears JL, Nuñez A, Liu HY.
J Virol Methods. 2009 Sep;160(1):29-37.
Comparison of crop rotation for Verticillium wilt management and effect on Pythium species in conventional and organic strawberry production
Njoroge SMC, Kabir Z, Martin FN, Koike ST, Subbarao KV.
Plant Disease. 2009 May;93(5):519-27.
Diversity, pathogenicity, and management of verticillium species
Klosterman SJ, Atallah ZK, Vallad GE, Subbarao KV.
Annu Rev Phytopathol. 2009;47:39-62.
Demystifying the nomenclature of bacterial plant pathogens
Bull CT, De Boer SH, Denny TP, Firrao G, Fischer-Le Saux M, Saddler GS, Scortichini M, Stead DE, Takikawa Y.
Plant Pathol. 2008;90(3):403-17.
Non-Journal Publications:
RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae - (Abstract Only)
Duressa, D., Anchieta, A.G., Chen, D., Klimes, A., Dobinson, K.F., Garcia-Pedrajas, M., Klosterman, S.J. 2013. RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae. Fungal Genetics Conference Proceedings. p. 194.
Molecular Identification of Phytophthora - (Book / Chapter)
Martin, F.N. 2013. Molecular identification of Phytophthora. In: Lamour, K., editor. Phytophthora: A Global Perspective. Boston, MA: CABI. p. 19-27.
Foliar Diseases of Apiaceae Crops in Coastal California - (Other)
Bull, C.T. and Koike, S.T. 2012. Foliar Diseases of Apiaceae Crops in Coastal California. Crop Notes (May/June). 1-4.
Novel Pseudomonas syringae strains associated with leaf spot diseases on watermelon (Citrullus lanatus) and squash (Cucurbita pepo) in California - (Abstract Only)
Rubio, I., Bourzar, H., Jardini, T.M., Koike, S.T., Bull, C.T. 2012. Novel Pseudomonas syringae strains associated with leaf spot diseases on watermelon (Citrullus lanatus) and squash (Cucurbita pepo) in California. Phytopathology. 102:S4.103.
Organic strawberry production manual - (Book / Chapter)
Koike, S., Bull, C.T., Bolda, M., Daugovish, O. 2012. Organic strawberry production manual. Organic Strawberry Production Manual. 148 p.
Verticillium comparative genomics yields insights into niche adaptation by plant vascular wilt pathogens - (Abstract Only)
Klosterman, S.J., Subbarao, K.V., Kang, S., Veronese, P., Gold, S.E., Thomma, B., Chen, Z., Henrissat, B., Lee, Y., Park, J., Garcia-Pedrajas, M.D., Barbara, D., Anchieta, A.G., Jonge, R., Santhanam, P., Maruthachalam, K., Atallah, Z.K., Amyotte, S., Paz, Z., Inderbitzin, P., Hayes, R.J., Heiman, D., Young, S., Zeng, Q., Engels, R., Galagan, J., Cuomo, C., Dobinson, K.F., Ma, L. 2011. Verticillium comparative genomics yields insights into niche adaptation by plant vascular wilt pathogens. Phytopathology. 101:S208.
Colonization of spinach (Spinacia oleracea L.) by GFP-tagged verticillium dahliae - (Abstract Only)
Maruthachalam, K., Klosterman, S.J., Subbarao, K.V. 2011. Colonization of spinach (Spinacia oleracea L.) by GFP-tagged verticillium dahliae. Phytopathology. 101: S115.
Development of a qPCR assay for quantification of verticillium dahliae in spinach seed - (Abstract Only)
Duressa, D.O., Rauscher, G.M., Mou, B., Hayes, R.J., Koike, S.T., Maruthachalam, K., Subbarao, K.V., Klosterman, S.J. 2011. Development of a qPCR assay for quantification of verticillium dahliae in spinach seed.Phytopathology. 101:S46.
Lettuce cultivar influences Xanthomonas campestris pv. vitians population levels - (Abstract Only)
Gebben, S., Hayes, R.J., Bull, C.T. 2011. Lettuce cultivar influences Xanthomonas campestris pv. vitians population levels. Phytopathology. 101:S59.
Identification of an emergent bacterial blight of garlic in Brazil - (Abstract Only)
Martins, O.M., Couto, M., Bull, C.T. 2011. Identification of an emergent bacterial blight of garlic in Brazil. Phytopathology. 101:S115.
Previous reports of bacterial diseases on crucifers attributed to Pseuomonas syringae pv. maculicola were caused by P. cannabina pv. alisalensis - (Abstract Only)
Rubio, I., Bull, C.T. 2011. Previous reports of bacterial diseases on crucifers attributed to Pseuomonas syringae pv. maculicola were caused by P. cannabina pv. alisalensis. Phytopathology. 101:S157.
A new disease of parsley (Petroselinum crispum) in California caused by a fluorescent pseudomonad related to Pseudomonas viridiflava - (Abstract Only)
Mauzey, S.J., Davis, C., Martins, O.M., Koike, S.T., Bull, C.T. 2011. A new disease of parsley (Petroselinum crispum) in California caused by a fluorescent pseudomonad related to Pseudomonas viridiflava. Phytopathology. 101:S116.
Bacterial Leaf Spot of Parsley: Characterization of a New Disease - (Other)
Koike, S.T., Bull, C.T. 2011. Bacterial Leaf Spot of Parsley: Characterization of a New Disease. University of California Press-Cooperative Extension. March/April 2011:4-6.
Show us your spots! Researchers need samples of bacterial leaf spots on celery, cilantro, parsley, and other crops - (Other)
Bull, C.T., Koike, S.T. 2011. Show us your spots! Researchers need samples of bacterial leaf spots on celery, cilantro, parsley, and other crops.. University of California Press-Cooperative Extension. Available:http://ucanr.org/blogs/blogcore/postdetail.cfm?postnum=4519&utm_source=RSS&utm_medium=RSS&utm_campaign=RSS%2BFeed.
SACNAS (the Society for Advancement of Chicanos and Native Americans in Science) Annual Meeting Proceedings - (Abstract Only)
Gebben, S.J., Bull, C.T. 2010. SACNAS (the Society for Advancement of Chicanos and Native Americans in Science) Annual Meeting Proceedings.. Society for the Advancement of Chicanos and Native Americans in Science. p. 75.
Identification of Pseudomonas cannabina pv. alisalensis previously isolated from diseased crucifers in Australia - (Abstract Only)
Rubio, I., Bull, C.T. 2010. Identification of Pseudomonas cannabina pv. alisalensis previously isolated from diseased crucifers in Australia.. Society for the Advancement of Chicanos and Native Americans in Science. p.75.
Irrigation water is an unlikely source of inoculum of Pseudomonas cannabina pv. alisalensis - (Abstract Only)
Mauzey, S.J., Bull, C.T. 2010. Irrigation water is an unlikely source of inoculum of Pseudomonas cannabina pv. alisalensis. Phytopathology 100:579.
A qPCR assay for detection and quantification of Verticillium dahliae in spinach seed - (Abstract Only)
Rauscher, G.M., Mou, B., Hayes, R.J., Koike, S.T., Maruthachalam, K., Subbarao, K.V., Klosterman, S.J. 2010. A qPCR assay for detection and quantification of Verticillium dahliae in spinach seed.. Phytopathology. 100:S107.
Identification of lettuce genes differentially expressed in a Verticillium dahliae-lettuce interaction by suppression subtractive hybridization - (Abstract Only)
Klosterman, S.J., Anchieta, A.G., Maruthachalam, K., Hayes, R.J., Subbarao, K.V. 2009. Identification of lettuce genes differentially expressed in a Verticillium dahliae-lettuce interaction by suppression subtractive hybridization. Phytopathology Supplement; APSnet (Plant Pathology Online).
Mitochondrial Genomics in the Peronosporales; Implications for Phylogenetics and Development of Molecular Markers - (Abstract Only)
Martin, F.N. 2009. Mitochondrial Genomics in the Peronosporales; Implications for Phylogenetics and Development of Molecular Markers. Phytopathology.
Real Equal Opportunities for All Plant Pathologists in the 21st Century - (Popular Publication)
Bull, C.T. 2008. Real Equal Opportunities for All Plant Pathologists in the 21st Century. Phytopathology News 42:54.
Taxonomy of Plant Pathogenic Bacteria - (Abstract Only)
Bull, C.T., Vinatzer, B.A. Taxonomy of Plant Pathogenic Bacteria. International Congress of Plant Pathology, Torino, Italy, August 24-29, 2008.
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