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United States Department of Agriculture

Agricultural Research Service

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Research Project: Comparative Genomic Systems for Molecular Detection and Control of Toxigenic Fusarium

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

2013 Annual Report


1a.Objectives (from AD-416):
The overall goal of this project is to contribute to the effective control of toxigenic Fusarium, especially those responsible for FHB of small grain cereals, in order to enhance food safety and crop production in the U.S. and around the world. The proposed project is designed to produce a robust evolutionary framework for understanding the genetic and phenotypic diversity, geographic distribution and population biology of toxigenic fusaria, and will result in novel technologies for the rapid detection, identification and control of toxigenic fusarial pathogens of critical importance to food safety and food security. This framework will also support and facilitate work by the global Fusarium research community. The specific objectives are: Objective 1: characterize the genetic diversity and mycotoxin potential of Fusarium head blight and other fusarial pathogens, develop novel pathogen detection technologies, and expand web-accessible informational database to facilitate the rapid and accurate identification of toxigenic fusaria via the Internet. Objective 2: Determine the global population structure of F. graminearum and identify genetic variation associated with population-level difference in growth, reproduction, and toxin accumulation phenotypes as a means to improve pathogen modeling and surveillance. Objective 3: Characterize the mechanisms that drive the diversification and adaptive evolution of virulence genes in Fusarium genomes as well as host defense genes involved in immunogenicity and disease response.


1b.Approach (from AD-416):
Toxins produced by plant-pathogenic Fusarium pose a significant threat to food safety and place a major burden on the world’s agricultural economy. The primary objectives of the proposed research are to:.
1)Characterize the genetic diversity and mycotoxin potential of Fusarium head blight (FHB) and other fusarial pathogens, develop novel pathogen detection technologies, and expand web-accessible informational databases to facilitate the rapid and accurate identification of toxigenic fusaria via the Internet,.
2)Determine the global population structure of F. graminearum and identify genetic variation associated with population-level differences in growth, reproduction, and toxin accumulation phenotypes as a means to improve pathogen modeling and surveillance, and.
3)Characterize the mechanisms that drive the diversification and adaptive evolution of virulence genes in Fusarium genomes as well as host defense genes involved in immunogenicity and disease response. These complementary objectives are directed at developing robust pathogen control strategies through elucidating the evolution, population structure, phenotypic diversity, host range, geographic distribution and adaptive potential of toxigenic fusaria. In addition, the planned research will produce enhanced methods for identification and characterization (e.g. toxin type, toxin accumulation potential, and host preference) of Fusarium responsible for mycotoxin contamination of cereals and other food. The information and molecular tools developed as a result of this project will address the needs of small grain cereal producers, food and feed processors, the U.S. Department of Agriculture (USDA) Federal Grain Inspection Service (FGIS), the USDA Animal and Plant Health Inspection Service (APHIS), and the Food and Drug Administration (FDA).


3.Progress Report:
A pilot project to identify genomic regions that could be used to assess population diversity and evolutionary relationships within and between Fusarium head blight (FHB) populations from five continents was completed. More than forty large genomic regions were sequenced across a panel of isolates representing more than 30 geographic populations, and each of these regions was analyzed to assess single nucleotide polymorphism content and phylogenetic utility. A subset of 20 regions was selected for use in population diversity analysis. These data are being used to determine the recent and potential future movement of Fusarium head blight pathogen populations and to detect introductions of invasive pathogen populations. These data will also be used to identify regions of the genome that are responsible for observed differences in growth, toxin production, and aggressiveness in order to improve disease modeling, detection, and control strategies. In addition, we completed studies of diverse FHB populations in France, Uruguay, and Brazil in order to evaluate host-preference and assess the potential threat posed by Fusarium head blight species and populations from outside the United States. Our findings indicate an increasing risk of exposure to nivalenol outside of Asia. Finally, in collaboration with scientists at the ARS Cereal Disease Laboratory, St. Paul, Minnesota, we identified genetic variation in the TRI1 trichothecene biosynthetic gene that is linked to the production of a novel trichothecene mycotoxin by Fusarium graminearum isolates in the Upper Midwest.

We completed a detailed analysis of genetic diversity within the mycotoxigenic plant pathogenic genus Fusarium in collaboration with agricultural scientists in the Netherlands, Norway, Denmark, Japan, and collaborators at the Pennsylvania State University and in USDA-ARS, Beltsville, Maryland. Portions of three genes were sequenced for more than 800 Fusarium isolates to assess evolutionary relationships and to develop a robust framework for predicting mycotoxin potential. These analyses identified 20 species complexes and nine single-species lineages within Fusarium. Molecular dating of the Fusarium phylogeny indicated that the trichothecene toxin-producing pathogens responsible for Fusarium head blight of cereals, the F. oxysporum vascular wilts of over 100 economically important crops (e.g., banana, cotton, tomato), and the fumonisin toxin-producing members of the F. fujikuroi species complex appear to have evolved relatively recently. Given the economic importance of Fusarium and its toxins to world agriculture and food safety, the well-supported evolutionary framework developed in the present study should help guide future comparative phylogenetic and genomic studies on this genus.


4.Accomplishments
1. Identification of unexpected Fusarium head blight diversity in new wheat production areas. Fungi within the Fusarium graminearum species complex are responsible for economically destructive diseases of wheat, barley, and other cereals world-wide. In addition, these fungi contaminate grain with trichothecene mycotoxins that pose a significant threat to food safety and animal health. As part of a project to establish a global picture of F. graminearum species complex diversity, ARS, Bacterial Foodborne Pathogens and Mycology Research Unit scientists at the National Center for Agricultural Utilization Research in Peoria, Illinois, determined the prevalence of F. graminearum complex species and toxins associated with diseased wheat in Uruguay. The results indicated that F. asiaticum and the nivalenol toxin type predominated in diseased wheat from areas where rice production is common. These results are similar to those we recently published indicating that F. asiaticum and the nivalenol toxin type may have been introduced into a major rice-producing region of the United States. This is a significant concern for food safety and animal health, because nivalenol is considered more toxic than the deoxynivalenol, which is the most common toxin type in much of the United States, Europe, and South America. Significant differences in aggressiveness and fungicide sensitivity were also observed between different species and toxin types indicating the need to consider this pathogen diversity in development of disease control programs. As such, the results are critical to promoting food safety and cereal production through improved detection of novel F. graminearum species complex pathogens and through plant quarantine and variety improvement efforts that account for the entire spectrum of F. graminearum species complex pathogens and toxin types.

2. Determination of the toxigenic and pathogenic diversity within Fusarium. Fusarium species comprise one of the most economically important groups of fungi. These fungi are responsible for diseases of a wide variety of agriculturally important plants and are an emerging group of human pathogens. In addition, the toxins produced by some species of Fusarium pose a constant threat to plant and animal health and food safety, causing multi-billion U.S. dollar losses to world agriculture annually. ARS, Bacterial Foodborne Pathogens and Mycology Research Unit scientists at the National Center for Agricultural Utilization Research in Peoria, Illinois, used DNA sequence data to clarify the limits of diversity within Fusarium and to assess the distribution and evolution of toxigenic and pathogenic diversity within this group of fungi. In addition, we published an up-to-date review of the diversity, geographic distribution, host preferences, and trichothecene mycotoxin potential of Fusarium head blight pathogens that cause significant diseases of cereals and contaminate grain with deoxynivalenol (DON) and other toxins. These data will be of interest to plant pathologists, mycotoxicologists, plant breeders, and quarantine officials interested in the identification and differentiation of Fusarium, enable prediction of the toxigenic or pathogenic potential of poorly studied species within this group, and provide a robust framework for future comparative analyses of this agronomically and medically important group of fungi.


Review Publications
Aoki, T., Ward, T.J., Kistler, H.C., O'Donnell, K. 2012. Systematics, phylogeny and trichothecene mycotoxin potential of Fusarium head blight cereal pathogens. Mycotoxins. 62(2):91-102.

Ratani, S.S., Siletzky, R.M., Dutta, V., Yildirim, S., Osborne, J.A., Lin, W., Hitchins, A.D., Ward, T.J., Kathariou, S. 2012. Heavy metal and disinfectant resistance of Listeria monocytogenes from foods and food processing plants. Applied and Environmental Microbiology. 78(19):6938-6945.

Short, D.P., O'Donnell, K., Thrane, U., Fog Nielsen, K., Zhang, N., Juba, J.H., Geiser, D.M. 2013. Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. nov. and F. petroliphilum stat. nov. Fungal Genetics and Biology. 53(2013):59-70.

O'Donnell, K., Rooney, A.P., Proctor, R., Brown, D.W., McCormick, S.P., Ward, T.J., Frandsen, R.N., Lysoe, E., Rehner, S.A., Aoki, T., et al. 2013. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genetics and Biology. 52:20-31.

Lee, S., Rakic-Martinez, M., Graves, L.M., Ward, T.J., Siletzky, R.M., Kathariou, S. 2013. Genetic determinants for cadmium and arsenic resistance among Listeria monocytogenes serotype 4b isolates from sporadic human listeriosis patients. Applied and Environmental Microbiology. 79(7):2471-2476.

Ward, T.J. 2013. Identification and subtyping of Listeria monocytogenes. In: de Fillipis, I., McKee, M.L., editors. Molecular Typing in Bacterial Infections. New York, NY: Springer Science and Business Media. p. 27-38.

Short, D.G., O'Donnell, K., Zhang, N., Juba, J.H., Geiser, D.M. 2011. Widespread occurrence of diverse human pathogenic types of the fungus Fusarium detected in plumbing drains. Journal of Clinical Microbiology. 49(12):4264-4272.

Kasson, M.T., O'Donnell, K., Rooney, A.P., Sink, S.L., Ploetz, R.C., Ploetz, J.N., Konkol, J.L., Carrillo, D., Freeman, S., Mendel, Z., et al. 2013. An inordinate fondness for Fusarium: Phylogenetic diversity of fusaria cultivated by ambrosia beetles in the genus Euwallacea on avocado and other plant hosts. Fungal Genetics and Biology. 56(2013):147-157.

Last Modified: 9/1/2014
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