Skip to main content
ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Research Project #434131

Research Project: Management and Characterization of Agriculturally and Biotechnologically Important Microbial Genetic Resources and Associated Information

Location: Mycotoxin Prevention and Applied Microbiology Research

2021 Annual Report

The major goals of this project are to maintain and enhance the quality, diversity, and utility of the ARS Culture Collection holdings, including strains held in the ARS Patent Culture Collection, and to conduct and support microbiological research that advances agricultural production, food safety, public health, and economic development. Objective 1 provides for the curation and management of the ARS Culture Collection, including the acquisition and distribution of microbial strains and associated information. This objective provides scientists worldwide with access to high quality microbial germplasm through culture deposit and distribution services that facilitate research, publication, and technology transfer. Objective 2 is designed to improve understanding and utilization of microbial diversity through genetic and phenotypic characterization of strains in the ARS Culture Collection, and through the development of improved tools for microbial identification and characterization. Successful completion of goals under Objective 1 will provide scientists working on Objective 2 with access to microbial cultures, associated metadata, and tools to transfer research findings to the scientific community. Research conducted under Objective 2 will provide novel germplasm, microbiological expertise, and strain characterization data that enhances the value of the ARS Culture Collection and improves its curation. Objective 1: Efficiently and effectively acquire, distribute, back-up, and maintain the safety, genetic integrity, health, and viability of priority microbial genetic resources and associated information in the ARS Culture Collection. Objective 2: Enhance the value of priority microbial genetic resources in the ARS Culture Collection by conducting comparative phenotypic, phylogenetic and genomic analyses. Record and disseminate characterization data via the ARS Culture Collection database and other data sources.

More than 98,000 accessions consisting of microbial cultures of agriculturally, industrially, and medically important bacteria and fungi will be maintained in a secure centralized limited-access facility. These microbial genetic resources will be effectively preserved and secured, characterized to improve their utility, and made available to support agricultural and other research projects worldwide. In addition to maintaining and distributing currently held strains, high priority microbial genetic resources will be acquired and safeguarded so that these critical resources are widely available for microbial research and development. Microbial cultures will be characterized with a combination of genetic, genomic, and phenotypic approaches and analyses to elucidate their phylogenetic relationships, ensure accurate species identification, and enhance their utility for research and development.

Progress Report
The ARS Culture Collection, also known by the original acronym for the Northern Regional Research Lab (NRRL) in Peoria, Illinois, is one of the largest publicly accessible collections of microorganisms in the world. The ARS Culture Collection consists of a collection of strains that are open for public distribution and a collection of strains that are distributed in accordance with an international treaty on recognition procedures for patents involving microorganisms. The open collection currently maintains more than 98,000 strains of fungi and bacteria together with more than 7,000 strains held in the ARS Patent Culture Collection. The ARS Culture Collection is one of only two International Depositary Authorities recognized by the World Intellectual Property Organization that curate fungi and bacteria in the United States. In this capacity, The ARS Culture Collection facilitates technological innovation by enabling scientists to simultaneously fulfill microbial culture deposition requirements in association with patent applications in the United States and internationally. The major goals of the current project are to conduct and support microbiological research that advances food safety, public health, economic development, and agricultural production. In-house research in pursuit of these goals is focused on improved understanding and utilization of microbiological diversity together with efforts to enhance the value and accessibility of microbial germplasm in the ARS Culture Collection. Strains from the collection have contributed significantly to advances in agriculture, medicine, and biotechnology, and are cited in approximately 70,000 patents and scientific publications. Goals of the first objective include acquiring, safeguarding, and distributing priority microbial genetic resources to advance scientific discovery. This year, in response to ARS research program needs and customer requests, 46 new strains were accessioned into the open collection and 89 isolates were deposited in the ARS Patent Culture Collection. In addition, 2,722 NRRL strains were sent to 550 scientists from across the United States and 36 other countries. These strain distributions conservatively represent an in-kind contribution in support of microbiological research and biotechnological innovation. The utility and security of the collection was improved by adding or updating 2,945 strain history or inventory records. The ARS Culture Collection received approximately 6,000 isolates from the U.S. Quartermaster Collection in the mid-1970s. These strains, which represents a global collection of various fungi associated with the biodegradation of military supplies and other cellulose materials, as well as various plant pathogens, has been stored at NCAUR for the last 45 years. The data on the strains were stored on index cards, and only approximately 350 strains of specific research interest were accessioned. With the help of volunteer staff from multiple NCAUR research units we were able to digitize the entire U.S. Quartermaster Collection. These strains will then be officially accessioned into the ARS Culture Collection and made available to the general public. Research under the second objective is focused on generating and utilizing DNA-sequence based analyses of genetic variation and phenotypic data to characterize agronomically important microbes in the NRRL and to make these strains and associated metadata publicly available to promote agricultural production, biotechnological development, and food safety. This year, approximately 2,500 agronomically important toxin producing and plant pathogenic fungal strains in the ARS Culture Collection or from ongoing research studies within the Mycotoxin Prevention & Applied Microbiology (MPM) Research Unit were typed using single or multilocus DNA sequence data. One specific project initiated this year in support of Objective 2, was the generation of new whole genome data and accessioning of Claviceps purpurea isolates in the ARS Culture Collection. The cereal crop pathogen, Claviceps purpurea, which causes ergot on barley, wheat, and rye, poses a significant threat to agriculture and food safety because it produces toxic alkaloids which can cause severe poisoning in humans and livestock. To better understand the evolutionary history of this fungus, a researcher from the ARS Culture Collection, in collaboration with researchers at Colorado State University, Agriculture and Agri-food Canada and the Joint Genome Institute, looked for genes that would help explain why this pathogen has such a broad host range and why host resistance is limited in most modern crops. This year we sequenced the genomes of 24 isolates of C. purpurea and found that genes that control production of ergot alkaloids and other metabolites have been most important to the evolution of the fungus and its global distribution and host range, and not effector proteins, which are recognized by host resistance genes. The lack of effector diversity and the limited role in infection indicate that options for targeting host resistance are limited and that future control strategies will need to focus on cultural practices.

1. Discovery of 33 toxin-producing, plant pathogenic fungi new to science. During the past three decades, molds have caused epidemics of the plant disease called Fusarium head blight (FHB) of wheat and barley in the U.S. and elsewhere around the world. FHB is an economically devastating plant disease because it causes significant reduction in seed quality and yields, and because seeds are often contaminated with toxins that pose a serious global threat to agricultural biosecurity, food safety, and human health. Thus, this study was conducted to characterize the genetic diversity of a global collection of 171 Fusarium strains either known or predicted to produce toxins. This collection was used to assess species diversity, evaluate the potential to produce toxins, and cause disease on wheat. Analyses of DNA data revealed that the 171 strains comprised 74 species, including 33 that are new to science. These species were distributed among six species groups that corresponded to the type of toxins they produce. Results of a pathogenicity experiment revealed that only species within two of the six groups could cause FHB of wheat and contaminate grain with toxins. These data further suggest that the type of toxin produced contributes to the ability of these plant pathogens to cause disease. Results of this study will be of interest to plant disease specialists, quarantine officials, and plant breeders who are focused on minimizing the threat these toxigenic molds pose to U.S. and world agriculture. Moreover, knowledge gained from this research should assist plant breeders to develop cultivars with broad-based resistance to FHB.

2. Large-scale DNA study clarifies naming system within the mold genus Fusarium. Members of the mold genus Fusarium are the most economically destructive group of toxin-producing plant pathogens and emergent human pathogens. These fungi produce toxins that contaminate food and feed, making it unsuitable for consumption by humans and other animals. A recent proposal to use the name Neocosmospora for over 100 Fusarium species, many of which are of agricultural and medical importance, is being contested and causing considerable confusion within the global scientific community. Inconsistent use of names for Fusarium pathogens can cause problems for clinicians and plant pathologists, as they need to be aware that these molds are broadly resistant to the spectrum of antifungals/fungicides that are currently available. ARS researchers at Peoria, Illinois, in collaboration with 167 agricultural and medical scientists from 30 different countries, conducted the most detailed comparative genomics analyses of the genus Fusarium to date. These studies support the sole use of the name Fusarium for these pathogens. As such, this study will be of considerable interest to plant pathologists, toxicologists, medical mycologists, and quarantine officials worldwide. In our interconnected global economy, it is essential that clinicians, plant disease specialists, and quarantine officials throughout the world use the same name for the same pathogen.

3. Three fungal pathogens new to science are farmed by beetles as a source of food. Native to Asia, fungus-farming ambrosia beetles have recently emerged as a global threat to several economically important woody hosts, including avocado, citrus, cacao, Chinese tea, and rubber. These invasive pests and the pathogenic fungi they farm also pose a significant threat to urban landscapes and native forests here in the U.S. and abroad. An ARS researcher in Peoria, Illinois, in collaboration with scientists in Japan, Israel, Sri Lanka, and three universities in the U.S., characterized the fungal pathogens of avocado in Florida, Chinese tea in Sri Lanka, and a woody host in Singapore. The results based on a multi-gene phylogeny support recognizing each pathogen as a distinct species and provide for the first-time detailed information on their host range, geographic distribution, and genetic diversity. The research reported in this study will be invaluable to plant disease specialists and quarantine officials who are charged with preventing these economically important insect pests and fungal pathogens from entering the U.S. and other countries worldwide where they are not presently established.

Review Publications
Laraba, I., McCormick, S.P., Vaughan, M.M., Proctor, R.H., Busman, M., Appell, M., O'Donnell, K., Felker, F.C., Aime, M.C., Wurdack, K.J. 2020. Pseudoflowers produced by Fusarium xyrophilum on yellow-eyed grass (Xyris spp.) in Guyana: A novel floral mimicry system? Fungal Genetics and Biology. 144. Article 103466.
Gargouri, S., Balmas, V., Burgess, L., Paulitz, T., Laraba, I., Kim, H.-S., Proctor, R.H., Busman, M., Felker, F.C., Murray, T., O'Donnell, K. 2020. An endophyte of Macrochloa tenacissima (esparto or needle grass) from Tunisia is a novel species in the Fusarium redolens species complex. Mycologia. 112(4):792-807.
Smyth, C.W., Sarmiento-Ramirez, J.M., Short, D.P.G., Diéguez-Uribeondo, J., O'Donnell, K., Geiser, D.M. 2019. Unraveling the ecology and epidemiology of an emerging fungal disease, sea turtle egg fusariosis (STEF). PLoS Pathogens. 15(5). Article e1007682.
Vandepol, N., Liber, J., Desiro, A., Na, H., Kennedy, M., Barry, K., Grigoriev, I.V., Miller, A.N., O'Donnell, K., Stajich, J.E., Bonito, G. 2020. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity. 104:267-289.
O'Donnell, K., Al-Hatmi, A.M.S., Aoki, T., Brankovics, B., Cano-Lira, J.F., Coleman, J.J., de Hoog, G.S., Di Pietro, A., Frandsen, R.J., Geiser, D.M., Gibas, C.F., Kim, H.-S., Kistler, H.C., Laraba, I., Proctor, R.H., Ward, T.J., et al. 2020. No to Neocosmospora: Phylogenomic and practical reasons for continued inclusion of the Fusarium solani species complex in the genus Fusarium. mSphere. 5(5). Article e00810-20.
Laraba, I., McCormick, S.P., Vaughan, M.M., Geiser, D.M., O'Donnell, K. 2021. Correction: Phylogenetic diversity, trichothecene potential, and pathogenicity within Fusarium sambucinum species complex. PLoS ONE. 16(4). Article e0250812.
Senatore, M.T., Ward, T.J., Cappelletti, E., Beccari, G., McCormick, S.P., Busman, M., Laraba, I., O'Donnell, K., Prodi, A. 2021. Species diversity and mycotoxin production by members of the Fusarium tricinctum species complex associated with Fusarium head blight of wheat and barley in Italy. International Journal of Food Microbiology.