Location: Mycotoxin Prevention and Applied Microbiology Research
2019 Annual Report
Objectives
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.
Approach
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 public collections of microorganisms in the world, and currently maintains more than 98,000 strains of bacteria and fungi. This includes more than 7,000 strains held in the ARS Patent Culture Collection. This collection is one of only two International Depositary Authorities recognized by the World Intellectual Property Organization that curate bacteria and fungi in the United States. As such, the NRRL 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 this project are to conduct and support microbiological research that advances agricultural production, food safety, public health, and economic development. These goals are pursued through in-house research that improves understanding and utilization of microbiological diversity and through efforts to enhance the value and accessibility of microbial germplasm in the NRRL. NRRL strains contribute to significant advances in agriculture, medicine, and biotechnology, and are cited in approximately 70,000 scientific publications and patents.
The primary goals of the first objective are to acquire, safeguard, and distribute priority microbial genetic resources to advance scientific discovery. During the previous year, we accessioned 381 isolates into the ARS Culture Collection, including 194 isolates deposited into the ARS Patent Culture Collection, based on ARS research program needs and customer requests. During the same time period, more than 3,553 NRRL strains were sent to approximately 500 scientists from across the United States and 42 other countries. Using a conservative estimate of monetary value, these strain distributions represent a $710,000 in-kind contribution in support of microbiological research and biotechnological innovation.
To improve utility and security of the collection, 8,332 strain history or inventory records were added or updated. The server infrastructure was updated to the latest version of CentOS software. A new database of patent strain metadata and inventory records was developed and populated providing a complete digital inventory and electronically searchable database of patent strain metadata. The ARS Culture Collection webpage was improved based on customer feedback to facilitate quick access to key information. A backup collection of newly acquired strains held as lyophilized preparations was generated and relocated to an environmentally controlled and physically secure facility in Fort Collins, Colorado.
Research under the second objective is designed to generate and utilize DNA-sequenced based analyses of genetic variation and phenotypic data to characterize agronomically important microbes in the ARS Culture Collection (NRRL) and to make these strains and associated metadata publicly available to promote agricultural production, food safety, and biotechnological development. This year, we conducted DNA sequence-based analyses of genetic variation and phenotypic data to characterize agronomically important toxin-producing and pathogenic Fusarium strains in the ARS Culture Collection (NRRL).
Accomplishments
1. Advancement of agricultural research and scientific innovation through curation of one of the largest public collections of microorganisms in the world. Access to accurately identified microbial isolates is critical to microbiological research that advances agricultural production and utilization, food safety and public health, and economic development. During the last year, ARS scientists in Peoria, Illinois, facilitated a wide variety of microbiological research through curation of the 98,000 microbes in the ARS Culture Collection, and facilitated technological innovation by enabling scientists to simultaneously fulfill microbial culture deposition requirements in association with patent applications in the United States and internationally. The value and utility of this collection were increased through the addition of 381 novel isolates, including 194 isolates deposited in association with patent applications. In addition, 3,553 microbial isolates were distributed from the ARS Culture Collection in response to requests from scientists in the United States and 42 other countries. Using a conservative estimate of monetary value, these strain distributions represent a roughly $710,000 in-kind contribution in support of scientific research and innovation. The broad impact of this work is evidenced by the fact that microbial isolates from the ARS Culture Collection have been used in approximately 70,000 scientific publications and patents.
2. Discovery and characterization of a novel toxigenic pathogen of barley. The cereal disease called Fusarium head blight or scab reached epidemic proportions in various regions of the world during the past three decades. Head blight is an economically devastating disease of small grain cereals such as wheat and barley due to significant reductions in seed quality and yields, and because infested grains are typically contaminated with fungal toxins that pose a significant threat to food safety, human health, and agricultural biosecurity. ARS scientists in Peoria, Illinois, in collaboration with scientists in Brazil, discovered and characterized a novel head blight pathogen of barley. Genetic analyses of DNA sequence data confirmed that this pathogen was new to science. Whole genome sequence data and chemical analyses revealed that this novel pathogen could produce several compounds that are toxic to humans and animals. The discovery of a novel toxin-producing pathogen of cereals has alerted quarantine officials and plant disease specialists to include it in their active surveillance programs and it informs plant breeders that this pathogen diversity needs to be accounted for in programs directed at developing cultivars with broad-based resistance to Fusarium head blight.
Review Publications
Short, D.P.G., O'Donnell, K., Stajich, J.E., Hulcr, J., Kijimoto, T., Berger, M.C., Macias, A.M., Spahr, E.J., Bateman, C.C., Eskalen, A., et al. 2017. PCR multiplexes discriminate Fusarium symbionts of invasive Euwallacea ambrosia beetles that inflict damage on numerous tree species throughout the United States. Plant Disease. 101(1):233-240. https://doi.org/10.1094/PDIS-07-16-1046-RE.
Yatsiuk, I., Saar, I., Kalamees, K., Sulaymonov, S., Gafforov, Y., O'Donnell, K. 2016. Epitypification of Morchella steppicola (Morchellaceae, Pezizales), a morphologically, phylogenetically and biogeographically distinct member of the Esculenta Clade from central Eurasia. Phytotaxa. 284(1):031-040. http://dx.doi.org/10.11646/phytotaxa.284.1.3.
Zhou, X., O'Donnell, K., Kim, H.-Y., Proctor, R.H., Doehring, G., Cao, Z.-M. 2018. Heterothallic sexual reproduction in three canker-inducing tree pathogens within the Fusarium torreyae species complex. Mycologia. 110(4):710. https://doi.org/10.1080/00275514.2018.1491766.
Anelli, P., Peterson, S.W., Haidukowski, M., Logrieco, A.F., Moretti, A., Epifani, F., Susca, A. 2018. Penicillium gravinicasei, a new species isolated from cave cheese in Apulia, Italy. International Journal of Food Microbiology. 282:66-70. https://doi.org/10.1016/j.ijfoodmicro.2018.06.006.
