Location: Mycotoxin Prevention and Applied Microbiology Research
2018 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 Agricultural Research Service 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, which is one of only two international patent depositary authorities for bacteria and fungi in the United States. This 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 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 ARS Culture Collection (designated NRRL). NRRL strains contribute to significant advances in agriculture, medicine, and biotechnology, and are cited in 7,000 patents and more than 58,000 scientific publications.
The primary goals of the first objective is to acquire, safeguard, and distribute priority microbial genetic resources to advance scientific discovery. Over the course of this project, we accessioned approximately 224 isolates into the ARS Culture Collection, including nearly 110 isolates deposited into the ARS Patent Culture Collection, based on ARS research program needs and customer requests. During the same time period, more than 1,709 NRRL strains were sent to approximately 299 scientists from across the United States and 32 other countries. Using a conservative estimate of monetary value, these strain distributions represent a $340,000 in-kind contribution in support of microbiological research and biotechnological innovation. To improve strain access and security, approximately 5,075 strain history or inventory records were added or updated. The ARS Culture Collection webpage was improved based on customer feedback to facilitate quick access to key information. A backup collection of all strains held as lyophilized preparations was generated and relocated to an environmentally controlled and physically secure facility at 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. Research conducted during the first eight months of this new project has focused on characterization of agricultural and medically important fungi in the genera Fusarium, Penicillium, Talaromyces, and Aspergillus, as well as a diverse group of zygomycete fungi. Isolates have been characterized using a variety of genetic and phenotypic methods to improve species concepts, facilitate accurate species identification, and to advance understanding of genetic and phenotypic diversity within these groups of fungi. Data collected during the current reporting period are being analyzed and will be uploaded to the ARS Culture Collection database in conjunction with their publication.
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 2018, 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. During the first eight months of this project, the value and utility of this collection were increased through the addition of more than 220 novel isolates, including 110 isolates deposited in association with patent applications. In addition, 1,709 microbial isolates were distributed from the ARS Culture Collection in response to requests from scientists in the United States and 32 other countries. Using a conservative estimate of monetary value, these strain distributions represent a roughly $340,000 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 more than 7,000 patents and 58,000 scientific publications.
2. Improved framework for whole-genome analyses of plant-pathogenic fungi. Knowledge of the chromosome number (CN) of an organism provides genome biologists with key information needed to conduct informed whole-genome sequence analyses. Numerous research groups around the world are engaged in Fusarium comparative genomics research because these fungi are among the most important causes of crop losses. Fusarium also contaminate grain with toxins that are a threat to food safety and animal health, and are responsible for an increasing number of opportunistic infections. In collaboration with scientists in The Netherlands and Japan, ARS scientists in Peoria, Illinois, determined the CN of 33 genetically diverse Fusarium species. These data provide genome biologists with an invaluable reference to assist them in reconstructing the whole-genomes of genetically diverse fusaria, which will facilitate development of robust molecular diagnostic assays and significantly advance agricultural biosecurity.
Review Publications
Waalwijk, C., Taga, M., Zheng, S.-L., Proctor, R.H., Vaughan, M.M., O'Donnell, K. 2018. Karyotype evolution in Fusarium. IMA Fungus. 9(1):13-26. doi:10.5598/imafungus.2018.09.01.02
