Project : USDA ARS

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

Location: Mycotoxin Prevention and Applied Microbiology Research

2020 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 publicly accessible collections of microorganisms in the world. NRRL 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. NRRL 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, 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 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 NRRL. Strains from NRRL 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. During the reporting period, 292 isolates were accessioned into the NRRL open collection and 424 isolates were deposited in the ARS Patent Culture Collection, in response to ARS research program needs and customer requests. During the same reporting period, more than 9,434 NRRL strains were sent to approximately 950 scientists from across the United States and 53 other countries. These strain distributions conservatively represent an in-kind contribution of $1,886,800 in support of microbiological research and biotechnological innovation. The utility and security of the collection was improved by adding or updating 10,900 strain history or inventory records. 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 NRRL and to make these strains and associated metadata publicly available to promote agricultural production, biotechnological development, and food safety. During the rating period, DNA sequence-based analyses of genetic variation and phenotypic data were used to characterize agronomically important toxin producing and plant pathogenic Fusarium strains in NRRL.

Accomplishments
1. Discovery of three new plant pathogens farmed by foreign beetles. The recent and rapid global spread of wood boring, fungus-farming, ambrosia beetles from Asia is of significant concern because they can cause considerable damage to economically important hosts including avocado, cacao, rubber and citrus trees, and Chinese tea. They also pose a serious threat to forest ecosystems and urban landscapes. Scientists in Japan and Australia, and at two universities in the United States, in collaboration with an ARS scientist in Peoria, Illinois, used DNA and morphological data to characterize disease-causing Fusarium species on avocado in Queensland, Australia, rubber trees in North Borneo, and box elder in Florida. This research found three new Fusarium species and provided detailed information on the genetic diversity, host range, and geographic distribution of these important plant pathogens and the foreign insect pests that farm them as a source of food. This information will help enable quarantine officials and plant disease specialists to prevent these economically destructive foreign insects and fungal pathogens from entering the United States and other countries that are our trading partners.

2. Collections of microorganisms support life science. A review that focuses on the importance of preserving microbial collections to foster advances in biotechnology, agricultural, and medical research was prepared by 11 members of the U.S. Culture Collection Network (USCCN), including an ARS scientist in Peoria, Illinois. Because this review arose from discussions at several USCCN meetings, it focuses on U.S. collections. Preservation of biological collections has risen in priority due to a new appreciation for discoveries linked to preserved microorganisms. While many historic collections have been lost, rescued microbes have been used for discoveries in areas of health, biotechnology, and basic life science. For 80 years, the ARS Culture Collection (NRRL) has supported discoveries in microbiology by providing authenticated microorganisms and associated data. Currently, the NRRL is one of the largest public collections of microorganisms in the world, containing approximately 98,000 isolates of bacteria and fungi. The microbes maintained in the NRRL, including those obtained through acquisition of orphaned collections, are of critical importance to a wide variety of research projects around the world as evidenced by citation in more than 74,000 publications and patent applications indexed by Google Scholar. During the last four years, the ARS Culture Collection distributed over 23,000 microbial cultures in response to requests from scientists in 66 countries.

3. Novel fungal disease of mahogany trees discovered in Mexico. Big-leaf mahogany is valued for its high-quality wood and for use in urban landscapes in Mexico. Scientists in Mexico and at the University of Florida, in collaboration with an ARS scientist in Peoria, Illinois, discovered a new disease of mahogany trees during surveys of mango-producing areas in central western Mexico. The most conspicuous symptoms resembled those of mango malformation, which is the most important disease in the Mexican state of Michoacán. Using DNA data, most of the isolates recovered from symptomatic mahogany trees were identified as Fusarium pseudocircinatum or F. mexicanum. A pathogenicity experiment confirmed that these two species were able to induce malformation symptoms on big-leaf mahogany. Knowledge of the pathogens, host range, and geographic distribution are being used by plant disease specialists to prevent the spread of this disease to other big-leaf mahogany and mango growing regions of Mexico and other countries.

4. Novel antibiotic-producing bacteria discovered on squid eggs. Discovery of new antibiotics is becoming increasingly critical to combat the dramatic rise in multidrug resistant bacteria. Scientists at the University of Connecticut, the University of Texas-San Antonio, and the University of Florida, in collaboration with an ARS scientist in Peoria, Illinois, characterized several antimicrobial compounds produced by bacteria in the jelly coat of squid eggs. These antimicrobial compounds prevent overgrowth of fungi and other microorganisms. Using both experimental and analytical approaches, multiple bacteria associated with the eggs, and chemical extracts of the bacteria, inhibited the pathogenic mold Fusarium keratoplasticum and yeast Candida albicans. In addition to several compounds that may play a role in squid egg defense, nine compounds were discovered. The discovery of novel antimicrobials is critical to promoting public health globally because many antibiotics available to clinicians cannot be used to treat patients with life threatening infections caused by multidrug resistance microbes.

U.S. DEPARTMENT OF AGRICULTURE

Mycotoxin Prevention and Applied Microbiology Research: Peoria, IL