Location: Mycotoxin Prevention and Applied Microbiology Research
2023 Annual Report
Objectives
The major goals of this project will be most effectively achieved through strengthening the relationship between the ARS Culture Collection and the user community and fostering a synergistic relationship. To this end, we will implement a “virtuous cycle” of collection management (Graphical Project Summary) to achieve the project goals and enhance our connection to the user community.
Objective 1: Acquire, distribute, back-up, and maintain the safety, genetic integrity, health, and viability of priority microbial genetic resources and associated descriptive information in the ARS Culture Collection.
Sub-objective 1.A: Maintain the safety, genetic integrity, viability and accessibility of priority microbial genetic resources and associated information in the ARS Culture Collection.
Sub-objective 1.B: Enhance the diversity and utility of the ARS Culture Collection by acquiring germplasm representing type material or novel strains important to ARS and other microbial research programs.
Objective 2: Increase the value of priority microbial resources in the ARS Culture Collection for research and development by conducting integrated phylogenetic, physiological, phenotypic, and metabolomic analyses. Connect these multiple data types to accession records in the ARS Culture Collection, and deposit in appropriate public databases.
Sub-objective 2.A: Characterize 2,500 priority strains of bacteria and fungi.
Sub-objective 2.B: Update the metadata on strains in the ARS Culture Collection using the Ag Data Commons website to facilitate research by ARS and other scientists worldwide.
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, taxonomic accuracy, 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, metabolomic, and phenotypic approaches and analyses to elucidate their phylogenetic relationships, secondary metabolite profiles, ensure accurate species identification, and enhance their utility for research and development.
Progress Report
This is the first report for this new project begun March 2023 and continues research from the previous project, 5010-22410-021-000D, “Management and Characterization of Agriculturally and Biotechnologically Important Microbial Genetic Resources and Associated Information”. See that report for additional information. 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 7,500 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 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. In a typical year, the ARS Culture Collection distributes approximately 5,000 strains to over 400 scientists in as many as 65 countries. During the first months of this project, we have continued to distribute strains at this rate.
Research under the first objective is focused on maintaining the integrity of the existing collection and acquiring material to improve the taxonomic representation and utility of the collection. To this end the ARS Culture Collection acquired and accessioned 35 strains of Pezizomycetes, which is a group of fungi that is poorly represented in the collection. These strains have also had their genomes sequenced. As we have a limited number of Pezizomycetes in the collection, we also had to modify our preservation protocol to ensure the viability of these strains. This new standard operating procedure (SOP) will be used for future preservation of these type of fungi. We also completed the molecular identification and accessioned 96 strains of Trichoderma from the U.S. Army Quartermaster collection. This collection of over 6,000 microbial strains was taken in by the ARS Culture Collection in the late 1970s when the U.S. Army closed their research unit, and it represents a global collection of various fungi associated with the biodegradation of military supplies and other cellulose materials, as well as various plant pathogens. This collection was acquired and stored at NCAUR for the last 45 years but was never accessioned into the NRRL open collection or made publicly available. We generated 10 lyophilized preparations of each of these Trichoderma strains and are in the process of making them available for the scientific community to order through the ARS Culture Collection website.
The ARS Culture Collection is always working to improve the functionality of our website. Specifically, we would like to get feedback from the user community on how we can improve the layout of the website and any other topics related to our service and/or the strains and their related metadata in the database. During the first year of this project members of the culture collection team developed a series of questions for the survey.
Identification and classification of fungi and bacteria increasingly depends on DNA sequences of standardized genetic markers or entire genomes. The greatest value associated with strains in the ARS Culture Collection is this additional metadata generated by project scientists and collaborators including the DNA-based data generated for identification as well as metabolomic, phenotypic and physiological data generated by project scientists and collaborators. During our previous project, we were able to update the taxonomy of over 6,000 strains in the ARS Culture Collection using multilocus sequence typing (MLST). Research under the second objective will expand on this work by generating and analyzing phylogenetic, metabolomic and phenotypic data to better characterize agronomically important microbes in the NRRL to improve the taxonomic accuracy of these strains and identify potentially novel or useful secondary metabolites produced by these strains. This year we completed the DNA-based identification of 96 Trichoderma strains from the U.S. Army Quartermaster collection. This data was combined with Trichoderma sequence data we generated in the previous project along with Trichoderma type strain sequence data mined from GenBank to generate a DNA sequence database for rapid identification of unknown Trichoderma strains using the RPB2 gene sequence. We also completed the DNA-based identification and updated the taxonomy of 500 strains of Fusarium.
The other goal in this objective is to make the associated metadata publicly available to the scientific community to catalyze new areas of science, accelerate the speed of microbial product and biotechnology discovery, and promote sustainable agricultural systems and food safety. To this end the whole genome data of 83 Bacillus strains from the ARS Culture Collection are now publicly available on Genbank and links to this data was added to the ARS Culture Collection program page on the National Ag Library, Ag Data Commons website. The metabolome data of 400 strains of Streptomyces grown in five different media for a total of 2000 datasets was also completed and made publicly available this year. The data is hosted on the Global Natural Products Social Molecular Networking (GNPS) website in the GNPS-MassIVE Datasets.
Accomplishments
