Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2023 Annual Report
Objectives
Objective 1: Efficiently and effectively acquire, distribute, and preserve the fungal specimens and associated information in the U.S. National Fungus Collections.
Objective 2: Expand and enhance web-accessible databases that deliver information associated with the specimens in the U.S. National Fungus Collections, emphasizing accurate names, and information about plant-associated fungi, their host associations, and ecogeographical distributions.
The long-term goal of this project is to maintain and make available the specimens and information in the U.S. National Fungus Collections (USNFC) to enhance our ability to solve problems caused by fungi in agricultural systems and in our natural resources. Through curation and digitization, the staff of the U.S. National Fungus Collections carry out the USDA’s responsibility to maintain this unique scientific, mission-critical resource for use in perpetuity. Objective 1 will focus on the acquisition and cataloging of specimens, while Objective 2 will focus on making plant pathogen information available through a publicly accessible website.
Approach
Approximately one-million dried fungal specimens are contained in the U.S. National Fungus Collections. Specimens are housed in metal herbarium cabinets on moveable compactors in a relatively climate-controlled space. About 2,000 specimens are accessioned each year. Many of these are type specimens documenting previously undescribed fungi. Non-type voucher specimens that document research, especially on plant pathogenic fungi, are also accepted. Specimens are accessioned using standard procedures including archival quality supplies, and specimen information is databased as part of the accessioning process. Specimens in the U.S. National Fungus Collections are available on loan for examination by qualified scientists. The loan policy of the U.S. National Fungus Collections is posted on the management unit’s official ARS website. Typically 50 loans for a total of approximately 2,000 specimens are sent each year. Loans are tracked through a loan database, which generates overdue notices that are sent twice a year when necessary. All specimens are frozen at -20 C for three to five days before intial filing, after being returned from a loan, or after use by scientists on location to prevent the introduction of insect pests. Requests to use material for DNA analysis are considered if sufficient material exists to support such work without jeopardizing the integrity of the specimen. Excess DNA must be returned to the U.S. National Fungus Collections or be made available to other researchers upon request.
Database resources about plant-associated fungi will continue to be updated with newly published literature and as new specimens are accessioned into the U.S. National Fungus Collections. The nomenclature database will be updated when such expertise is available. This database provides the accurate scientific name for plant-associated fungal species as well as all synonyms and a synopsis of the host range, plant part affected, and geographic distribution. The accepted scientific name and the synonyms are linked so that one search on a fungal name returns the worldwide distribution, host range, literature, and specimens in the U.S. National Fungus Collections.
Herbarium specimens will be digitized as funds become available for discrete taxonomic groups and as specimens are accessioned or returned from loan. Data entry applications, online database queries, and website code are updated as needed and in accordance with ARS security requirements. The public website and internal data entry applications are currently maintained on a Dell PowerEdge 710 server. This hardware was purchased in 2010. It is anticipated that a new server will be purchased during or that a transition to cloud computing will be made under Departmental guidance during the lifespan of this project.
Progress Report
This report serves as the final report for Project 8042-22000-308-000D, “Management of Specimens and Associated Information in the U.S. National Fungus Collections, with Emphasis on Critically Important Plant Pathogens.” This project continues as 8042-22000-327-000D, “Expansion and Improvement of Plant-Associated Fungal Resources and Associated Descriptive Data in the U.S. National Fungus Collections and Databases.” Regarding Objective 1, 16 specimen loans were sent nationally and internationally although images were able to be substituted in about 10 cases in FY23. In addition, approximately 200,000 specimens were accessioned into the database over the life of the project. This database of specimens is currently searchable at https://mycoportal.org. Approximately, 130,000 unaccessioned historic specimens that had not been included in the database were imaged by contractors for optical character recognition (OCR) of the label text to facilitate the data entry for these specimens and entered into the database. Many of these represent type and valuable reference specimens. Nearly 25,000 unaccessioned myxomycete specimens were entered into the database with digitized specimen labels. These activities contribute to fulfillment of Objective 1 of this service project as they represent the core functions necessary to curate specimens in the U.S. National Fungus Collections as an international resource for use by scientists throughout the U.S. and the world. For the second objective, approximately 40,000 fungus-host-locality-literature reports were added to the database of fungi on plants around the world over the life of the project for a total of 828,926 reports. Approximately 6,500 new taxonomic or fungus-host literature records were added over the life of the project, and the fungus-host association database now accounts for 419,814 unique associations. This represents the most comprehensive database of fungi on plants in existence. Progress continues towards incorporation of historic fungus host data from 300,000 scanned index cards into the public fungus-host database.
Approximately 2,000 fungal names were updated in the curated database for scientific names of fungi on plants, which now totals approximately 80,087 reviewed names (42,508 accepted names). This allows users to synthesize and collate all data reported for all names associated with a single fungal species. Contractors working with the Mycology and Nematology Genetic Diversity and Biology Laboratory continue to assist in purging code and databases of unused elements. We are continuing a project to update the data entry system to modern and secure web-based modules. Literature and fungus-host data module development essentially complete. In addition to fungal databases, the server hosts databases for the USDA Nematode Collection and the Floral and Nursery Products Research Unit. These activities also contribute to fulfillment of Objective 2 of this project to develop on-line resources about the systematics of fungi and plant pathogens of importance to scientists and plant quarantine officials.
Accomplishments
1. Historic fungal specimens were documented. Preserved fungal specimens serve as references for names of important disease-causing fungi and document their presence in space and time. The potential economic impacts of misidentification or unknown geographic distributions of plant pathogens exceeds $10 billion per year. ARS scientists and staff in Beltsville, Maryland, photographed and inventoried approximately 10,000 historic specimens to document their presence worldwide. Accurate names and information are essential for the control of fungal diseases and prevention of entry of invasive fungi into the U.S. Plant disease diagnosticians, plant pathologists, and plant quarantine officials will use this information to accurately identify and manage plant disease outbreaks.
2. United States agricultural imports and exports were facilitated by fungus-host databases. Over $200 billion in trade flows through ports each year. Knowledge of the plant host associations and geographic distributions of plant pathogenic fungi is critical to controlling the spread of plant diseases. ARS scientists in Beltsville, Maryland, accessioned over 2,500 world-wide records of fungus-host distributions from peer-reviewed literature into the U.S. National Fungus Collections Fungal Databases. These data are used daily by quarantine officials to accurately track plant pathogenic fungi and prevent their entry into or the further spread in the U.S. while maintaining the approximately $110 billion and $130 billion agricultural import and export markets, respectively.
