Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2019 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 is for Project 8042-22000-308-00D, “Management of Specimens and Associated Information in the U.S. National Fungus Collections, with Emphasis on Critically Important Plant Pathogens.” Regarding Objective 1, approximately 12 specimen loans were sent nationally and internationally, consisting of approximately 175 specimens. In addition, approximately 2,000 specimens were accessioned into the collection for use by future researchers. Approximately, 30,000 unaccessioned myxomycete specimens have been identified in the Collections and nearly 17,000 label images have been captured to facilitate the data entry for these specimens. 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 12,000 fungus-host-locality-literature reports were added to the database of fungi on plants around the world for a total of 806,361 reports. 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. 1,052 fungal names were updated in the curated database for scientific names of fungi on plants, which now totals 76,856 reviewed names. This allows users to synthesize and collate all data reported for all names associated with a single fungal species. Data are available at https://nt.ars-grin.gov/fungaldatabases/.
Contractors working with the Mycology and Nematology Genetic Diversity and Biology Laboratory continue to assist in purging code and databases of unused elements. We have also begun a project to update the data entry system to modern and secure web-based modules. Literature and fungus-host data module development is well underway, with the literature module nearly completed. 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. Identitifying plant pathogenic fungi. ARS scientists in Beltsville, Maryland, have verified or updated the names for approximately 1,052 plant pathogenic fungal species. Accurate names are essential for the control of fungal diseases and prevention of entry of invasive fungi into the U.S. for which estimates place potential economic impacts at greater than $10 billion per year. Plant disease diagnosticians, plant pathologists, and plant quarantine officials will use this information to accurately identify and manage plant disease outbreaks.
2. Documentation of fungus-plant associations facilitates trade. 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 12,000 records of fungus-host distributions from around the world into the U.S. National Fungus Collections Fungal Databases based on peer-reviewed literature reports. These data are used daily by quarantine officials to accurately track plant pathogenic fungi and prevent their entry into or the further spread of these organisms in the U.S. while maintaining the approximately $110 billion and $130 billion agricultural import and export markets, respectively.
3. Fungal plant pathogen reference specimens digitally imaged. The spread of invasive and emerging pathogens is estimated to cause economic impact greater than $10 billion per year. ARS scientists in Beltsville, Maryland, identified 1,500 reference specimens housed in the U.S. National Fungus Collections representing 720 species of plant pathogenic fungi and captured 6,000 digital images to aid in the rapid identification of plant pathogenic fungi. This information is critical to disease management and prevention of the movement of disease-causing fungi. Plant disease diagnosticians, plant pathologists, and plant quarantine officials will use this information to accurately identify and manage plant disease outbreaks.
Review Publications
Rossman, A.Y., Allen, W.C., Castlebury, L.A., Seifert, K., Verkley, G. 2018. Proposals to conserve Amorphotheca resinae against Cladosporium avellaneum, Ditiola mucida (Holwaya mucida) against Acrospermum caliciiforme (Crinula caliciiformis), Lophodermium seditiosum against Leptostroma austriacum, Pezicula sporulosa against Gloeosporium longisporum (Cryptosporiopsis longispora), and Tapesia yallundae (Oculimacula yallundae) against Cercosporella herpotrichioides (Pseudocercosporella herpotrichioides) (Ascomycota: Leotiomycetes). Taxon. 67(3):636-638. https://doi.org/10.12705/673.18.
Ju, Y., Hsieh, H., Dominick, S.B. 2016. The Xylaria names proposed by C.G. Lloyd. North American Fungi. 11(1):1-31.
