Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2018 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 Enhancing Plant Protection through Fungal Systematics, which started 1/18/2018 and continues research began under 8042-22000-285-00D, “Curation of the U.S. National Fungus Collections and Associated Information Resources.” Since this project was initiated, regarding Objective 1, approximately 13 specimen loans were sent nationally and internationally, consisting of approximately 300 specimens. In addition, approximately 150 new specimens were received for deposit into the collection for use by future researchers. 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 2500 new fungus-host reports were added to the database of fungi on plants around the world for a total of 793900 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. 1921 fungal names were updated in the curated database for scientific names of fungi on plants, which now totals 75,870 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 (MNGDBL) continue to assist in purging code and databases of unused elements. In addition to fungal databases, the MNGDBL server hosts databases for the USDA Nematode Collection and the Floral and Nursery Products Research Unit (FNPRU). 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
