Location: Mycology and Nematology Genetic Diversity and Biology Laboratory
2021 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, no specimen loans were sent nationally and internationally, although images were able to be substituted in about 10 cases. In addition, approximately 40,000 specimens were accessioned into the database that is currently searchable at https://mycoportal.org for use by future researchers. Approximately 65,000 unaccessioned historic specimens that had not been included in the database have been imaged to date by contractors for optical character recognition (OCR) of the label text to facilitate the data entry for these specimens. Many of these represent the type and valuable reference specimens. These activities fulfill Objective 1 of this service project as they represent the core functions necessary to curate specimens in the United States National Fungus Collections as an international resource for use by scientists throughout the United States and the world. For the second objective, approximately 12,000 fungus-host-locality-literature reports were added to the fungi database on plants around the world for a total of 820,000 reports. Approximately 900 new literature records were added, and the fungus host association database now accounts for 413,065 unique associations. This represents the most comprehensive database of fungi on plants in existence. Progress continues to incorporate historic fungus host data from 300,000 scanned index cards into the public Fungus-Host Database.
Approximately 4,000 fungal names were updated in the curated database for scientific names of fungi on plants, totaling approximately 78,781 reviewed names (41,348 accepted 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 are 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 the fulfillment of Objective 2 of this project to develop online resources about the systematics of fungi and plant pathogens of importance to scientists and plant quarantine officials.
Accomplishments
1. Recent rules in naming fungi can confuse the identities of plant pathogenic fungi. Recent changes in the rules for naming fungi can confuse the identities of plant pathogenic fungi. ARS scientists in Beltsville, Maryland, have verified or updated the names for approximately 4,000 plant pathogenic fungal species. Accurate names are essential for controlling fungal diseases, and preventing entry of invasive fungi into the United States, 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 identify and manage plants disease outbreaks accurately.
2. Facilitation of 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 world-wide records of fungus-host distributions from peer-reviewed literature into the United States National Fungus Collections Fungal Databases. Quarantine officials use these data daily to accurately track plant pathogenic fungi and prevent their entry into or the further spread of these organisms in the United States while maintaining the approximately $110 billion and $130 billion agricultural import and export markets respectively.
3. Georeferencing of fungal plant pathogens. The spread of invasive and emerging pathogens is estimated to cause an economic impact greater than $10 billion per year. However, exact location information is limited for many of the historic collections that are available for study. ARS scientists in Beltsville, Maryland, georeferenced specimens housed in the United States National Fungus Collections representing approximately 50,000 species of plant-associated fungi from Central and South America, Texas, Florida, California, and several other heavily agricultural states. This information will aid in the rapid identification and tracking of plant pathogenic fungi through space and time. These data are 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 identify and manage plant disease outbreaks accurately.
4. Digital imaging of fungal plant pathogens and associated information. The spread of invasive and emerging pathogens is estimated to cause an economic impact greater than $10 billion per year. ARS scientists in Beltsville, Maryland, identified 779 reference specimens housed in the United States National Fungus Collections representing 414 species of plant pathogenic fungi and captured nearly 10,000 digital images, including specimen labels and specimens to aid in the rapid identification of plant pathogenic fungi, uploading nearly 40,000 total images to the aggregated site at https://mycoportal.org. 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 identify and manage plant disease outbreaks accurately. Approximately 80,000 specimen labels from oomycete, myxomycete, phycomycetes, and true fungi, including 65,000 images contained in historic bound volumes of specimens, mostly from the 1800s and early 1900s.This will enable many researchers to view the information online without the need to request specimens or photographs from ARS staff.
Review Publications
Udayanga, D., Miriyagalla, S.D., Herath, I.S., Castlebury, L.A., Ferdinandez, H., Manamgoda, D.S. 2020. Foliar pathogenic fungi: growing threats to global food security and ecosystem health. Ceylon Journal of Science. 49(5):337–353. https://doi.org/10.4038/cjs.v49i5.7801.
Petrovic, K., Skaltsas, D.N., Castlebury, L.A., Kontz, B., Allen, T.W., Chilvers, M.I., Gregory, N., Kelly, H., Koehler, A.M., Kleczewski, N., Mueller, D.S., Price, P.P., Smith, D.L., Mathew, F.M. 2021. Phomopsis seed decay of soybean (Glycine max L.) is endemic in the United States, but new fungi are involved. Plant Disease. https://doi.org/10.1094/PDIS-03-20-0604-RE.
