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United States Department of Agriculture

Agricultural Research Service

Research Project: THE U.S. NATIONAL FUNGUS COLLECTIONS AND DEVELOPMENT OF ON-LINE RESOURCES ABOUT FUNGI

Location: Systematic Mycology and Microbiology

2012 Annual Report


1a.Objectives (from AD-416):
Objective 1. Curate specimens in the U.S. National Fungus Collections as an international reference resource for use by scientists throughout the world. Objective 2. Develop on-line resources about the systematics of fungi, especially plant pathogens of importance to scientists and plant quarantine officials.


1b.Approach (from AD-416):
Objective 1. At the U.S. National Fungus Collections standard procedures are followed as detailed in reference books. Newly acquired specimens are “fumigated” by freezing prior to accessioning. Information about each newly acquired specimen at the U.S. National Fungus Collections (BPI) is entered in the Specimen Database with its unique accession number and barcode sticker. The dried fungal specimens are placed in acid-free boxes or in packets made of archival paper and the label is attached. Specimens are housed in standard metal herbarium cabinets on moveable compactors in limited climate-controlled space. The loan policy and guidelines of the U.S. National Fungus Collections are posted on the SMML website. Student technicians assist with filing specimens, pulling and mailing loans, and upgrading specimens. Newly acquired specimens and returned loans are frozen to prevent pest infestation before being incorporated into the collection. The herbarium is monitored for pests and specimens are frozen as necessary. Requests to use material for DNA analysis are considered favorably as long as sufficient material exists to support such work without jeopardizing the integrity of the specimen. Excess DNA is to be returned to the U.S. National Fungus Collections where it is stored in a –80 C freezer.

Objective 2. On-line database resources about fungi developed at the SMML will continue to be updated and increased as new specimens are accessioned and new data are published. As funding permits, the nomenclature file will be updated. Additions to the on-line identification systems are made as additional taxa are studied and described by the associated scientists. As unique sequences, i.e. DNA barcodes, are developed for these species, there will be a link to these GenBank sequences. Descriptions and illustrations of invasive fungi will be placed on the Internet as they become available. New software will be evaluated especially Adobe Flex software to facilitate the ability to work efficiently with these databases. Computer programs and operating system software and hardware will be continually under review and incorporated as deemed necessary and useful.


3.Progress Report:
Progress was made in both objectives all of which fall under National Program 301, Component 1, Crop Genetic and Genomic Resources and Information Management. Activities on this service project focus on problem 2B, plant and microbial genetic resource and information management. With the move to a new building the infrastructure for the U.S. National Fungus Collections has been updated with new cabinets and increased environmental controls. This past year seventy-nine loans were sent nationally and internationally with an equal number returned. An emphasis was placed on obtaining the return of loans that were more than five years overdue. About 8000 new specimens were accessioned. With the advent of genetic analysis, mycological study has been revolutionized often requiring destructive sampling of specimens. Personnel at the U.S. National Fungus Collections have been revising policies and discussing these issues with agricultural scientists so that research can be supported while protecting specimens for methods available in the coming centuries. These activities contribute to fulfillment of objective 1 of this service project as stated in the plan to curate specimens in the U.S. National Fungus Collections as an international reference resource for use by scientists throughout the world. About 40,000 new fungus-host reports were added to the worldwide database of fungi on plants around the world for a total of over 850,000 reports. This represents the most comprehensive database of fungi on plants in existence. The 300,000 card file reporting fungi on plant hosts was scanned and an application developed that allows these reports to be edited and included in the fungus-host reports. The nomenclature of an additional 12,000 scientific names of fungi on plants now totaling 65,000 names was verified allowing users to synthesize data reported for synonymous names of one species. All data are available at: http://nt.ars-grin.gov/fungaldatabases/. The descriptions and illustrations of about 100 plant pathogenic fungi including those encountered at ports of entry were updated on the SMML Website. Several of these plant pathogens have been discovered in the U.S. These descriptions and associated information were included in the CABI Invasive Species Compendium. Contractors working with SMML have implemented a new security system for remote access to data entry and revised code on the public web pages to remove potential security issues. The contractors continue to assist in addressing security issues and in purging code and databases of unused elements. SMML hosts databases for the Nematology Laboratory (NL) and Floral and Nursery Products Research Unit (FNPRU). SMML contractors developed a mechanism to allow NL database updates to be available immediately to users. In addition the FNPRU seed and fruit identification applications were upgraded, secured and consolidated. These activities contribute to fulfillment of objective 2 of this service project to develop on-line resources about the systematics of fungi, especially plant pathogens of importance to scientists and plant quarantine officials.


Last Modified: 9/29/2014
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