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United States Department of Agriculture

Agricultural Research Service

U.S. National Fungus Collections

Fungi and Bacteria: U.S. National Fungus Collections

U.S. National Fungus Collections

By Amy Y. Rossman and David F. Farr


U.S. Department of Agriculture, Agricultural Research Service, Sytematic Botany and Mycology Laboratory, BARC-West, 10300 Baltimore Boulevard, Building 011A, Room 304, Beltsville, MD 20705


To recognized institutions and scientists


5,600 volumes; 75,000 pamphlets and reprints

Number of

1,100,000 collections; 125,000 taxa, including species and varieties




Amy Y. Rossman, Phone: (301) 504-5364, fax: (301) 504-5810, e-mail, expertise in Ascomycetes, particularly the Hypocreales, Calonectria, Nectria, Ophionectria, plant pathogenic fungi

David F. Farr, Phone: (301) 504-5274, fax: (301) 504-5810, e-mail,expertise in Coelomycetes, particularly Septoria, Stagonospora, plant pathogenic fungi, data management

Mary E. Palm, Phone: (301) 504-5327, fax: (301) 504-5810, e-mail, expertise in Deuteromycetes, particularly Kirramyces, Plectosporium, plant quarantine fungi

Gary J. Samuels, Phone: (301) 504-5279, fax: (301) 504-5810, e-mail, expertise in Ascomycetes and their asexual states, including Hypocrea-Trichoderma, Nectria-Fusarium, Hypocreales, biocontrol fungi

Internet Access

Home page

Telnet access: Type "" (then type "login user" and enter the password "user").

The U.S. National Fungus Collections is a mycological institution that includes the world's largest herbarium of dried fungus specimens, together with technical reference literature and data files. The collection serves as a base for research and service in national and international mycology and plant pathology. Many of the technical resources and specimen data are available over the Internet through a telnet system or the World Wide Web. These resources can be accessed by contacting one of the mycologists listed above or by entering the system through the World Wide Web.


Fungus collections of the Smithsonian Institution were transferred to the U.S. Department of Agriculture (USDA) in 1869 as the foundation of the Pathological Collections. Later they became the Mycological Collections and finally the U.S. National Fungus Collections, as changes in the title reflected a broadened role and status of the technical resources. In 1885, when the herbarium had fewer than 3,000 collections, F. Lamson Scribner assumed charge as the first Federal pathologist. He was followed by Franklin S. Earle in 1891, and Flora W. Patterson in 1896. Patterson organized programs and assembled a staff that notably influenced subsequent development of the U.S. National Fungus Collections. Emphasis was on the taxonomy of plant pathogens, but significant pathogens and closely related potential pathogens were also listed for nearly every fungus family.

The presence in America of the bubble disease of mushrooms, which threatened the entire industry, was first recognized in 1909 by scientists working at the U.S. National Fungus Collections. This group of scientists also was responsible for the earliest American investigations of "plaster molds" and other important pathogens of mushrooms. Before the Plant Quarantine Act was passed in 1912, Vera K. Charles and Patterson conducted pathological inspection of imported plants. Among their interceptions was the dangerous potato wart disease caused by Synchytrium endobioticum, which they identified for the first time in the United States on imported potatoes.

In 1917, the Plant Disease Survey was organized as a distinct project coordinated with the Pathological Collections. Cooperation between these units stimulated progress on taxonomic and host-distribution inventory of American pathogens, as documented by specimens in the U.S. National Fungus Collections. At first, nearly all research and service activities of the Pathological Collections were the personal responsibility of Patterson and Charles. In addition to Charles' studies of mushrooms, she did research on the fungal pathogens of insects. In 1941, this work culminated in the publication of a comprehensive checklist of entomogenous fungi of North America. The scientific staff working at the U.S. National Fungus Collections was increased by the appointments of Anna E. Jenkins in 1912, Edith K. Cash in 1913, and William W. Diehl in 1917. Jenkins was the foremost authority on spot-anthracnose fungi, which cause leaf and blossom disease and scab of many economically important plants. The representation of these fungi in the U.S. National Fungus Collections is the most comprehensive and taxonomically authoritative anywhere. Cash was widely recognized for her investigation of cup fungi (discomycetes), which also include major plant pathogens. Diehl's work culminated in the publication of the only modern monograph on Balansia, a genus of pathogens significant in causing sterility in grasses.

Patterson retired in 1923, and James R. Weir was in charge of the U.S. National Fungus Collections until 1927. While in charge of the collections, he prepared a comprehensive report on the fungi that cause diseases of the Hevea rubber tree. In 1927, Cornelius L. Shear collaborated with B.O. Dodge in the publication of a pioneering report on the life histories and heterothallism of red bread-mold fungi. This was the study that later brought Neurospora into prominence as an experimental genetic organism and opened a broad new field of genetic research.

After 1927, when John A. Stevenson succeeded Weir in charge of the collections, buildup of the herbarium and associated reference material was intensified. Stevenson had worked in Puerto Rico as a plant pathologist. He retained his interest in tropical pathology while in charge of the Mycological Collections. As a result, he collaborated extensively with tropical plant pathologists, such as F.D. Wellman, in development of the herbarium, specimen identification, preparation of geographical and host compendia, and research publications. Working relationships also were developed with outstanding national authorities, such as J.L. Lowe and G.B. Cummins, specialists in the taxonomy of wood-decay polypores and rust fungi, respectively. Ross W. Davidson was employed in 1928 to work with the U.S. National Fungus Collections. After a few years, his transfer to the Office of Forest Pathology stimulated further cooperation with that organization in the acquisition of wood-decay fungi as herbarium specimens.

In 1947, Paul L. Lentz joined the research staff associated with the U.S. National Fungus Collections. His interests in the classification and biology of wood-decay fungi resulted in a monograph on Stereum in 1955 and led then to the recognition and description of the fungus that causes pecky cypress. In 1958, Marie L. Farr came to the U.S. National Fungus Collections as a taxonomic specialist in the myxomycetes. She also worked extensively with black mildews and other fungi prevalent in the tropics as leaf parasites, epiphytes, and hyperparasites. Chester R. Benjamin was placed in charge of the U.S. National Fungus Collections as Stevenson's successor in 1960. Within a few years, he increased the staff by adding mycologists. John L. Cunningham, a specialist in rust taxonomy, arrived in 1965, as did Francis A. Uecker, whose specialization was in the cytology and developmental morphology of pyrenomycetes. Kent H. McKnight reestablished a program on mushroom taxonomy and ecology in 1966. The following year, Lekh R. Batra was employed to continue his diverse research projects in the classification of discomycetes, hemiascomycetes, and fungus-insect relationships. After Benjamin's departure in 1971, Lentz assumed charge of the U.S. National Fungus Collections and its associated research. Joseph F. Ammirati was employed in 1973 as an agaricologist, and he was succeeded by David F. Farr, who joined the mycology staff in 1974 to work primarily with noncultivated mushrooms and later to become the expert in computer technology.

With Paul Lentz's retirement in 1983, Amy Y. Rossman became director of the U.S. National Fungus Collections and continued the program of specimen data computerization. Her knowledge of plant pathogenic fungi in general and the Hypocreales continued the tradition of research on fungi important to U.S. agriculture. Under the guidance of Farr, two research associates—Gerald F. Bills and George P. Chamuris—provided the expertise for the relational database that resulted in the monumental account of 13,000 species of fungi reported on plants and plant products in the United States. A companion volume on the vascular plant hosts was completed by Lois A. Brako, who was assisted by Rossman and Farr.

Following the retirement of M.L. Farr and McKnight, in 1989 Gary J. Samuels was hired to develop a program on the systematics of fungi useful in the biological control of plant diseases. This work concentrated on Hypocrea-Trichoderma (figs. 9 and 10), with molecular expertise provided by Robert Meyer and, later, by Stephen Rehner. Tackling this extremely difficult but important group of fungi has required a team effort using morphological and molecular approaches. Samuels' strains of Trichoderma isolated from tropical specimens of Hypocrea are combined with asexual isolates to determine systematic relationships that are the basis for predicting their effectiveness. In 1994 Samuels worked with Rehner to discover a technique for producing sexuality in asexual strains of Hypocrea (fig. 9). Dr. Francis A. "Bud" Uecker retired on January 3, 1995. He was working on the systematics of plant pathogenic fungi in the genus Phomopsis, in which over 1,000 species have been described (fig. 11). Morphological and molecular approaches were used to determine whether these fungi are host specific.

Figure 9. Sexual reproduction in Hypocrea poronioidea shown as ascocarps developing in culture
Figure 10. Asexual reproduction in Hypocrea illustrated by the branching conidiophore of Trichoderma

Figure 10. Asexual
reproduction in
Hypocrea illustrated
by the branching
conidiophore of

Figure 9. Sexual reproduction
in Hypocrea poronioidea
shown as ascocarps develop-
ing in culture

Notable among the original or early acquisitions of the Pathological Collections are the exsiccati from J.B. Ellis, G.L. Rabenhorst, and H.W. Ravenel. Other early collections are from T.J. Burrill, G.W. Clinton, B.D. Halsted, E.W.D. Holway, M.E. Jones, W.A. Kellerman, and A.B. Langlois. Specimens were submitted from the U.S. Exploring Expedition under Commodore Wilkes, 1838-42, and also from the U.S. North Pacific Exploring Expedition under Commanders Ringgold and Rogers, 1853-56. The earliest American collections of fungi were those by L.D. von Schweinitz. Many of the Schweinitz collections and those by M.A. Curtis and other early American mycologists are in the U.S. National Fungus Collections. Thousands of collections also were contributed by mycologists and plant pathologists of the USDA. Some of the most extensive are from G.G. Hedgecock, Jenkins, Shear, Stevenson, and Weir.

 Figure 11. Black pycnidia of Phomopsis developing in culture on stems of alfalfa

Figure 11. Black pycnidia of Phomopsis
developing in culture on stems of alfalfa

In 1924, the valuable G. Bresadola herbarium from Italy was purchased for the U.S. National Fungus Collections, and the E.A. Rau herbarium, including types, was acquired as a gift. The C.G. Lloyd herbarium was obtained in 1927. With more than 59,000 collections, it may be the largest fungus herbarium ever assembled by one person. Weir's herbarium of wood-decay fungi, acquired in 1928, also numbered many thousands of collections.

Other major acquisitions include the P.C. Standley collection from Honduras and Costa Rica; L.W. Nuttall fungi from West Virginia; remainders of the J.B. Ellis herbarium; the Sbarbaro collections from Europe; New York and Colorado collections by Shear; collections by E.A. Burt; specimens from the former Division of Cereal Crops and Disease (Bureau of Plant Industry); collections contributed by the Horticultural Crops and Diseases Division (USDA); the herbarium of R. Ciferri from the Dominican Republic; O.A. Reinking's Philippine collections; the G.L. Zundel smut herbarium; E.R. Bethel's herbarium of Colorado fungi; the W.H. Long collections of rust fungi and gasteromycetes; C.E. Chardon's herbarium of parasitic fungi from the West Indies and Central and South America; Japanese fungi from N. Hiratsuka; type specimens of P.A. Karsten's European wood-decay fungi; remainders of the Chinese National Herbarium; the J.H. Faull rust fungi; Elizabeth B. Morse's mushrooms; E.F. Guba's collections of Pestalotia; and the entire mycological herbaria of Goucher College, Stanford University, the Missouri Botanical Garden, and the Brooklyn Botanic Garden, including the large personal herbarium of F. Bubak and the collections of D. Griffiths and G.M. Reed.

In 1953, the fungus herbarium of the New Haven, Connecticut Forest Service Field Station was transferred to the U.S. National Fungus Collections. Another acquisition is the herbarium of the Connecticut Agricultural Experiment Station at New Haven including the smut fungi of G.P. Clinton. Another addition was the myxomycete herbarium of T.H. Macbride and G.W. Martin from the State University of Iowa, as well as myxomycetes from C.J. Alexopoulos, T. Brooks, and D. Reynolds. As a result of these acquisitions, the myxomycetes section in the U.S. National Fungus Collections is now among the most notable in the world (fig. 12). The same is true of the polypore and rust collections, as well as several other outstanding sections of the herbarium. Collections also have been received from such well-known scientists as R. Allen, J.P. Anderson, R.K. Beattie, W.W. Calkins, G.W. Carver, F.S. Earle, F.D. Fromme, F.D. Hall, J.R. Hansbrough, A.G. Johnson, C.L. Lefebrve, A. Liberta, W.H. Long, W.A. Orton, J. Rick, W.H. Snell, A.B. Seymour, E.F. Smith, F.L. Stevens, N.E. Stevens, W.T. Swingle, B.C. Tharp, S.M. Tracy, M.B. Waite, H.J. Webber, F.H. Wellman, F.A. Wolf, and many others. S. Ahmad in Pakistan and K.S. Thind in India have contributed numerous collections. Also, a policy was established by Patterson and followed by her successors for the acquisition of all sets of fungi exsiccati as they became available by purchase or exchange.

Figure 12. Fruiting bodies of Physarum roseum, also known as the slime molds

Figure 12. Fruiting bodies of
Physarum roseum, 1 of the
60,000 specimens of Myxo-
mycetes, also known as the
slime molds, in the U.S.
National Fungus Collections

As the herbarium grew, a reference literature collection and extensive data files were developed. The library was built up principally as the personal collection of Stevenson, who donated it to the Smithsonian Institution. In 1976, an understanding between the Smithsonian Institution and the Agricultural Research Service provided for permanent maintenance by the research staff of the U.S. National Fungus Collections. Technical indexes also serve as sources of reference information in the U.S. National Fungus Collections. These include the New Taxa Index, which includes 210,000 entries; the Plant Pathogens Index, which consists of 1,200,000 cards; a herbarium fungus and host index of 200,000 records; and an index of type specimens.


The specimens in the U.S. National Fungus Collections have been assembled from every major area of the world. They are used often for direct comparison with suspected pathogens. Approximately 100 loans are made each year for research throughout the world. Records for a recent, typical year show that services by the staff of the U.S. National Fungus Collections included assistance with fungal nomenclature and synonymy, fungal identification, herbarium specimen data, records of distribution and pathogenicity, information on mold prevention, information on mushroom poisoning and the eradication of mushrooms, and identification of poisonous mushrooms. Services were provided for such individuals as mycologists, plant pathologists, extension pathologists, and physicians as well as the lay public, and for institutions, including experiment stations, universities, biology publishing firms, research laboratories, government offices, museums, and hospitals.

The facilities, program, and staff of the U.S. National Fungus Collections are particularly strong in dealing expertly with mycological problems of foreign origin. The herbarium and major data files have been built up with emphasis on foreign material. Many compendia on foreign pathogens have been produced by use of these data. Support also is provided to the plant quarantine program of USDA's Animal and Plant Health Inspection Service. As international travel and commodity shipments increase, continuing development of technical information on the mycology of foreign countries is necessary for plant protection in the United States.


Databases developed at the U.S. National Fungus Collections provide access to information about fungi, primarily those associated with plants or otherwise of agricultural importance. These databases are maintained and expanded by members of the Systematic Botany and Mycology Laboratory (SBML), U.S. Department of Agriculture, Agricultural Research Service.The databases can be accessed directly on the laboratory's web site (click on the link above) or on telnet (telnet address="telnet") through either of two public menus. Terminal emulation must be set to VT100, the default setting at the terminal emulation prompt. Other settings for terminal emulation are listed after this prompt. To access the databases after connecting via telnet, type the words "login user" and enter a password of "user." The USER menu will appear. To access the APHIS menu with additional databases for plant-associated fungi from throughout the world, type "login Aphis" and enter the password "Aphis."

The two public menus, USER and APHIS, provide access to databases maintained at the U.S. National Fungus Collections. The databases of specimens in the U.S. National Fungus Collections, relational databases for the book entitled Fungi on Plants and Plant Products in the United States (available from APS Press), and references for the identification of plant pathogenic fungi can be accessed through both menus. In addition the USER menu includes the database of books in the J.A. Stevenson Reference Library, the Index to Saccardo's Sylloge Fungorum, the International Mycological Institute's Index of Fungi, 1940-1980, and the database of C.H. Peck type specimens. The APHIS menu includes access to the database of Q37 hosts, primarily horticultural crops, Rhododendron, conifers, and about 200,000 unedited reports of fungi on plants from the world literature. The APHIS menu also has an option for searching all of the fungal databases.

Specimens in the U.S. National Fungus Collections. The U.S. National Fungus Collections is the repository for over 1 million fungal specimens worldwide and is the largest such collection in the world. Information associated with these specimens constitute an enormous data resource, especially about plant-associated fungi. Data from the labels of about 650,000 (65 percent) of the specimens have been entered into a database. These labels have information on the host on which the fungus was found and the locality in which the specimen was collected. Sixty percent of these specimens are from the United States and thus represent a large body of information about the fungi in this country. Data entry has been completed for the Uredinales (rusts), the Ustilaginales (smuts), the Polyporales (polypores), the Deuteromycetes (imperfect fungi), the Ascomycetes, and the C.G. Lloyd collections. Data from about 50,000 specimens and from approximately 10,000 newly accessioned specimens are entered each year.

Fungi on Plants and Plant Products in the United States. The relational databases used to produce the book Fungi on Plants and Plant Products in the United States are available. These databases include the reports of fungi on vascular plants and plant products according to their distribution by state. The reports are taken from over 4,000 literature sources, primarily published between 1950 and 1987, and include 13,000 fungal species on 9,000 vascular plant hosts representing 78,000 unique host-fungus combinations. The data can be searched using the scientific name of the host genus, host genus and species, fungus genus, or fungus genus and species. The common name of the host can be used to determine its scientific name. If an obsolete scientific name is entered, the database will automatically correct the name and search under the accurate scientific name. The accepted fungal names are listed with their accurate scientific names, authors, basionym, synonyms, alternate state names, geographic distribution—both worldwide and by state, host range, and relevant literature for identification. A database is maintained on the scientific and common names of the vascular plant hosts.

References on the systematics of plant pathogenic fungi. An outstanding database of current references on the systematics of plant pathogenic fungi is maintained by the mycologist for the Animal and Plant Health Inspection Service (APHIS), Dr. Mary E. Palm. She reviews the worldwide literature received at the Agricultural Research Service's SBML for important references on world distribution, taxonomy, and biology of plant pathogenic fungi and bacteria. At present more than 16,000 references have been entered, and additional references are added periodically. Keywords for each piece of literature are derived primarily from fungus and host scientific names and country. Records can be retrieved by using author names, year of publication, or keywords. In addition data are maintained that were published in the book A Literature Guide for the Identification of Plant Pathogenic Fungi (available from APS Press). The database includes comments about each genus and a listing of important fungal diseases caused by species in that genus. A database of the over 5,000 books in the John A. Stevenson Reference Library is also available.

Index to Saccardo's Sylloge Fungorum. A database was developed for all the fungal names included in Saccardo's 26-volume work, Sylloge Fungorum, published from 1881 to 1931 and in 1972. About 117,000 fungal names are indexed, often with more than one citation.

International Mycological Institute's Index of Fungi, 1940-1994. A database on the International Mycological Institute's Index of Fungi, volumes 1-6 covering 1940-1994, is available. It can be searched by genus or species of fungus and gives the reference (volume and page) to the Index of Fungi.

Type specimens of Charles Horton Peck at the New York State Museum. A database of type specimens of taxa described by Charles Horton Peck is also available. This database and the specimens are maintained at the New York State Museum in Albany, NY.

Fungi on Q37 Horticultural Crops, Rhododendron, and Conifers. As part of a project for the Animal and Plant Health Inspection Service, information has been collected on a worldwide basis for the fungi found on some Q37 hosts or plants in growing media, primarily horticultural crops including members of the Bromeliaceae. In addition fungi found on the genus Rhododendron (published by Parkway Publishers)and conifers have been reported and reviewed. This information has been compiled into a database that includes information on 3,300 fungi and 89 host genera. The approach and format are identical to those used in Fungi on Plants and Plant Products in the United States. The database can be queried for fungi reported on a particular host and for information on the taxonomy, worldwide distribution, and host range of each fungus.

Unedited Reports from the Literature of Fungi on Plants Throughout the World. Records of the literature reporting fungi on vascular plant hosts from outside the United States are entered daily into a database. In surveying the literature for the Q37 database, all of the reports from each literature source are entered. The database includes more than 200,000 reports of fungus on plants throughout the world. Most of the data in this file have not yet been reviewed and edited by SBML personnel. Thus, there is no information about synonymy, common names, or distribution of either the fungi or the hosts.



Detected first-known American case of industry-threatening bubble disease of mushrooms


Discovered first-known importation of dangerous potato wart disease in America


Revealed major, newly recognized group of plant pathogens as represented by citrus-scab fungus


Characterized all known pathogens and diseases of Hevea rubber trees in South America


Established fundamental significance of Neurospora to development of modern research in fungal genetics


Developed comprehensive taxonomic key in English to all known genera of fungi


Completed research on entomogenous fungi with checklist of fungal pathogens in insects in America


Monographed Balansia, a genus of fungi causing sterility in grasses


Organized definitive system for use in specialized hyphal morphology for classifying wood-decay fungi


Monographed Stereum, an important genus of wood-decay and tree-disease fungi


Documented all known fungi of Puerto Rico in the most comprehensive technical inventory available for a specific, large tropical area


Monographed Myxomycetes of American Tropics


Monographed the phragmosporous species of Nectria and related genera in the Hypocreales


Monographed the species of Tubeufiaceae, many of which are parasitic on leaf fungi


Published checklist of species described in Cercospora leaf spot fungi


Completed a world list of Phomopsis names with notes on nomenclature, morphology, and biology, including over 1,000 species with their hosts and type specimens


Published a comprehensive account of the Fungi on Plants and Plant Products in the United States, including 13,000 accepted fungal species on 9,000 vascular plant hosts


Described the fungus causing dogwood anthracnose as the previously unknown species, Discula destructiva; this description served as the basis for research on this important disease


Published world monograph of Monilinia, fungi causing brown rot of stone fruits and other diseases


Produced an index to the 200,000 species of fungi as the Index to Saccardo's Sylloge Fungorum (available in print and electronic form)


Established public access to data files of over 650,000 herbarium specimens as well as databases of fungi on vascular plants both inside and outside the United States


Published book on the scientific and common names of 7,000 vascular plants in the United States, a companion volume to fungi on plants and plant products


Developed checklist and account of fungi reported on Rhododendron throughout the world

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Last Modified: 2/6/2002