Mycology

1 - Mycology 2 - Page 1- Ordering ARSEF Isolates 3 - Page 2 - ARSEF Catalogues

SERVICES AND HISTORY OF THE ARSEF COLLECTION

 

Deposition and Exchange of Cultures Ordering ARSEF isolates (see next page) Diagnostic Services Acknowledging ARSEF Strains in Publications Searching ARSEF and Electronic Catalogs (see page 2 for PDF catalouges) Release of ARSEF Cultures from Containment or Quarantine History and Goals of ARSEF

Deposition and Exchange of Cultures

The ARSEF collection accepts isolates of fungi and related eukaryotic microorganisms (oomycote and selected protozoans) for deposition and long-term preservation. The ARSEF encourages depositions of entomopathogenic fungal cultures of strains used in published studies, as well as the insect hosts from which these fungi were isolated into the associated herbarium of voucher and reference specimens. We especially welcome fungi isolated from emerging insect or other invertebrate (nematode, mite, wasp among others) hosts as well as fungal taxa not previously isolated and cultured from invertebrate hosts.

Depositors may reserve the right to limit redistribution of any culture deposited with ARSEF for a limited period of time (usually up to 5 years) upon consultation with the curator for the purposes of securing patents or finishing publications. For patented strains, please consult with the curator for restrictions or an MTA.

Depositors can receive subcultures of their own depositions at any time and are not subject to limitations on numbers of free cultures.

Exchanges of cultures between ARSEF and other research or general collections of fungal cultures are encouraged, but subject to restrictions, if applicable, and guidelines that are fair and beneficial to both parties and must be arranged in advance with curators of each collection.

Please contact the curator before shipping any cultures or specimens! 

While we aim to accept most requests for accessioning isolates, the curator reserves the right to decline shipments or accessions, depending on the current needs and priorities of the collection. For international contributors shipping cultures from countries outside the United States, it is essential to contact the Curator to obtain the appropriate importation permit from the U.S. Department of Agriculture, Animal and Plant Health Inspection Services, Plant Protection and Quarantine (APHIS-PPQ). Cultures shipped without appropriate documents may be destroyed by APHIS or in customs and those shipped without prior approval of the curator may be autoclaved or disposed of upon arrival.

To improve the associated metadata in our database, ARSEF requests to include as much of the following information as possible in your submission. Please e-mail to the Curator (kathryn.bushley@usda.gov) the following information prior to shipping your isolates.

 

• Taxonomic identification to extent known: Scientific name (Genus and species if possible and taxonomic authority) of the fungus or identification to the lowest possible taxonomic rank (Family, Order, Class, SubPhyla, Phyla, Kingdom)
• Common name (if known)
• Method and any associated data used for taxonomic assignment:
• DNA sequence
• Morphological identification (any microscopy images)
• Collection metadata (This information is required):
• Date of collection
• Name of collector
• Date of isolation and name of isolator
• Invertebrate host (if present) or substrate isolated from (e.g. soil, plant)
• Substrate of Invertebrate host (e.g. Insect collected feeding on plant)
• Bodypart (e.g. abdomen, leg, gut, head, brain, etc.)
• Any collection, accession, or other identifier number(s) applied by the collector or sender
• Culture medium on which culture was isolated and is growing on
• Any special requirements or conditions required for growth (e.g. medium, temperature, pH)

Diagnostic Services

Specimens and cultures of unidentified fungi from invertebrates can be submitted to ARSEF for diagnosis, after consultation with the curator. This service is an important function of the ARS Collections of Entomopathogenic Fungi and is provided without charge but is generally limited to initial identification based on morphological characters. We do not currently provide free identification requiring multi-locus sequencing. However, for selected isolates of interest to the collection, we may be able to provide sequencing of the fungal ITS barcode region to identify to genus or family.  

Acknowledging ARSEF Strains in Publications

We request that all publications using or referring to strains obtained from ARSEF acknowledge the U.S. Department of Agriculture, ARS Emerging Pests and Pathogens Research Unit and list the ARSEF accession numbers of these strains in the publication and any depositions to public sequence databases (e.g. NCBI GenBank or EMBL). We would greatly appreciate receiving of all past, current, and future publications or even periodic notification about research in progress involving the use of ARSEF strains. We track research on the collection and such information is also useful for other users of the collection to avoid duplication of work and provide background and context on particular isolates. In the future, we aim to include a doi link to publications associated with ARSEF isolates on the website, so supplying this information may even increase readership and citations of your article.

Accession numbers of strains from commercial culture collections such as the American Type Culture Collection (ATCC), Centraalbureau voor Schimmelcultures (CBS), United Kingdom National Culture Collection (IMI), and other registered general service collections are listed in this catalog to provide complete information about specific isolates.

Representation of cultures obtained from ARSEF as being from ATCC, CBS, IMI or UAMH or any other general service culture collections violates trademark laws, and persons doing so are subject to prosecution. Cultures received from ARSEF should be referred to by their ARSEF numbers only even if they are co-deposited in other culture collections.

 

Searching ARSEF and Catalogs

The complex software application used to manage all aspects of the operation and recordkeeping of the ARSEF collection was designed and executed using 4th Dimension (now 4D) relational database software by Timothy S. Larkin and more recently updated and rewritten by Jody Bevans (Argus Productions Inc.).

Due to security concerns from an unfortunate hacking event at another USDA collections database site, the searchable version of ARSEF culture accession data is currently offline. We are transitioning to a cloud-based solution at the National Agricultural Library and anticipate having a searchable online catalogue back online in fall of 2023 (Stay Tuned!). A searchable PDF catalog of the complete collection and specific catalogues of frequently requested fungal or host taxonomic groups are linked on page 2 of this site. If you are unable to use these to find the information you need, please e-mail the Curator (Kathryn.Bushley@usda.gov) with your needs and we can generate a custom search that will be returned as quickly as possible by email. We apologize for this inconvenience.

Release of ARSEF Cultures from Containment or Quarantine

Neither the curator nor any employee of ARSEF or of the Emerging Pests and Pathogens Research Unit is entitled to authorize the release of any culture it provides from laboratory containment or quarantine in the United States or elsewhere. Recipients of ARSEF cultures are responsible for obtaining all appropriate and necessary permissions from or for providing official notifications to appropriate regulatory agencies in the receiving country. Neither the curator or any employee of ARSEF will be held responsible or liable for any unauthorized release from containment or quarantine. APHIS permits are required to ship and work with most of the isolates in our collection (see Requesting ARSEF isolates for more information). 

History and Goals of ARSEF

The goal of the ARS Collection of Entomopathogenic Fungal Cultures (ARSEF) is to provide fundamental support for basic and applied research on the fungal pathogens of invertebrates.

Since its establishment in the early 1970s, this collection has provided general research resources for the isolation, collection, preservation, and distribution of fungal strains from insects, other arthropods, and nematodes. ARSEF actively seeks to acquire and, on request, to distribute strains under active study for use in research programs. The basic research subjects directly associated with the collection include fungal systematics, fungal cytology, pathobiology, and methodologies for long-term preservation of fungal germplasm. The culture collection and its associated collection of microscope slides and herbarium specimens provide invaluable support for taxonomic research on and the diagnoses of fungal pathogens of invertebrates. Identification services for specimens and cultures have always been available free of charge upon request. We strive to provide users with accurately identified and pure (uncontaminated) fungal cultures. The taxonomies used to identify the fungi in the collection are continuously updated to reflect their current supported classifications. The curator of the collection welcomes all correspondence about nomenclatural or taxonomic changes or possible misidentifications involving any ARSEF strains.

The ARSEF collection began as the Richard Soper (RS) research collection in a USDA-ARS laboratory at the University of Maine, Orono (UMO), and its cultures were at initially designated by a UMO or RS prefix before being renamed as ARSEF in 1985. In 1978, the ARS Insect Pathology Research Unit relocated to Ithaca, NY, to work with the Boyce Thompson Institute (BTI) on the Cornell University campus. The Insect Pathology Research Unit became the Plant Protection Research Unit (PPRU) in 1985,and was renamed in 2016 as the Emerging Pests and Pathogens Research Unit (EPPRU).

The ARSEF collection moved from BTI in 1990 into new facilities in the US Plant, Soil and Nutrition Laboratory which was, in turn, rededicated in 2008 as the Robert W. Holley Center for Agriculture and Health to commemorate the completion by Dr. Holley and his team in this building of the first sequencing of any nucleic acid for which he received the 1968 Nobel Prize for Physiology or Medicine. This remains the only Nobel Prize ever received by any ARS scientist.

The Emerging Pests and Pathogens Research Unit operates the ARSEF culture collection for the USDA Agricultural Research Service; the collection is not now and never has been owned or controlled by the Boyce Thompson Institute. ARSEF is one of the largest germplasm collections in the ARS, and is globally recognized for its active support of research on fungal pathogens of invertebrates. ARSEF and its associated herbarium are registered under the ARSEF acronym since 1985 with the World Data Center on Microorganisms (WDCM, under the auspices of the World Federation of Culture Collections) and with the Index Herbariorum (maintained by the New York Botanical Garden).

From 1977 through 2008, all ARSEF strains were preserved by immersion in liquid nitrogen. Since the late 1990s, the collection has been lyophilizing (freeze-drying) those isolates that could tolerate such treatment while still maintaining cryogenic stocks of all isolates. ARSEF ships freeze-dried units of all isolates whenever possible; all isolates not available in such an inactive form are shipped as living cultures on appropriate culture media. Requests for cultures are filled in the order in which they are received, with an average processing time for most requests being 4-6 weeks, but often less when only lyophilized isolates are included in a shipment.

 

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