The Microfungi Collections Consortium: A Networked Approach to Digitizing Small Fungi with Large Impacts on the Function and Health of Ecosystems

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Digitization TCN: Creating The Microfungi Collections Consortium: A Networked Approach to Digitizing Small Fungi with Large Impacts on the Function and Health of Ecosystems

Microfungi TCN
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Project Summary

Microscopic fungi (microfungi) represent a diverse assemblage that is distributed worldwide and includes bread molds, plant pathogens, powdery mildews, rusts, slime molds, and water molds. A large percentage of these organisms are harmless or even beneficial, but some cause disease and death in animals, plants, and other fungi resulting in major economic loss and serious negative implications for human and ecosystem health. Despite their importance, little is known about their distribution, diversity, ecology, or host associations. This project is a collaborative effort involving 38 institutions in 31 states and aims to consolidate data from specimens housed in biodiversity collections for 2.3 million microfungi specimens and make these data available through online resources. The consolidation and increased accessibility of these data is critical to inform and promote new and innovative research, education and community engagement around this little-known but important group of organisms.

Specimen data generated by this project will be used to assess natural and human-induced environmental changes on microfungi distributions, and evaluate the impact of these changes on the function and health of ecosystems. This project fills a critical gap in the national digitization effort by contributing images, digitizing specimen label data, and linking associated ancillary data for over 1.2 million North American specimens of microfungi. Additionally, nomenclature and taxonomic information will be updated to reflect the newest practices as dictated by the International Codes for Nomenclature. These data will provide a foundation for making informed decisions by agribusinesses, educators, forest managers, government agencies, horticulturalists, policy makers, researchers, and the general public. The broader education goals of this project will be facilitated through the development and implementation of a teaching module for high school biology on the economic importance of microfungi. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biological Collections program and all data resulting from this award will be available through the national resource (

Current Research

Proposed research questions include:

  • What are the effects of anthropogenic disturbance to the environment on the temporal and spatial distribution and phenology of microfungi? Human-induced impacts may include downstream effects due to land use changes in agricultural and natural ecosystems, the introduction of herbicides, fungicides, and pesticides, and increased atmospheric pollution.
  • Can we use historic and current distributional patterns of microfungi as models for the early detection of invasive species to reduce their potential deleterious effects? Can we use these same data to detect endemism and biodiversity hotspots in microfungi?
  • How do climatic changes influence the dispersal, distribution, and functioning of soil microfungi?

Project Websites & Social Media

Microfungi Collection Consortium (


Citizen Science & Outreach Projects

WeDigBio @ UIUC 2015

Project Leadership

Project sponsor: University of Illinois at Urbana-Champaign (NSF award 1502735)

Principal Investigator (PI): Andrew Miller – Illinois Natural History Survey
Biological Informatician: Phil Anders – Illinois Natural History Survey
Data Curator: Diego Barroso – Illinois Natural History Survey
Project Consultant: Scott Bates – Purdue University North Central

Project Collaborators

Map of Collaborating Institutions

Barbara Kennedy, Richard Pyle – Bernice Pauahi Bishop Museum
Julia Kerrigan – Clemson University
Cathie Hodge, Scott LaGreca – Cornell University (NSF award 1502748)
Melissa Islam, Vera Evenson – Denver Botanic Garden
Tatyana Livshultz – Drexel University, Academy of Natural Sciences
Thorsten Lumbsch – Field Museum of Natural History
Don Pfister – Harvard University, Farlow Herbarium (NSF award 1502767)
Deborah Lewis – Iowa State University
Jennie Kluse – Louisiana State University & Agricultural and Mechanical College
Michael Vincent – Miami University
Alan Fryday – Michigan State University
Roy Halling – New York Botanical Garden (NSF award 1502699)
Marc Cubeta – North Carolina State University (NSF award 1503564)
Joey Spatafora – Oregon State University
Cathie Aime – Purdue University (NSF award 1502887)
Brian Geils – USDA Forest Service, Rocky Rocky Mountain Research Station
Jim White, Ning Zhang – Rutgers University, Chrysler Herbarium (NSF award 1502788)
Dennis Desjardin – San Francisco State University
Alex Weir – State University of New York, College of Environmental Science and Forestry
Lisa Castelbury – U.S. National Fungus Collections
Martha Powell – University of Alabama
Betsy Arnold – University of Arizona
Steve Stephenson – University of Arkansas
Brent Mishler, Andrew Doran – University of California - Berkeley (NSF award 1502663)
Matthew Smith – University of Florida, Florida Museum of Natural History (NSF award 1502763)
Marin Brewer – University of Georgia, Georgia Museum of Natural History
Robert Lichtwardt – University of Kansas
Tim James – University of Michigan (NSF award 1502703)
George Weiblen – University of Minnesota (NSF award 1502745)
Robert Kaul – University of Nebraska
Carol Ann McCormick – University of North Carolina - Chapel Hill
John Hayden – University of Richmond
Karen Hughes – University of Tennessee - Knoxville
Mary Ann Feist, Sharon West – University of Wisconsin (NSF award 1502915)
Larry Schmidt – University of Wyoming
Mary Barkworth – Utah State University
Lori Carris – Washington State University

Unfunded Collaborators

Acadia University
Brown University
California State University Chico
Foray Newfoundland and Labrador Fungarium
Royal Ontario Museum Fungarium
Université de Montréal, Cercle des Mycologues de Montréal Fungarium
University of Alabama Chytrid Culture Collection
University of British Columbia Herbarium
Universidad de Buenos Aires
Virginia Polytechnic Institute and State University

Protocols & Workflows

Project Resources
Digitization workflow


Bates, S. T., Chapman, R. M., Islam, M. B., Schwabe, A., Wardenaar, E. C., & Evenson, V. S. 2016. Phylogenetic placement of the secotioid fungus Araneosa columellata within Agaricus. Mycotaxon, 131(1), 103-110.

Delgado, G. and O. Koukol. 2016. Microfungi from Nicaragua in a Historical Collection Kept at the Herbarium of the Charles University in Prague. Cryptogamie, Mycologie 37(1):15-36.

McCluskey, K., Alvarez, A., Bennett, R., Bokati, D., Boundy-Mills, K., Brown, D., ... & Dye, G. (2016). The US culture collection network lays the foundation for progress in preservation of valuable microbial resources. Phytopathology, 106(6), 532-540.

Bates, S. T., Golday, J., Kunnen, R. L., & Pilla, N. J. 2017. CHECKLIST OF INDIANA FUNGI I: MACROFUNGI. In Proceedings of the Indiana Academy of Science (Vol. 126, No. 1, pp. 12-34).

Heads, S.W., A.N. Miller, J.L. Crane, M.J. Thomas, D.M. Ruffatto, A.S. Methven, D.B. Raudabaugh, and Y. Wang. 2017. The oldest fossil mushroom. PLoS one, 12(6), p.e0178327.

Hodge, K. T., Hajek, A. E., & Gryganskyi, A. 2017. The first entomophthoralean killing millipedes, Arthrophaga myriapodina n. gen. n. sp., causes climbing before host death. Journal of invertebrate pathology, 149, 135-140.

Miller, A.N., and S.T. Bates. 2017. The Mycology Collections Portal (MyCoPortal). IMA Fungus MycoLens 8(2): 65–66.

Ranadive, K., Jagtap, N., & Khare, H. 2017. fungifromindia: the first online initiative to document fungi from India. IMA Fungus, 8(2), 67-69.

Thiers, B.M., and R.E. Halling. 2018. The Macrofungi Collection Consortium. Applications in Plant Sciences 6(2): e1021. doi.10.1002.aps3.1021

Bates, S.T., Miller, A.N., and the Macrofungi Collections and Microfungi Collections Consortia. 2018. The protochecklist of North American nonlichenized Fungi. Mycologia 110(6): 1222–1348. doi: 10.1080/00275514.2018.1515410

Professional Presentations

Miller, A.N., S.T. Bates, and T. Iturriaga. 2018. Discovering fungal hot spots through the MyCoPortal. International Mycological Congress 11, San Juan, Puerto Rico. July 2018. (Symposium)

Miller, A.N., P. Anders, N. Cobb, B. Brandt, and E. Gilbert. 2018. Integrating source modifiers with sequence data through a new GenBank submission module in Symbiota. Biodiversity Collections Network (BCoN) Data Integration and Attribution Workshop, University of Kansas, February 12-14, 2018.

Miller, A.N. 2017. MyCoPortal. North American MycoFlora 2.0 Workshop, July 16, Athens, GA.

Miller, A.N. 2017. Digitization and data sharing of fungal specimens. IX Latin American Mycological Congress, Lima, Peru, August 24. (Keynote Address)

Miller, A.N., N.S. Cobb, and B.D. Brandt. 2016. Symbiota Biodiversity Data Management System. 8th Brazilian Mycological Congress, October 3-6, Florianópolis, Brazil. (Keynote)

iDigBio Summit V, 2015

Miller, A.N., D.J. Barroso, P.J. Anders, and S.T. Bates. 2019. The MyCoPortal: Past, Present, and Future. Abstracts of the Mycological Society of America Meeting. Published online. (Abstr.)

Miller, A.N., S.T. Bates, and P.J. Anders. 2019. The Symbiota Sequence Submission Tool. Society for the Preservation of Natural History Collections, Chicago, IL, May 29.

Other project documentation

Symbiota Webinar Series