The Macrofungi Collection Consortium

Digitization TCN: The Macrofungi Collection Consortium: Unlocking a Biodiversity Resource for Understanding Biotic Interactions, Nutrient Cycling and Human Affairs (MaCC)

Macrofungi TCN
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Current Research
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PENs

Project Summary

Mushrooms and related fungi (macrofungi) play a critical role in the lives of plants and animals, including humans, yet their diversity is underestimated. Understanding this diversity will be critical in analyzing impacts of habitat change, nutrient cycling in ecosystems, and distributions and diversity of host organisms. Scientists in the U.S. have been studying these fungi for the past 150 years, resulting in a legacy of approximately 1.4 million dried scientific specimens conserved in 35 institutions in 24 states. These institutions have now joined in an effort to digitize and share online all data associated with macrofungi specimens. The resulting resource will enable a national census of macrofungi, never before attempted, and will allow researchers to better understand the diversity of these organisms and the relationship between macrofungi and the organisms with which they form intimate relationships.

Organized into clubs across the country, citizen mycologists play an important role in documenting macrofungi diversity, and these enthusiastic individuals are the conduit between professional scientists and the general public for critical information about wild edible and poisonous fungi. Citizen mycologists will join the collections institutions in this project to help to create the on-line resource. The project will fund two workshops for high school teachers to promote classroom study of fungi. University students employed by the project will gain work experience in digitization and formal training about fungi. Students will share the knowledge they gain through oral and video presentations. This award is made as part of the National Resource for Digitization of Biological Collections through the Advancing Digitization of Biodiversity Collections program and all data resulting from this award will be available through the national resource (https://www.idigbio.org).

Current Research

Herbarium collections of fungi with conspicuous spore-bearing structures commonly known as macrofungi (e.g., mushrooms, boletes, puffballs, club fungi, morels, stink horns, truffles and cup fungi) are the subject of this Thematic Collections Network. We propose to unite established and nascent collections of macrofungi into the Macrofungi Collections Consortium (MaCC) of 35 institutions that collectively will digitize collection information from about 700,000 specimen labels, capture 110,000 images of fungal specimens and digitize about 500,000 critical ancillary items such as photographs, field notes and fieldbook pages. The result will be a dataset of almost 1.4 million enriched specimen records that includes essentially all the macrofungal collections deposited in U.S. herbaria during the past 150 years. The data generated through this project will allow researchers to address the questions: To what extent do the diversity and distribution of macrofungi determine the diversity and distribution of the organisms with which they form commensal or symbiotic relationships, and by extension, how will changes in macrofungal diversity and distribution affect those organisms and ultimately human affairs?

So far, approximately 650,000 items have been newly digitized (includes specimens, specimen labels, photographs, field notes, field book records), and 1,933,000 specimen records have been added to the Mycoportal (http://mycoportal.org/portal/index.php). This total includes specimens digitized prior to the start of this project as well as newly digitized specimens. The Portal contains 54,000 are skeletal records (i.e. locality data yet to be added), 1,824,000 are records with complete text locality information, and approx. 300,000 records have complete locality data with geocoordinates. The MycoPortal also has been populated with 509,000 images (approximately 25,000 of these are living fungi, the remainder are images of dried fungi, labels, and field notes), 41 checklists, including a checklist for North American fungi with more than 15,000 entries). With eight months remaining in the grant, we have already exceeded the number of specimens to be digitized through this project by 50,000, and the Mycoportal contains more than 300,000 more records than originally anticipated.

Three training courses were held at NYBG for 12 participants in the project, and three training courses were held at participant institutions for 10 participants. A 125 page training manual was prepared to guide the training sessions. The procedure manual provides step-by-step instructions for all aspects of the project, with the majority of time spent on learning to set up the camera equipment, capturing images of specimen labels and specimens, creating skeletal records, and uploading data to the portal. Follow up included phone calls and emails with NYBG staff, and sessions via phone or skype with Portal Manager to review data upload procedures for newly digitized data as well as helping institutions to configure existing data for upload. All training documents were placed on the project website for additional reference.

Approximately 200 people have been actively engaged in the Macrofungi Collection Consortium project across the funded institutions, including 42 senior personnel, 32 paid staff, and 126 student workers (or recent graduates). At least 33 presentations or articles have been produced for a scientific audience, and 55 presentations or publications (including blogs) have been produced for a general audience. Instead of developing our own crowdsourcing application, we decided to join forces with Notes from Nature, a Zooniverse crowdsourcing application (13). To date, approximately 50,000 records have been transcribed.

At least 12 presentations or articles have been given to a scientific audience about the project during the period 1 July – 31 March, and 15 Presentations, publications (including blogs) about the project have been presented or published for a general audience. About 200 university students (not including student workers on the project) have attended demonstrations, lectures or tours relating to the MaCC project.

The first high school teacher training course for the project was held at North Carolina State University in Raleigh, NC 5-7 August 2013 for five high school teachers from North Carolina, one Assistant Professor (Dr. Mozley-Standridge) and four undergraduate students from Middle Georgia State College. The workshop taught participants about macrofungi in both the field and the lab, and included training in the use of the MycoPortal, and ways to use macrofungi and the MycoPortal in high school biology courses to meet curriculum standards for North Carolina. A second course for high school teachers will be offered in conjunction with the annual meeting of the Mycological Society of America at University of California, Berkeley in June 2016.

Two PEN awards have supplemented the original consortium: University of Vermont and University of Maine. The project is currently in a one year no-cost extension that will continue the project through June 2016.

Project Websites & Social Media

Mycology Collections Portal (http://mycoportal.org)
Macrofungi Collection Consortium (https://sites.google.com/site/macrofungicollectionconsortium)
NYBG award announcement

Project Leadership

Project Sponsor: New York Botanical Garden (NSF award 1206197)

Principal Investigator (PI): Barbara Thiers

Collaborating Award PIs: Rytas Vilgalys, Meredith Blackwell, Peter White, Richard Baird

Project Collaborators

Map of Collaborating Institutions

College of the Atlantic
Cornell University
Davis & Elkins College
Denver Botanic Garden, Sam Mitchel Herbarium of Fungi
Duke University
Eastern Illinois University
Field Museum of Natural History
Fort Lewis College
Harvard University, Farlow Herbarium (NSF award 1206216)
Iowa State University
Louisiana State University & Agricultural and Mechanical College
Miami University
Middle Georgia State College - E&O participation
New York Botanical Garden
New York State Museum
North Carolina State University (NSF award 1206196)
Oregon State University
Purdue University
Rutgers University
San Francisco State University
State University of New York at Cortland
State University of New York at Syracuse
University of Arizona
University of California, Berkeley (NSF award 1207526)
University of California, Santa Cruz
University of Central Oklahoma
University of Florida, Florida Museum of Natural History
University of Illinois at Urbana-Champaign (NSF award 1205935)
University of Illinois at Urbana-Champaign, Illinois Natural History Survey
University of Michigan (NSF award 1206134)
University of Minnesota, Bell Museum of Natural History
University of Montana
University of North Carolina
University of South Alabama
University of Tennessee
University of Washington (NSF award 1206115)
University of Wyoming
Utah State University
Virginia Polytechnic Institute and State University

Unfunded collaborators:
United States National Fungus Collections
University of South Florida

Publications

1. Heads, Sam W., Andrew N. Miller, J. Leland Crane, M. Jared Thomas, Danielle M. Ruffatto, Andrew S. Methven, Daniel B. Raudabaugh, and Yinan Wang. "The oldest fossil mushroom." PloS one 12, no. 6 (2017): e0178327.
2. Bates, Scott T., Robert M. Chapman, Melissa B. Islam, Anna Schwabe, Erik CP Wardenaar, and Vera S. Evenson. "Phylogenetic placement of the secotioid fungus Araneosa columellata within Agaricus." Mycotaxon 131, no. 1 (2016): 103-110.
3. Dentinger, Bryn T.M., Ester Gaya, Heath O'Brien, Laura M. Suz, Robert Lachlan, Jorge R. Díaz-Valderrama, Rachel A. Koch, M. Catherine Aime; Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life, Biological Journal of the Linnean Society, Volume 117, Issue 1, 1 January 2016, Pages 11–32, https://doi.org/10.1111/bij.12553
4. McCluskey, K., Barker, K. B., Barton, H. A., Boundy-Mills, K., Brown, D. R., Coddington, J. A., ... & Greene, S. (2017). The US Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing. mBio, 8(4), e00982-17.
5. 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.
6. Siegel N, Nguyen N.H., Vellinga E. C."C. Pholiota olivaceophylla, a forgotten name for a common western North American snowbank fungus, and notes on Pholiota nubigena," Mycotaxon, 2014.
7. Nguyen, N.H., F. Landeros, R. Garibay-Orijel, K. Hansen & E.C. Vellinga. "The Helvella lacunosa species complex in western North America: cryptic species, misapplied names and parasites.," Mycologia, v.105, 2013, p. 1275. doi:10.3852/12-391
8. Bruns, Thomas D. “The North American Mycoflora Project - the First Steps on a Long Journey.” The New Phytologist 196, no. 4 (December 2012): 972–74. doi:10.1111/nph.12027.

Professional Presentations

iDigBio Summit V, 2015

PENs

Digitization PEN: Partnership to Existing Macrofungi Collection Consortium--Digitization of an Important Regional Collection of Macrofungi at the Pringle Herbarium

The University of Vermont's Pringle Herbarium (VT) will join the Macrofungi Collection Consortium (MaCC), a Thematic Collections Network (TCN) dedicated to increased understanding of mushrooms and their allies (macrofungi). The Consortium includes 35 institutions' botanical gardens, natural history museums and universities from 24 states. For this project, all 3,000 macrofungi specimens at the Pringle Herbarium will be digitized, and the resulting data and images will be released for worldwide computer access through the MaCC's online MycoPortal and the iDigBio shared portal. The macrofungi collections at the Pringle Herbarium will provide a unique focus on the macrofungi of northern New England and significant representation from the early, poorly documented period from 1840-1910.

Adding these collections to enhance the Macrofungi Consortium will increase the research possible on the impact of macrofungi on their host plants over time and space and how these changes impact human health and economic enterprise. University of Vermont undergraduates will perform the digitization and imaging and in the process increase their understanding of research on biological diversity. The Pringle Herbarium will engage the local community of macrofungi enthusiasts with mushroom identification workshops to stimulate amateur interest in the impact of fungi on human affairs. 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 (iDigBio.org).

Project Sponsor: University of Vermont & State Agricultural College (NSF Award 1401510)

Principal Investigators (PIs): David Barrington

Partnership to the Macrofungi Collection Consortium for the Richard Homola Mycological Herbarium

The goal of this project is to add 8,000 macrofungi specimens from the Richard Homola Mycological Collection at the University of Maine to the Macrofungi Collection Consortium (MaCC). Label information for each specimen will be digitized along with supplementary 35mm color slides, field notes, and scanning electron micrographs of spores. The data and images will be publically accessible through the MyCoPortal and iDigBio websites for research and public use. Student training, course development, and public engagement through workshops are also goals of this project.

A primary goal of the MaCC is to understand the diversity of macrofungi and their symbiotic partners. Additionally, understanding how these attributes, diversity and interactions, have changed over time, and informed human endeavors is critical. Maine covers half of the area of New England and contains a diversity of habitats, including eastern deciduous forest and northern boreal forest, which support a remarkable diversity of fungi. The Homola herbarium contains extensive collections from Maine by Dr. Homola and will fill historical and geographic gaps in the MaCC data. 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 (iDigBio.org).

Project Sponsor: University of Maine (NSF Award 1503574)

Principal Investigators (PIs): Seanna Annis