Evolution of the North American Mycoflora Project
Submitted by: Bill Sheehan and D. Jean Lodge
The North American Mycoflora Project is changing. In August 2020, we will announce a new name and logo, a new DNA sequencing partner with new protocols, as well as a more expansive and inclusive vision of engaging citizen scientists and professional mycologists.
Our mission remains unchanged: to equip citizen and professional scientists with the tools to document the diversity and distribution of fungi across North America. We are evolving to better address our ultimate purpose: to increase awareness of the critical role of fungi in the health of our ecosystems and allow us to better protect them in a world of rapid climate change and habitat loss.
Origin. The original idea for a North American funga was the brainchild of UC Berkeley mycologist Tom Bruns and colleagues. With remaining NSF grant funds they convened a one-day workshop of professional and amateur mycologists at the MSA Annual Meeting at Yale University in 2012 to explore creating a funga for all North American macrofungi. The enterprise was called the North American Mycoflora Project. Funding never materialized but the North American Mycological Association (NAMA) kept the idea alive through a Mycoflora Committee, chaired first by Richard Jacob and then by Stephen Russell. In 2016 Bill Sheehan surveyed all NAMA clubs (half responded) and presented results in articles published in The Mycophile and Fungi Magazine.
. The survey showed considerable interest in vouchering and sequencing within clubs but no coordination between clubs.
Mycoflora 2.0. In 2017, Bruns and Sheehan organized a workshop at the MSA Annual Meeting in Athens, Georgia, to explore reframing the mycoflora project as a co-created citizen science project. After the meeting an independent nonprofit organization was formed, North American Mycoflora Project, incorporated.
NAMP, Inc., launched operations at the start of 2018 with the focus of helping nonprofessional mycologists document, sequence, and voucher fungal specimens to advance Bruns’s vision of a North American funga. We received startup funding for sequencing grants from MSA, NAMA and a generous anonymous donor, as well as individual contributions made on the MSA website and elsewhere. Russell created the technological infrastructure for NAMP, including creating the mycoflora.org website and building up a website, MycoMap, that he had created originally to manage the sequences he was obtaining for the Hoosier Mushroom Society’s Mycoflora of Indiana. Russell, who has since stepped away to pursue graduate studies, also managed initial DNA sequencing for all of NAMP which was done in his home lab and at the academic labs of Cathie Aime at Purdue University, Todd Osmundson at University of Wisconsin-La Crosse, and Rytas Vilgalys at Duke University.
During 2019 we focused on putting our all-volunteer organization on a sound footing by developing an active Board of Directors, recruiting a great team of volunteers, implementing sound fiscal and accounting practices; developing tracking systems for projects, specimens, and orders; and conducting outreach to projects via a newsletter and social media.
Where we stand now. NAMP awarded 65 sequencing grants to 50 projects in spring and fall of 2018. Together with paid (fee-for-service) sequencing, more than 3,500 specimens have been sequenced to date, with results posted on MycoMap (with some also on Genbank and MyCoPortal). Emily Cantonwine at Valdosta State University (GA) directed a student summer project to estimate the scientific contributions of NAMP projects. The team evaluated 1,650 sequences generated by 34 NAMP projects. One finding: of 290 specimens searched in MyCoPortal, 7 had not been reported before on MyCoPortal, 11 were first reports for the United States, and 44 were first reports for the state.
BLASTs of sequences from projects suggest that numerous new taxa await description, but that will require technical expertise by experts. Jean Lodge has analyzed over 50 sequences and also found that some North American species that were previously synonymized under a European name will need to be resurrected (one example here. Lodge and Rosanne Healy started polling experts willing to help analyze sequences; further engagement of mycologists in analyzing sequences is a work in progress.
NAMP has generated a lot of excitement among a broad range of mushroom enthusiasts as evidenced by the number and diversity of projects started. During our first two years we’ve registered more than 160 citizen science projects spanning a broad geographic range from Alaska to Puerto Rico and Hawaii to Greenland. Projects range in scale from local to regional to continent-wide and include forays and taxon-focused projects (such as PNW Cortinarius, Inocybe of Quebec; projects on Russulas, Boletes, Bankeraceae, polypores, crust fungi, and others). Forty-one percent of projects are led by individuals without any organizational affiliation while 35% of projects are affiliated with (not necessarily sponsored by) NAMA or with NAMA-affiliated mushroom clubs. Other affiliations include civic organizations (such as the Great Plains Nature Center, Potter Valley Tribe), educational institutions (such as Valdosta State University, Glen Urquhart School), government organizations (such as Northwest Territories, Florida Department of Agriculture and Consumer Services) and national parks (such as Boston Harbor Islands, Glacier National Park). There’s even a project that aims to find and sequence mushrooms described by Charles McIlvaine around Philadelphia more than a century ago.
We have learned a lot during our first two years. Key challenges that we are now addressing include dependence on volunteers for coordinating sequencing activities; rising expectations without the capacity to communicate effectively with project participants; reliance on sequencing at academic labs that resulted in bottlenecks; and the lack of robust tracking mechanisms to determine which specimens have been accessioned by fungaria, or posted to Genbank or to MyCoPortal. Analysis of 95 Sanger sequences from BOLD indicated we had poor DNA recovery from polypores, corticioid fungi, and some Ascomycetes, so we revised our protocols based on advice from experts. Ongoing challenges include developing a sustainable funding model for core operations and demonstrating the value of citizen science to professional mycologists.
Why “reboot”? We are changing our name because most of the world does not yet know that fungi are their own kingdom, parallel to plants and animals. Which means fungi don’t get the attention and protection they deserve. To change this, we need to stop using language that propagates this confusion, including the term “mycoflora.”
We are also expanding our tent to be more welcoming and accessible to people who love fungi but lack scientific training. We have learned that there are many competent naturalists who are eager to learn about fungi (a number likely in the hundreds of thousands) but are intimidated by the notion that they must learn DNA sequencing and voucher all specimens to participate in NAMP. So, we aim to become a welcoming home for people eager to learn, as a first step, about proper documentation of fungi and posting observations on public, databased platforms. If 100,000 or 1 million citizen scientists learned to take and post geo-tagged field photos, not only would we be building an important body of ecological and taxonomic data, we would also be creating a pool of individuals who will want to learn more about science and move up to the next level. Our goal is to engage many more people, especially young people, in what we’re calling Level 1 activities, and then provide resources and encouragement to those who want to do more complex (and scientifically useful) sequencing and vouchering (Levels 2 and 3, respectively).
We’re working on setting up our sequencing pipeline through BOLD, the Barcode of Life Data system, based at the Center for Biodiversity Genomics at the University of Guelph. Ontario. Initially we are using BOLD’s Sanger sequencing because they can analyze high volumes at low cost with a predictable turnaround time. Our hope is that a partnership with BOLD will clear the bottlenecks we have had with academic labs and offer other advantages such as easy GenBank submission. BOLD is also collaborating with us on a pro bono SMRT Sequel metabarcoding trial. BOLD’s metabarcoding with SMRT Sequel technology yields long reads that include the SSU and much of the LSU in addition to the ITS region, and multiple single-strand reads per specimen which should eliminate problems encountered using Sanger sequencing caused by heterokaryons and non-concerted evolution of ribosomal DNA gene copies. While low-cost metabarcoding could open up a range of new opportunities, it requires large batch (950) submissions in ten 96-well plates. The SMRT trial is being coordinated by Danny Haelwaters and Todd Osmundson and includes a wide range of macrofungal DNA extracts submitted by collaborators that had previous Sanger sequencing attempts (some successful and some failed).
We have new opportunities to partner with professional mycologists. NAMP Board members Bitty Roy and Jean Lodge are collaborating with others on an NSF proposal to engage citizen scientists from NAMP projects to work with mycologists to survey certain NEON and LTER sites for macrofungal sporocarps. Sequences from specimens will be compared with sequences from fungal environmental DNA samples from the same sites to test hypotheses about the ecology, geographic distribution and evolution of sexual versus asexual forms. In addition, a newly funded NSF grant to Matt Smith and Gregory Bonito includes training for citizen scientists to collect Pezizales across North America.
The future. We live in exciting times. Citizen science has taken off in a major way; platforms such as iNaturalist and eBird demonstrate that hundreds of thousands can participate in documenting the ecosystems around them. This is amplified by other advances in technology, whether it’s increasingly sophisticated smartphones or home PCR labs. And in a world where life is increasingly lived indoors and spent in front of screens, people are more compelled than ever to escape and spend time outdoors, engage with the natural world and help protect it.
While these are tailwinds that will add to our momentum, we are also propelled by a sense of urgency. Fungi are the cornerstone of many ecosystems, and changes in their distribution and incidence can be signals of habitats under threat or the results of climate change. Conservation relies on these kinds of data points. What’s more, the overwhelming majority of fungi have not yet been described; there are simply not enough mycologists out there able to do the describing and species are going extinct before they can be cataloged. This moment in time marks an opportunity for NAMP to become more than our original vision, to reach a larger audience, and create a greater impact. A rebooted NAMP is focused on harnessing the power of citizen science for fungi. We want to tap into the passion and local knowledge of tens of thousands of volunteers by inspiring them to take high-resolution color photographs and record geographic location and other metadata of the fungi they find. Combined with sharing on the internet and sequencing DNA, this crowdsourced fungal exploration and discovery can have profound consequences. By collaborating with professional mycologists, not only can citizen scientists generate new scientific knowledge; they can also help revitalize the academic field of mycology.