Creating a Local Mycoflora. The eDNA .... Labs: Rytas Vilgalys, Alejo Rojas (Duke Univ.) Todd Osmundson .... Facebook Mycoflora 2.0 Discussion Group.
CITIZEN SCIENCE IS MUSHROOMING! UPDATE ON THE NORTH AMERICAN MYCOFLORA PROJECT Bill Sheehan, Ph.D., President North American Mycoflora Project, Inc
iDigBio Gainesville, Florida Summer Solstice 2018 1
A massive-scale, distributed effort, motivated by passion and use of technological coordination, that enlists citizen scientists, working with professional mycologists, to
document, voucher & sequence all the macrofungi of North America in order to create a continent-wide Mycoflora.
Macrofungi Collection Consortium
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Mycoflora Background Creating a Local Mycoflora The eDNA Conundrum
Plans, Challenges, Vision
Mountain Lake Biological Station, July 2016
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2012 Scientific Goal
Create the first mycoflora for macrofungi in North America
Mycoflora aka Funga, Mycota
• Photos, descriptions, keys • Distribution maps, time of year • Microscopic images • • • •
Online, dynamic & free Links to original observations (MO, iNat) Links to vouchered specimens (fungaria & MyCoPortal) Links to sequences (Genbank) 8
Why is a Mycoflora Important? 1. Macrofungi are Important
Fungi are critical to human well-being Agriculture (pathogens; mycorrhizae) Medicine (drug discovery) Climate Science (carbon cycle)
Fungi provide vital ecosystem services Mycorrhizal fungi are key to plant health. Decomposers drive the carbon cycle.
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Plant Helpers Mycorrhizal
Carbon Recyclers Wood & Leaf Rotters
Why is a Mycoflora Important? 1. Macrofungi are Important
2. Fungi are Understudied
Fungi are critical to human well-being Agriculture (pathogens; mycorrhizae) Medicine (drug discovery) Climate Science (carbon cycle)
Fungi provide vital ecosystem services Mycorrhizal fungi are key to plant health. Decomposers drive the carbon cycle.
McGraw-Hill
3. All biology is built on accurate species determinations 11
• Sequence DNA • Voucher specimens
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The project stalled.
1. Not enough money Estimated cost for professionals to start creating a North American Mycoflora:
$18 million over 10 years
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2. Too many undescribed species • 19,390 described taxa of N. American macrofungi (in 1.7 million macrofungal records digititized, on MyCoPortal)
• 2-4 cryptic species for every described one? > 40,000 species to describe At the current rate of new species discovery, it would take professional mycologists
> 2000 years to produce a comprehensive Mycoflora for North America macrofungi
3. Not enough professionals Mycological Society of America
… “the steady hemorrhaging of prestige, funding and positions from taxonomy for more than three decades” …
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Quentin Wheeler New Phytologist (2014) 201: 370–371
SOURCE: Inoculum, March 2016
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But lots of potential volunteers! Membership of NAMA-affiliated clubs vs MSA 10,200
High Schools & Colleges 963
NAMA
MSA
3 Million students every year 16
Citizen Science Movement Public participation in scientific research
crowdandcloud.org
Distributed Technology 17
Fungi are Perfect for Citizen Science 1. Stationary 2. Can collect ‘em 3. Sequence DNA 4. Fascinating!
http://fungimap.org.au/
Wikimedia Commons
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Mycoflora 2.0 Workshop July 16, 2017
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2017 Focus: Citizen Science
How to make it easy and cheap for amateurs, working with professionals, to document, voucher and sequence fungal specimens.
The Time Is Right • Amateur mycological community is ready
• Professional community is on board • Significant funding is in place • DNA sequencing is inexpensive and readily available
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Mycoflora Background Creating a Local Mycoflora The eDNA Conundrum
Plans, Challenges, Vision
www.mycoflora.org
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MycoMap Project Dashboard
www.mycomap.com
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70 Mycoflora Projects as of 6/17/2018
National State-level Regional County Natural Area Institutions Taxon-focused
1 13 30 4 5 1 16
mycoflora.org/people/participants 25
Mycoflora Fund for Sequencing • General Fund
$20k (MSA) + others
• NAMA Fund
$10k (Stamets) + $10k (NAMA)
• DNA Sequencing
$10-$12 each 4,000 specimens
• First Round
May 1, 2018 - 35 approved x 30 specimens Next Round: Sept. 15th
mycoflora.org/participate/apply-for-funding 26
Which Species Do We Want? “Starting out, we have no formal requirements or recommendations on the species to be selected for sequencing.” - Website FAQ “In the beginning, everything is gold!” - Tom Bruns Clubs & individuals can sequence whatever they want to pay for.
Mycoflora Protocols 1. Document
2. Voucher 3. Sequence 4. Create a Local Mycoflora 28
Mycoflora Protocols
mycoflora.org/resources/protocols
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STEP 1. Document Photograph in the field. Smartphones are good for field documentation. 30
Photograph with numbered field slips
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OPTIONAL: Document at home
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Post photos & notes online Create Species List Export spreadsheet, send with vials & specimens
Join or create Project Export spreadsheet, send with vials & specimens
Fungarium uploads to MycoPortal, which then links back to original observation on MO or iNat 33
STEP 2. Voucher Dry specimens
Print labels
NESCO Professional $68
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Mail specimens & spreadsheet to fungarium Local Fungarium
or
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STEP 3. Sequence A. Collect Tissue Sample, mail to lab Or mail dried specimen (extra $$) Labs: Rytas Vilgalys, Alejo Rojas (Duke Univ.)
Todd Osmundson (UW-La Crosse)
B. Analyze Results on MycoMap.com (largely automated) 36
MycoMap Project Dashboard
www.mycomap.com
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MycoMap Project Dashboard
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STEP 4. Create Local Mycoflora
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Mycoflora Project Types Foray Events
Online Forays
Ongoing Projects
High Schools & Colleges
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A Model for Citizen Science • We’ve developed the least common type of citizen science project in which volunteers are actively involved in all steps of the scientific process (‘co-created’ sensu Shirk et al. 2012) • We’re engaging amateurs in cutting edge science via DNA sequencing. • We’re working with the least studied kingdom of multicellular organisms (fungi). 41
Mycoflora Background Creating a Local Mycoflora
The eDNA Conundrum Plans, Challenges, Vision
eDNA Reveals Stunning Biodiversity eDNA = sequencing all DNA present in an environment
Microbes (bacteria, protists, viruses & fungi)
are ubiquitous hyper-diverse hyper-abundant super-important 43
Phylogeny
You Are Here
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Biodiversity: The New Pie of Life
% Species
Most biodiversity is microbial
Larsen et al., 2017. Inordinate fondness multiplied and redistributed: the number of species on Earth and the new pie of life. The Quarterly Review of Biology, 92(3), pp.229-265.
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Question: What’s the role of eDNA in documenting biodiversity?
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Do Specimens Still Matter? • Most eDNA cannot be associated with known organisms. • “Fresh well-documented specimens remain critical to reconstruct robust phylogenies, link sequence data to morphology, and supply ecological data on hosts and substrate associations.” Truong et al. New Phytologist (2017) 214: 913–919
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Most mushroom species fruit infrequently 21-year Study in Switzerland
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Number of Species
N = 408 macrofungi species 5 plots in 75 ha reserve
50% of species collected only in 1 or 2 years 53 32 18 1
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3
4
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5
20 13
12
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7
8
14
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7
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7
1
10
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Frequency Group Straatsma et al. 2001
Most mushroom species fruit infrequently Number of Species
Wildacres Foray, NC – 19 years N = 1,042 species
57% species collected only in 1 or 2 years
Frequency Group
From Gabrielle Zeiger
Mycoflora Project • Primary value: vouchered & sequenced specimens to build up public gene reference libraries to improve DNA identifications.
• In several years, we may add environmental sequencing to complement specimen-based collecting.
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Take-aways 1. eDNA is needed to fully understand biodiversity. 2. Specimens are needed to make sense of eDNA data.
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Mycoflora Background Creating a Local Mycoflora The eDNA Conundrum
Plans, Challenges, Vision
Next Steps & Future Directions
• Develop online forays • Build expert registry/network • Public launch (beyond clubs) • High schools & colleges • eDNA sampling
Challenges
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Engaging busy experts & professionals (registry)
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Finding sufficient curated fungaria space
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Translating data into new species descriptions & monographs
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Building organizational capacity, including $$
Our Vision
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Enlist and empower citizen scientists to contribute to important conservation work.
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Help Revitalize professional mycology.
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Re-connect people to nature through mushrooming.
Acknowledgements Key Collaborators
Partners & Supporters
Cathie Aime Tom Bruns Rosanne Healy Joan Kutcher Todd Osmundson Alejo Rojas Barbara Thiers Roo Vandergrift Rytas Vilgalys
NAMP, Inc. Board Bill Sheehan, President Christian Schwarz, Vice president Alija Mujic, Treasurer & MSA Liaison Stephen Russell, Secretary
Mycological Society of America North American Mycological Assn. Botanical Research Institute of Texas Fungi Perfecti GenBank iDigBio iNaturalist Mushroom Observer MyCoPortal New York Botanical Garden Radical Mycology
Stay Informed Facebook Mycoflora 2.0 Discussion Group www.facebook.com/groups/mycoflora.2.0/
Email List mycoflora.org/resources/email-list 57