FUNDIS August 2023 Newsletter
Letter from the Director
FUNDIS Friends and Family,
Hello from the Telluride Mushroom Festival! I’m honored to share the fungal conservation progress seen by the FUNDIS team with the Telluride community this year. The high mountain forest precipitates inspiration, fascination, and sustenance for the Kindom of life that we love and respect so dearly.
Last night we hosted our first ever FUNDIS Fundraiser Dinner and Art Auction: a foraged feast for fungal conservation. Support and generosity was astounding. Our hosts
Peter Waldor, Gabriel Waldor, and Lisa Allee offered their serene mountain home for Chef Phoebe Tran to create masterpiece dishes centering around local mushrooms. We are humbly grateful for her and her kitchen staff’s devotion to our mission, as well as for the support from FUNDIS President Adam DeMartino, Art Auctioneer John Michelotti, Brandon Pitcher, event volunteers, and over 15 artists who donated unique items for the cause. Local crafted mushroomy cocktails were donated by Dry Land Distiller, cultivated mushrooms to help fill out the meal (it’s a dry year in parts of the Rockies!) supplied by Mile High Fungi and Fungal Focus, and foraged mushrooms supplied by FUNDIS Communications Lead Mandie Quark, Alan Rockefeller, James Chelin, and CA FUNDIS Collector Taye Bright.
We raised over $5,000 last night during this first ever FUNDIS fundraiser! This will help us document and protect fungi for our California Fungal Diversity Survey statewide initiative and create even more community science resources for North America. We cannot protect fungi without your support, and boy, we felt it last night.
In addition to the Telluride excitement, I’m a excited to share that FUNDIS is opening up FREE DNA sequencing for our FUNDIS Local Projects in a collaboration with Stephen Russell and Mycota Lab. Read the details below and start preparing your specimens! Stay tuned with our newsletter and social media within the next month to learn about how to submit your specimens.
If you’re at the Telluride Mushroom Festival, say hi!
In Fungi,
Gabriela D’Elia
FUNDIS Director
L to R: Alex Blunk (Smallhold Mushrooms), hosts Peter Waldor and Lisa Allee, FUNDIS Director Gabriela D’Elia, Art Auctioneer John Michelotti, FUNDIS President Adam DeMartino, Chef Tiffany Tran, and Chef Phoebe Tran
DNA Sequencing Collaboration with Stephen Russell and Mycota Lab
FUNDIS is proud to announce that we will be reopening DNA sequencing to the public!!! This initiative is made possible thanks to a partnership with Stephen Russell and Mycota molecular laboratory services @mycota_lab provided by the Hoosier Mushroom Society, a non-profit 501(c)(3) organization. FUNDIS and Stephen Russell are currently in alignment for this sequencing initiative, with a co-mission of advancing the knowledge of fungi across North America, particularly progress towards cataloging biodiversity. To get your specimens sequenced for FREE, you can join or start your own FUNDIS Local Project RIGHT NOW, by visiting our website!! Photo credits @mushroom_madman
California Sequencing Update
If summer must have a theme, then let this be the summer of sequencing! Thanks to our Mediterranean climate, most of California sees virtually no precipitation between May and September. The notable exceptions to this being the coast, where enclaves of fog blanket the landscape with a gentle supply of moisture and the high mountains which where afternoon thunderstorms are common in late-summer. As collecting for the CA FUNDIS project has slowed, we have shifted focus towards generating and analyzing the DNA barcodes of our finds.
When the CA FUNDIS project began, we were using Sanger sequencing to generate DNA barcodes, a process which is slow and expensive. As of June, we have officially transitioned to doing in-house sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencing platform. With this platform we are able to generate DNA barcodes for hundreds of specimens at the same time, and for a fraction of the cost of Sanger. While this sequencing technology is not new, it has only been adopted by a few folks in the fungal DNA barcoding circle. To ensure our data quality standards are met, we have generated hundreds of sequences for comparison using both Sanger and ONT Nanopore sequencing.
To date we have attempted sequencing on over 2300 specimens, more than half of our expected total for the project. Our team of Sequence Validators have analyzed and approved over 600 of those sequences. Once a sequence has been validated, we will add it to the iNaturalist observation for the collection and anyone can follow our progress using a custom iNaturalist link: https://www.inaturalist.org/observations?project_id=150883&field:DNA%20Barcode%20ITS=
By analyzing DNA barcode data, we can begin to paint a picture of species distribution across California. Since many fungi are hard to identify by simply looking at them, misidentification is common. Sometimes within what appears to be a single species there are distinct genetic differences that indicate there may actually be multiple species using that name. Case and point, Helvella vespertina, a fairly distinctive ascomycete found in a variety of habitats in California. DNA barcoding was able to show that the ones found growing near oaks (now Helvella dryophila) are very different from the ones growing near conifers. Alas, our sequencing efforts have shown there to be a third member of this group. In this case our Helvella aff. vespertina associates with a very unusual partner. In fact, our CA FUNDIS work has shown there to be a unique collection of fungi that associate with one California's signature plant communities - chaparral. Specifically the chaparral dominated by Chamise (Adenostoma fasciculatum). Here is one of the 4 records we have of this Helvella https://www.inaturalist.org/observations/152337744
In addition to uncovering associations with unique plant communities, we have also surveyed specific geographical locations that have had little fungal collecting work done. Carrizo Plain, a wildflower viewer’s paradise and remnant of California’s mostly-displaced grasslands has yielded some very interesting finds. The Cedars, a desolate and rugged expanse of serpentine soil is home to the wettest Sargent’s Cypress (Cupressus sargentii) forests in the state. Our expeditions there have turned up some really exciting finds. Anyone can explore our project on iNaturalist (https://www.inaturalist.org/projects/ca-fundis) and peruse our collections from these unique places using the map tool.
Harte Singer
FUNDIS Sequencing Lead
Northeast Challenge Update
The Northeast Challenge is ALIVE - and thriving!! This July officially marked Year 2 of the FUNDIS Northeast Rare Fungi Challenge! Now in August, we are nearing the peak of prime mushroom season Northeast North America. The rain has been cooperating nicely this year, with many places receiving ample amounts of rain to support fungal fruits. So, if you are a local Northeasterner please keep your eyes peeled for interesting fungal species, especially those in our Rare Fungi Challenge.
If you think you found a target species in the NE Challenge please add your observations to iNaturalist. Our Challenge will automatically register any observation that is IDed as a target species. Consider creating other observations of nearby fungi in the same critical habitat. And remember to always obtain permission to foray on the land, whether from the property owner or your local forestry authority. See the photos below of NE Challenge species Boletus purpureorubellus found last summer in New Jersey (iNat ID: 135063897) by Keara Giannotti
We are also excited to announce our new Northeast Rare Fungi Challenge Coordinator is Hannah Huber, who we are currently welcoming to the team. In the future she will be tasked with updating you about current news and happenings in the Northeast. Stay tuned for some cool updates about rare fungal finds in the Northeast from Hannah!
West Coast Challenge Update
A species from our West Coast Rare Fungi Challenge was recently found! Hygrophorus goetzei, commonly known as the Rosy Snowbank Wax Cap, is only known from hemlock forests near snowmelt in California, Oregon, Washington, and Vancouver BC in Canada. Last month FUNDIS Collector Luca Hickey @species.i.see uncovered this elusive gem at the summit of Etna Mountain! Their original field description (iNat ID: 166633852) is as follows: “In mixed age Tsuga mertensiana forest at the uphill edge of a receding snowbank. Pileus light pink, sticky-tacky. Lamellae thick, off-white to pale pinkish gold, decurrent. Stipe light pinkish, dry.”
This graceful little pink mushroom has been a sought-after species among mycologists, and is 1 of 20 species in the FUNDIS West Coast Rare Fungi Challenge. These 20 fungi are rare, under-documented, or potentially threatened species that are of great importance to conservationists. Luca's discovery of Hygrophorus goetzei marks a breakthrough and adds to our collective knowledge of fungal diversity in western North America.
Interview with a Sequence Validator
Sequence Validators working for FUNDIS have the job of taking the DNA sequence data that is the result of DNA barcoding efforts and making a determination about sequence identity. They first clean up the sequences to make sure the data seem reasonable, which might differ based on the method of sequencing (whether Sanger or Nanopore). They then run the clean sequence of DNA bases through a program called BLAST so they can see how the sequence of the fungus that they are working with relates to other species that have similar sequences. The Validator can then make an intuitive determination of the species based on many factors including morphological similarities and geographical location of the specimen. Even if the sequence is a 100% match to a ‘known’ fungus in the database, the validator should continue to investigate if the researchers who uploaded the sequence match are trustworthy, and if the meaning they ascribed to the sequence seems realistic. The Sequence Validator role is best fulfilled by someone who is comfortable investigating and using their intuition to make a best guess for species determination using all of the available data.
With that being said, we are pulling back the curtain to show you one face behind our sequence validation work. Now presenting a conversation between FUNDIS Communications Lead Mandie Quark and Sequence Validator Scott Ostuni.
Mandie: So I just want to start off with your experience before FUNDIS. You came into the Sequence Validator job already knowing how to process DNA sequences, right? Tell me how your interest was sparked.
Scott: Yes, I got into looking at DNA barcodes last year after I was hunting a bunch of interesting mushrooms and decided to send some off for sequencing. I was finding these crazy albino chanterelles with a friend and I contacted Alan [Rockefeller] and he said to send them to Alvalabs. At the last minute I decided to send another mushroom, a Psilocybe, which ended up with a really cool result when they ran the ITS sequence [universal barcode for fungi]. Turns out it was a new species only found in Florida, that I ended up naming Psilocybe niveo-tropicalis. So I started editing the sequence data because I was seriously interested in this species. Then I got more genes [than ITS] sequenced and learned how I could make contigs [put the forward and reverse reads together] and read the data myself. After that I caught the sequencing bug and started collecting a bunch of other mushrooms to send off for sequencing. When the data came back I didn’t have anyone to interpret it for me, so I started to learn how to do it myself.
Mandie: So, you have no formal scientific training? No advanced degree?
Scott: I do not. Just the passion to learn and discover more about the fungi I find in the wild.
Mandie: Cool, that’s really interesting! And likely very inspirational for our audience to read. You’re a great example of a community scientist in action.
Mandie: So, how did you hear about the FUNDIS Sequence Validator job?
Scott: I saw it posted on social media. When I was hired I had been following FUNDIS on Instagram for about a year.
Mandie: Cool, that means my posts are reaching the right people! So, do you know how many sequences you’ve validated since you were hired [in May]?
Scott: 200 so far
Mandie: Excellent work, Scott! So what has been an interesting part of the Sequence Validator job, or something that you didn’t expect?
Scott: The whole process actually has been new because we are using Mycomap BLAST, which I wasn't using when I was doing this on my own. But, after using Mycomap, I can now see that NCBI BLAST is outdated.
Mandie: So, just to be clear, you’re doing this work for CA FUNDIS, but you’re also still sequence validating in your spare time?
Scott: Yes, and that's what makes the FUNDIS job accessible to me. I like it enough that I am willing to do the work in my spare time, as well as on the clock for FUNDIS. I live in Florida, but as you know the work for FUNDIS is specifically focused on mushrooms in California, because that is where our research project is being conducted. But I am also going back and validating sequences from iNaturalist observations in Florida, just for fun. I filter the Florida observations by ones that contain ITS barcodes and I noticed that people (probably graduate students) have added ITS data to their observations and then never validated the sequences. So I am running the same FUNDIS protocol for these cool unidentified things in Florida and I am able to identify mushrooms that were never identified before. This is just in my spare time in addition to my work for CA FUNDIS.
Mandie: Wow, what a service you are doing for the Florida community! And the mycology community in general. Thanks Scott!
Scott: You’re welcome!
Mandie: What are some cool things you have found out since you have been exploring the DNA sequences generated from California fungi?
Scott: Well there is this Clitoboid mushroom (iNat ID: 145988498) going under the name Leucocalocybe mongolica could potentially be a misnomer. FUNDIS is interrogating this further, although this is not something I have worked on directly. Another cool Gymnopilus collected a few weeks ago (iNat ID: 148506957) matched 100% with collections from the East Coast that were found across the state of Pennsylvania with the provisional name sp-PA01. Wood lovers can grow throughout the US and this is a wood lover [a similar ecological niche as the aforementioned Psilocybe Scott named], but it is neat to find 100% sequence matches on both coasts because it doesn’t happen super often.
Mandie: Anything else of note?
Scott: Well, there was that cool one that I told you about last week. The range of Galerina castaneipes was extended to California, when it was only previously known from Oregon and Washington. But honestly, new stuff is coming out all the time. Recently I found a 100% sequence match between two species of Leptonia that look completely different, a thin dark purple one and a bulky pink capped one that’s triple the size. In that case, it may be that only microscopy could be used to more reliably determine the species identity.
Mandie: Are there any weird parts about the Sequence Validator job?
Scott: Yeah, it's kinda like virtual speed dating mushrooms - haha! I don't actually know a ton of West Coast species, so there is a certain dissociation between the mushroom in the field in California and me sitting here at the computer in Florida. What adds to the dissociation is that many of these mushrooms only have provisional names instead of species names. But I am grateful to be learning a lot- more everyday. It’s like a 2-way street because I am exposed to stuff [California fungi] that I wouldn’t normally ever stumble upon in my everyday life. So I am able to familiarize myself with new genera which adds to my knowledge base. And the way the other side of the street runs, the new-to-me California mushrooms I am familiarizing myself with are helping me better identify the mushrooms I do encounter in daily life on the East Coast.
Mandie: What else do you like doing?
Scott: Well, I live in Florida, but I love going mushroom hunting in WNC in the summertime.
Mandie: No way, I love West North Carolina! It's one of my favorite places, and the fungal diversity is off the chain!
Scott: You're right, and I feel like it's the best when I randomly drive up there with no planning. Florida is so hot in the summer and the mountains of WNC are a great place to escape the heat.
Mandie: Random wrap-up question - what's your favorite color?
Scott: The color of the next mushroom I see!
Mandie: Great answer