North Spore was excited to take part in the 43rd annual Telluride Mushroom Festival in Telluride, Colorado late last month. Among the many mycological luminaries present was Alan Rockefeller, a photographer, and expert in DNA sequencing and microscopy. We sat down for an interview to reflect on his 20 years collecting, documenting, and studying fungi predominantly found in North America. This interview has been edited and condensed for clarity. For a full version, check out the video below!
Lou: Thanks for talking with us Alan. Who are you and what do you do?
Alan: I'm Alan Rockefeller and I study mushrooms. Mostly I do photography, DNA barcoding and microscopy. I really like mushroom identification, taxonomy, and documenting all mushrooms, especially rare species or unusual species, or even trying to get the best picture I possibly can of something that's common.
Lou: What got you into this in the first place?
Alan: I think it was Christmas Day 2001, and I was walking through the woods and there were mushrooms everywhere. I was like, “Wow, some of them must be poisonous, some of them probably hallucinogenic, some of them probably edible. There's got to be people out there that know what these are.”
But I didn't know who those people were or how to get a hold of them. So I just started taking a closer look at them. I've always been pretty into nature and doing a lot of hiking, but at that point I was working in tech and I was struggling to justify all the time I was spending in nature because, sure, it's good exercise, but like, what am I really doing with my life out there?
So, I started paying closer attention to the mushrooms, and after a while I was like, “Instead of just like wasting my time walking down these trails, I [should] have a goal.” [That goal became] trying to learn these mushrooms, trying to get the best picture I possibly can of all the mushrooms. And then I felt like I was making really good use of my time in the woods.
Lou: Everybody loves to spend time in the woods, so you found a great way to justify it. And over the years, you've made really significant contributions to the field of mycology. Can you talk a little bit about some of the discoveries you've made?
Alan: You make discoveries every day you're out in the woods.
Once you learn which ones are cool and which ones are rare, which ones have names and which ones don't, you might discover 30 or 50 new species in an afternoon. That might seem like a lot because for a botanist, if they discover two or three new species of plants in their life, that's a good botanist.
What I do like to do, is try to get the best picture I possibly can of it and then release that picture into the public domain. Then get a good DNA sequence that goes along with that collection that I photographed, (and then put that) DNA sequence in the GenBank so it’s publicly accessible forever.
I put these pictures on Mushroom Observer and iNaturalist and Wikipedia. These are like citizen science mycology site. As for Wikipedia, when the general public wants a good picture of the species, they can be confident that it's correctly identified.
I really like to combine the DNA sequence with quality microscopy. So you put that all together and you get a really in-depth picture of what this organism is, and then the next time you see it, you just feel like so much more of a connection to it. It's like seeing an old friend.
Lou: There is a particular genus that you've done a lot of work on that has a lot of meaning for people, and that’s psilocybe. Can you talk a little bit about your work with psilocybe in particular?
Alan: Everybody loves psilocybe because they're mysterious, hallucinogenic and have a lot of medicinal benefit. It's also understudied, especially in the modern sense with DNA sequencing.
There's a lot of [wild] psilocybe out there that we just don't know much about. A lot of species were described 100 years ago and there's no photo of them, or the only photo that exists is black and white. It's really fun to go out to these places where it was seen 60 years ago and get a modern photo of it, get some DNA sequences in the GenBank, and verify that it is what I think it is with some high quality microscopy.
Psilocybe is cool to study for a lot of reasons. One reason is because people love psilocybe and draws a lot of people into mycology. So my main goal with this is to get people more engaged with nature.
And it has this really profound effect. They have to go out into these crazy habitats to find psilocybe. And by the time they find them, they're already hooked on all mushrooms and they start getting really into Russula and Psathyrella because they start to notice the differences between everything.
They realize that the stuff they're seeing in their travels are rare and understudied and it opens up a whole Pandora's box. Many people have told me that I've really changed their life.
Some people say they were on a bad path, maybe experimenting with or addicted to hard drugs, even into crime. But then they started spending a lot of time in nature and it drew them away from all of that. Now, their whole life is about spending a time in the woods, camping, photography, and that kind of stuff.
It's much more fulfilling than a life where you're trying to get high all the time or take things from people or anything like that. It just seems like it's really good for your soul to be out in nature a lot. I think that's encoded into our DNA. Everything humans do is encoded into our DNA, good and bad, but being out in nature, it brings out the good side of humanity.
Lou: Tell us a little bit about how you approach taking good photographs.
Alan: I've been taking photographs since, I don't know, 2003 and all of my work before 2010 is completely unusable. When I'm teaching people how to take good photographs, sometimes I'll search for my early photographs so I can show them what not to do.
I learned to take good pictures just by taking a lot of really bad pictures, and my photos didn't start to turn out the way I really wanted them to until I started focus stacking.
Focus stacking is where you combine a whole bunch of pictures into one final image and it really bends the laws of physics in several different ways. It makes it easy for people who are not experts of photography to take amazing pictures. Before focus stacking, I had to teach people to get the ISO and the aperture just right.
Whereas with focus stacking, you set the camera down, you press the button and then you bring all the images back and put them together in the computer. Even if it's the first image you've ever focus stacked, it's going to look amazing. The reason it looks amazing is because the aperture is all the way open, and the ISO is all the way down.
And of course, it's really important to find good mushrooms. Photograph high quality specimens that are not dried out, ideally in several stages in development. Even if it's just a single mushroom and you're shooting up against the sky, if it's focused stacked and if it's lit right, it'll look amazing.
Mycena sanguinolenta growing on a Pinus radiata cone from the north island of New Zealand
Lou: What does a mycologist need to see in order to identify a mushroom? I've been that person whose sent a picture to an expert and it was a blurry cap. That's how I began too. So what are some things that people should think about when they're photographing mushrooms?
Alan: To actually communicate through photos what a mushroom is, it's important to get a picture in situ. That means before you pick it, take a picture of it.
The second most important thing is the underside (ex. gills, pores, folds, etc.). Just being able to see the underside, especially the underside of a mature mushroom, is impotant [for identification]. When you get the underside, you don't want to cut it off. You want to pop the mushroom out from below. If you just grab the stem you’ll usually leave this big fingerprint on it.
The the gill color of a mature mushroom will match the spore print color, unless it's white spored. By being able to look at a bunch of different mushrooms and see how the gills change color as the spores mature, gives you a lot of insight into what it actually is.
[Lastly] I like to have a few different specimens and a few different stages of development all in one frame. That way you can see in one image all of the different stages of development, how it looks when it just starts out, how it looks when it's like almost rotten, and everything in between.
Lou: Besides photography, you mentioned DNA sequencing. DNA sequencing, along with a good photograph, is the most accurate way to identify and examine fungal specimens. What does this process entail?
Alan: Microscopy is how things used to be identified, but it takes so much time and a lot of experience to get any useful information. DNA sequencing is a much better way to identify mushrooms and it's actually pretty easy. It's more difficult than cooking eggs, but it's easier than baking bread.
[First] I get the best picture I can and then I usually throw it on my dashboard for three or four days until it's completely dry. You can also use a food dehydrator or maybe just leave it in a window depending on what it is.
I like these really quick DNA extractions. I mix up a few chemicals, usually a base like sodium hydroxide and some kind of stabilizers like EDTA (Ethylenediaminetetraacetic acid) and a buffer like tris. [Then] you take just a little bit of the mushroom, maybe just one or two milligrams and put it in a little tube with some of your extraction buffer and heat it up for a few minutes. Then some of the DNA will be in solution.
[Next] you run a chemical reaction called PCR, a polymerase chain reaction. And what this does is it amplifies a certain gene, doubles it, copies it billions of times. The whole genome of the mushroom is like 40 million base pairs long. So it's a book that's 40 million characters long.
You end up with billions of copies of this little gene. And there are certain genes that we use more than others. The most common one is the ITS or Internal Transcribed Spacer. This gene is awesome because it does absolutely nothing, but it's really variable between species. So I take a little bit of this mushroom extract, throw it into a PCR reaction with ITS primers and a couple of hours later it's done.
Then I can either run gel electrophoresis to see if that works or just skip that step and send it off to Sanger sequencing. There are labs all over the country and all they do is Sanger sequencing. They take DNA from all sorts of laboratories, hospitals, and any kind of place that runs PCR. You can run them at home, but it's not recommended because the chemicals are expensive when not buying them at scale and the machines need a lot of maintenance.
What I do is I run PCR - if I run it in the morning, I'll fill out the order form at around noon and then about 2:00 - 3:00 p.m. this guy will stop by my house and ask for the samples and I'll take them out of the freezer and hand them to him. About midnight the results come in and it ends up costing me like $5 or $6 per sample.
That's almost free compared to how cool the data is. The most important thing that it does is that it ties collections together. If the holotype (a single type specimen upon which the description and name of a new species is based) of a specimen has been sequenced and you have a holotype sequence, if your sequence matches the holotype, then you know exactly what it is.
So you're tied together with the holotype. More often, there's no holotype sequence, so it takes a little bit more thinking. What it will definitely do is tell you the thing that you found is exactly the same as the thing that somebody else has found. So you can see where does this thing occur on the map?
Then you can start thinking about what names people usually apply to this and what part of the world that was described from. And if any of your sequence matches are from that part of the world. If they're not, you've either discovered a new species or it's one of these forgotten species. And you can untangle that with microscopy and dig into the literature.
DNA barcoding is really effective but if the DNA barcoding doesn't give me the answer, then I dig into the microscopy. The thing about microscopes is that it’s really time consuming. The way I learned is the wrong way to do it, which is to sit down with the microscope for a couple of hours a day for several years. What you should do is just talk to an expert that can just tell you how to do it or join a Facebook group like Fungal Microscopy or something like that.
But in any case, if you really want the full picture, you mix the high quality photo with the DNA barcode and the microscopic information, and then you really understand what you've been finding.
Lou: Tell us a little bit more about how somebody just getting into this can really make a difference and not just turn this from a hobby into real work that's furthering science.
Alan: That's one of the really cool things about mycology. People that don't have any kind of scientific degree can actually make a big difference because there's so much to discover and there are not very many people that are paid to make these discoveries.
If you want to make a big difference in mycology, all you have to do is go out into the woods and collect mushrooms, but instead of just throwing them all into a basket, you [can] take good pictures of them and carefully document whatever features are there that don't show up in your photograph. That's usually taste, smell, nearby trees, and chemical reactions.
Then, throw it into a tackle box or a Tupperware and bring it back, upload these photos to Mushroom Observer or iNaturalist to create a permanent biodiversity record, and then dry these mushrooms and send them to somebody that does DNA barcoding.
Indigo Milk Cap (Lactarius indigo) photographed by Alan Rockefeller and available on iNaturalist
Once you get the DNA barcode back, you can really see, “How common is it? Does it have a name? Do I have to do a bunch more research on that?” And then for your collections, you can give them to a herbarium (fungarium).
It's a library for mushrooms, but they save dried mushrooms forever. And most things in the herbariums don't have good photos and most of them don't have DNA sequences. So if you can have really good photos and attach a DNA sequence to that, then your herbarium collections will be much more valuable than most of the things that they have.
Very often after you really dig into the microscopy and the DNA barcode, you realize that it's a new species, or maybe it's more obvious than that, and you'll just see it and say, “Yeah it’s a new species.”
You don't have to have any kind of academic credentials to publish a new species. You don't even have to go through a peer review anymore. You can just make a collection, document it really well and go ahead and publish it, and then people will use that name for eternity.
Lou: That's amazing. I hope many more people take that advice and start to do it.
Alan: And that's something we really need done because a very large percentage of mushrooms that we find don't have names and we need names for them because we need to be able to communicate what we found.
For example, say you find this mushroom and you analyze it using analytical chemistry. You run it through a mass spec, you find some cool new medicine or some valuable molecule. You need to be able to communicate which mushroom this is. If it's one of the unnamed species, which is very likely, you can't really communicate that effectively. So we need names for all the mushrooms.
Also just for conservation. If there's a rare mushroom that doesn't have a name, you can't really say, “Oh, this forest needs to be protected because this thing only occurs there.” If you give something a name and then say, okay, this species only has been found in this one little spot, you probably shouldn't chop this spot down.
You know, that actually carries some real weight.
Lou: Do you think you'll be working with mushrooms for the rest of your life?
Alan: I think that's the best use of time for me. You know, I used to do computer security, a lot of breaking into computers and computer hacking stuff and that was really fun. But I did not feel like I was making good use of my time, not really changing the world in any way.
Whereas I think with mushrooms I can make much better use of my time. I could spend a lot of time outdoors. It's a lot more interesting than computers. So yeah, I think I'll be studying mushrooms forever.
Lou: We appreciate the work you're doing. It's making a huge difference. Thank you for talking with us.
Alan: Thank you for having me on.