We all know what DNA is but what is eDNA?
Described as another tool in the toolbox for wetland ecologists, we find out in this episode's conversation with Jenet Dooley from the Alberta Biodiversity Monitoring Institute and Brian Eaton from InnoTech Alberta's Environmental Impacts team, it's more than that. It's an emerging technology that at its most basic level it's a process and technology for detecting animal species; but it's also the means to more effectively collect and contribute to a vast library of the DNA of the varied animals, elusive and common, that inhabit Alberta's wetlands.
As with most emerging technologies, all of the eDNA applications have yet to be determined. It's up to the entrepreneurs out there to see how it can be used!
Jenet has been the Wetland Ecologist at the Alberta Biodiversity Monitoring Institute since February 2019. Prior to working at ABMI, she worked as a consultant applying the Alberta Wetland Policy. She periodically teaches Freshwater Ecology and Management at the University of Alberta Augustana campus. She earned her doctorate at the University of Florida in 2016 and has a bachelors of environmental engineering from Miami University in Ohio. Her graduate studies focused on wetland ecology and the relationship between noise and land use intensity.
Brian is an ecologist with research experience in terrestrial and aquatic systems, examining pure and applied questions across a wide array of taxa. He has 25+ years of experience in applied ecological research, including studies in oil and gas, forestry, and agricultural systems. Brian has worked in a variety of experimental venues, from aquaria to large-scale mesocosms to purely field-based research, including wetlands, lakes, streams, rivers, and a variety of terrestrial habitats. Most recently, Brian and his colleagues have been exploring the use of environmental DNA to detect species – including fish, amphibians, semi-aquatic mammals, and invertebrates - in aquatic systems in Alberta. Brian manages the Environmental Impacts Team at InnoTech Alberta.
Learn more by reading the CBC article on the elusive tiger salamander.
Jon: On today's episode, we're featuring Brian Eaton from InnoTech Alberta and Jenet Dooley from the Alberta Biomonitoring Institute. We're going to be talking with Brian and Jenet about an emerging technology called eDNA, which is another tool in the toolbox for wetland ecologists and their study of animals in Alberta. This a fascinating conversation that takes lots of twists and turns. So hang tight, welcome to Shift.
Brian, why don't you tell us what eDNA is?
Brian Eaton: Okay. eDNA stands for environmental DNA. It's the idea that you can collect samples from the environment, from different media, such as water or soil. What we're doing is capturing fragments of DNA that are in that environment and they might be still in cells. You can think of bacteria. You can think of small plants, other types of small multicellular organisms, like zooplankton, and some of the DNA might be in cells that have started to break down. You actually get fragments of DNA that are floating free in solutions. So there's ... it's a mix of things. It's quite complex. What we try to do with eDNA approaches is to collect that material and then we run it through a series of molecular analysis steps to try and relate those fragments back to specific species through using things called primers or probes.
Katie: What's the application for eDNA? What is it being used for?
Brian Eaton: eDNA can be used for lots of things. Right? It actually is a fairly new technology and we're still finding new ways to apply it. Some of the simple things that have been done are to look at single species that are of interest. Say rare species or elusive species that are hard to sample in other ways. It can also be used for things like invasives, because if you can detect an invasive species early in the invasion cycle, it's much easier to control than later on when it becomes more prevalent. Think of the pine beetles that got into Alberta and how much they ... how quickly they spread. If we'd been able to detect them very early on in the invasion cycle and then try and control them, that might have been a less impactful event in Alberta.
Katie: I think it's really fascinating that we can detect all that just from a sampling in the water. There was an article out this past summer about salamanders, and I actually had no idea we even had salamanders in Alberta. What other kind of things are you guys using this for other than species detection and working with the ABMI and Jenet?
Brian Eaton: Yeah. We've worked on a number of different projects around eDNA, but we're just really starting to get into it. We've looked at fish communities, for example, in compensation lakes up north. The idea being that when you have an impact in some of these areas, you have to build a lake that compensates for the habitat that's been lost. Then how do you sample to see if the appropriate fish species have gotten into that lake and are actually thriving. Traditional sampling can detect some of those fish species quite easily, but other ones that occur at low levels of abundance can be very difficult to detect. You can actually have a negative impact on the fish population as a whole, when you're trying to use things like nets or electofishes or whatever, to try and figure out if the guys that aren't there in great abundance are actually there. eDNA allows you to actually sample for organisms without actually ever seeing or interacting with the organisms. For things that are sensitive, it provides a much safer way for them and for you to do some of that sampling and detection.
Katie: Is it possible that we have species in Alberta that we don't even know exist?
Brian Eaton: Yes.
Brian Eaton: Particularly in terms of invertebrates and things like that. I don't know if you know, but there's way more invertebrates than vertebrates, so things like insects and spider and things like that, very many more species than things with backbones. The invertebrates in the world are only partially described at this point. We don't even know what proportion. But if you think about the tropics, we think there's huge percentages of species running around down there that haven't been described by science. I think Jenet is nodding her head so she agrees me.
Katie: Yeah. Jenet, what do you think about this?
Jenet Dooley: Yeah, I was just going to say, even without using eDNA, using our traditional monitoring methods at the ABMI, we're finding new species all the time. Especially like Ryan was talking about, mites, aquatic macroinvertebrates, the little buggy things that people aren't looking at all the time, we're finding new ones to Alberta every year.
Jon: Now when you say more traditional ways of monitoring, what are some of those more traditional ways as opposed to eDNA?
Jenet Dooley: Yeah. I've heard eDNA referred to as remote sensing, even just, because what Brian was just saying, it's a non-invasive way of monitoring species. You don't have to interact with them directly. Those traditional methods you are. You're actually sending people out in the field to directly observe the presence of those species.
Jon: I see.
Jenet Dooley: Or collect them and then bring them back to a lab to have more in depth taxonomic identification.
Jon: I get you. The eDNA analysis then is just ... is it essentially just taking a scoop of water and then analyzing it offsite?
Jenet Dooley: Yeah. A scoop and a filter, I would say.
Jenet Dooley: You've got to pull that material out of the water and then you're left with just filter paper to transport and to preserve.
Jon: The filter paper then has those little bits of DNA?
Jenet Dooley: Yep, that's right.
Jon: Give us a sense of how many different beings are in the DNA that you're finding. Is it two, three, dozens, hundreds?
Jenet Dooley: Hundreds. I'd definitely go with the hundreds, depending on where you are, but for sure. Our wetland environments are very biodiverse, hundreds of different macroinvertebrates just in one wetland. Then you think of amphibians, waterfowl, there's ... even your mammals are coming and drinking out of that water and interacting with the water. Right? So hundreds of species.
Katie: Let's talk about the ABMI then. Jenet, why don't you tell us what is the ABMI, and what are you guys working with InnoTech and Brian on?
Jenet Dooley: Sure, yeah. ABMI is the Alberta Biodiversity Monitoring Institute. We have a rich history of studying the biodiversity across the province using many different methods. We look at things from mammals, big moose, all the way down to the macroinvertebrates in the benthic areas of wetlands, like I mentioned. We've been doing it for about 15 years. Every year we're out sampling a couple hundred sites across the province and collecting data on all these taxonomic groups.
Katie: The great thing about the ABMI too, is that you guys are neutral parties, right? You're not political in any way, you're not affiliated. When you guys are helping organizations like InnoTech or any land developers or whatever the case is, you guys are really bringing a neutral party and a unbiased opinion of what's going on in the land to the table.
Jenet Dooley: Yeah, that's right. We collect all this data across the province and then there's a group of us at the ABMI that analyze that data. We're publicly funded from the province so we are just telling you what the data's saying. We're not ... we don't have specialty groups that are paying us to look at things in a certain way. We have standard methods that we follow. No matter what the question is, we're still using the same methods. Yeah. That's one of our core principles. We aren't adding opinions, we're scientific ... we stay scientifically credible and neutral.
Jon: Just the facts.
Jenet Dooley: Just the facts, that's a good way to put it.
Jon: Okay. Brian, why don't you tell us a little bit about the collaboration between InnoTech Alberta and ABMI in the context of this eDNA work?
Brian Eaton: Sure. I'd just like to back up a little bit and say that the ABMI has been an organization that has adapted new and emerging technologies as they make sense for the work that they do. Early on in the program, 15 years ago or whatever, they were doing winter track counts, for example, for mammals. They've since transitioned to things like wildlife cameras. They used to send people out to listen to birds at dawn in July, which is three o'clock in the morning, four o'clock in the morning. Right? Which is crazy. Now they use automated recording units that actually automatically record bird song at certain times of the day, for months. Then they can go back and retrieve those. This organization, or this Institute, has been very good about adopting and assessing new technologies to include into their program. I think that's great.
Jon: It's fascinating.
Brian Eaton: It's important, right?
Jenet Dooley: Well, it's in our interest. We've got a big province to cover.
Jon: Sure. Who wants to get up at three o'clock in the morning?
Jenet Dooley: That's right.
Brian Eaton: I used to be in camp with birders. I hated those guys because I would get up and do my stuff at nine or 10 and they would come, get up at three o'clock in the morning. Quads would start, wake us up. It was nasty.
Jon: Oh wow, okay.
Brian Eaton: Yeah.
Jon: They're just hitting the sack when you're getting up?
Brian Eaton: Yeah. I should have gone and shooken their tents every day or something just to wake them up somewhere.
Jenet Dooley: [inaudible 00:10:05].
Brian Eaton: They would go to bed about six in the evening. Yeah. I would say up till midnight. Anyway. Yeah. The idea that ABMI likes to assess new technologies that may be adaptable for their needs is what's really led us to this collaborative project. Right? It's the idea being that eDNA is an emerging technology. Although the term was first used, I think in 1987 in a scientific paper, it actually wasn't applied to things like freshwater ecosystems and tried to understand macroscopic life, so big things, until the late two thousands, 2008, 2010 area. it is a relatively new application of this emerging technology. Because technology keeps changing, it's allowing us to do new things that they couldn't do back then when it was originally conceived. Right? Now this collaboration is about looking at how eDNA can augment or compliment the work that ABMI is doing already. Right?
We actually have started by looking at amphibians as a target group. There's a couple different ways to do eDNA and one is to look at specific species. You might have five or 10 species that you're interested in. We use a certain approach to look at that. We develop primer sets for each species. We'll collect our sample, we'll run it through a certain analysis and then we'll be able to tell if one or more of those species is present in a site. Right? That's where we start.
Jon: Can I interject real quick?
Brian Eaton: Yep.
Jon: Okay. So you've got these five or six species that you have in mind that you're going to look at. Then earlier on, you guys mentioned that when you're scooping up the water and filtering it and analyze it, you're discovering new invertebrates and new vertebrates. Do you discover new vertebrates too? New ...
Brian Eaton: There's actually two-
Jon: ... mammals?
Brian Eaton: Yeah. There's two different approach, two major approaches, to analysis. One is to develop primer sets for a target species. Even though you have DNA from say a thousand individ ... or a thousand species in a sample, you would only pull out the hits for those target species that you're looking for. Right? The other approach is to use something called high throughput analysis or high throughput eDNA analysis. The idea there is that you would use what's called a universal primer and you might look for all the fish or all the mammals or all the invertebrates, right?
Jon: I see.
Brian Eaton: From that sample. But it's done in a high throughput way.
Jon: It's through that high throughput where you'll find those anomalies, so to speak, that we've ... this is a new species.
Brian Eaton: A new species to Alberta. One thing that does rely on is having a library of information about the different species that might be in the sample. For instance, if a species was found in Ontario and has never been found in Alberta, but we have the genetic information about that species in our library, when we do that bioinformatic step at the end of the analysis, then that would pull that out. If it's a species completely unknown to science, we'd just get a ... well, we wouldn't know what it was. Right? Somebody would have to try and find it and then describe it.
Jon: Has this happened?
Brian Eaton: I actually don't know. I'm pretty sure that range extensions have been ... they've found places where species have occurred in new places when they've been known somewhere else. I'm not sure that eDNA has ever been the basis for looking for a new species or not, to be honest. It would be interesting.
Jon: It'd be fascinating. Yeah. Yeah, no kidding.
Jenet Dooley: There's a lot of work happening now just to get that library and that catalog of genetic material for all the species we already know about. That's actively happening now.
Brian Eaton: Yeah.
Katie: The purpose of that, Jenet, then ... to have this library that exists, what would it be used for?
Jenet Dooley: It would be used in the analysis that Brian's talking about. You have to have that library in order to get the hit from your sample.
Jenet Dooley: Basically you're matching up the library sample and the sample from your environmental sample to match them up.
Katie: In my mind, you were talking about this library and because my little boy, my son, is obsessed with dinosaurs, what's coming to mind right now is the potential for Jurassic park to happen. Are we using this library for anything other than just awareness or to pinpoint where these species are? Is there potential to use this beyond that? I'm not talking about the Indominus Rex, but-
Jon: Yes, you are totally talking about that.
Katie: Okay, kind of.
Jenet Dooley: Yeah. Brian and I were talking about this recently, that there is potential to look at historical records through cores, through sediment or ice. As long as you have the DNA record for those species that are present from the past, you could look at a historic sample. Take a core in a lake, then you're getting ... at the very top, you're getting samples from very near history, what has recently been in the lake. But the further you go down in that core, the longer ago those species were present. You can start to get-
Jon: Right. Is that how you guys are building your library then? Taking core samples and going, okay, here's most recent DNA and then going back?
Jenet Dooley: I mean, the ABMI is currently involved in helping add to these libraries, but we're doing that with samples that we have from our traditional methods. I'm talking about macroinvertebrates a lot, which is interesting, but-
Brian Eaton: Because they're cool.
Jenet Dooley: They are cool and they don't get enough attention so I'm happy to. But in our traditional sampling methods for macroinvertebrates, we're taking nets and going out into the wetlands and actually scooping bugs up, putting them in jars, bringing them back to the lab and then identifying them. We still have all those samples from these years and years of sampling. We have all those bugs in jars. We're actually going back and these libraries of genetic material if they're missing the DNA sequence for specific species, and we have a sample of it, we're sending them that, the biomass from the actual species, which then can be analyzed to get the genetic material.
Jon: So you can fill in those missing spaces?
Jenet Dooley: Yep.
Jon: Okay. That's for the macroinvertebrates where you're saving the bugs, but those microinvertebrates is ... am I using that ... is that the correct term? That's what we're picking up with the eDNA, the water and the filters?
Brian Eaton: Well, the eDNA, the filters will pull out zooplankton, I think that's what you're talking about. Things like that, small stuff, but it also pulls out any DNA that's been shed by macroinvertebrates, by amphibians, by birds, by mammals. Some of those cells could be in feces, when you urinate. When frogs go and reproduce in wetlands, there's a bunch of gametes running around by themselves, right? Blah, blah, blah. There's lots, of course, different types of DNA.
Brian Eaton: What Jenet is talking about, for example, is building that library. The way this was explained to me is if we're doing high throughput analysis, and we're looking at community level or information, for example, say you had a universal primer for birds, and you can think of all birds having these areas of DNA that are conserved. They're the same for all birds. I think of them as bookends. If you look at a bookcase and it has multiple shelves and there's a shelf for birds and all those birds would have the same book bookends, right? Then the stuff in between varies. You can think of those pieces of information between as different books. You'd have different titles, right? You might have 30 titles within that area and they're all birds, but they're different birds, right?
Jon: I see, okay.
Brian Eaton: Some of the books might not have titles yet and they need to get titled, right? Then you'd have a shelf for mammals, a shelf for birds, a shelf for invertebrates, a shelf for fish, right? That's how that piece works. That's a different approach than the targeted individual species approach. It's more expensive, but it's less expensive per species once you get to about 15 species or more. Right? Then you can actually start to look at whole communities and say, we've detected all the fish for which we have information about those DNA fingerprints, for example, instead of saying, well, we're going to look for pike and stickleback. Because then if you did the community level analysis, you get pike and stickleback and Fathead minnow, and blah, blah, blah. You get all these different species potentially if your primer's a good one or your universal primer is a good one.
Jon: Okay. I want to step back here real quickly, because I still don't fully understand the partnership between ABMI and InnoTech and what we're doing and what the objective is here.
Jenet Dooley: Okay.
Jon: Jenet, I want to take-
Brian Eaton: [crosstalk 00:19:04] science. Yeah.
Jon: No. Oh, it's fascinating. It is absolutely fascinating. But I really want to get to that crux of the biscuit here, what the two organizations are doing. Jenet, you want to take a crack?
Jenet Dooley: Sure. I'll take a crack. Basically COVID shook everything up at ABMI. We weren't able to do our normal monitoring. We usually hire 30 to 40 field techs and house them throughout the summer. They have two weeks of training. They're in close quarters for a long time and then they're traveling across the province together to do this monitoring work. Well, when COVID happened, we knew we weren't going to be able to do that safely. We were looking for alternatives, projects that we could do safely without our field techs that we weren't able to hire that year.
Our first thought was to use ... to do projects that are using technologies that are remote or you don't have to directly observe like the ARUs, the autonomous recording units, or camera traps that we talked about earlier. These are technologies that ABMI already had in place. They're good candidates to use for projects because you just have to set them out, they do their thing, then at the end of the sampling period, you go and pick them up. A lot easier to do under COVID conditions.
We usually target birds with our ARUs. Throughout the years we've picked up amphibians because they're calling too. If you just have something out there recording all the sound, you're going to get everything that makes sound. We have some data on amphibians, but we haven't really focused on them as a target of our monitoring. We saw that this opportunity with COVID, it was an opportunity that we could really-
Jon: Was a silver lining?
Jenet Dooley: It was a silver lining. We could focus on amphibians. We made working groups to come up with projects and we invited Brian to be a part of our working group because ABMI and InnoTech actually have a longstanding partnership. InnoTech is a, or ABMI I guess, is a remote organization. We have people that are housed under other organizations, but collectively we're ABMI. InnoTech's one of those organizations. We already have a longstanding partnership. Somebody at ABMI knew of Brian and his expertise with amphibians and brought him in on the working group. Yeah, that enabled us to come up with this project where we were pairing ARUs and eDNA at wetlands around Edmonton to see what we picked up on with each of the technologies and how they compared.
Katie: You know-
Jon: Enters the Tiger Salamander.
Jenet Dooley: That's right. That's right. The popular Tiger Salamander.
Katie: Jon, as Jenet was talking, you know what I was thinking about? Do you remember our interview we had with Copperstone Technologies, Craig Milne, and how he uses a helix robot to enter areas that are dangerous for-
Jon: Difficult to traverse for people.
Katie: Yeah. He uses it with mining and stuff. To me, that's what was ... I was putting all this together in my head. The helix robot and the work that the ABMI is doing, the two of them and maybe that technology could come together somehow. Anyway, sorry, that was just a shameless plug for our listeners.
Jon: Are you listening, Craig? Craig Milne from Copperstone call Brian and Jenet.
Jenet Dooley: Yeah, let's get some robots going here.
Brian Eaton: We have explored the idea of using drones and things to collect samples too. There's actually a drone boat that somebody built, so it could suck up water samples and then it's actually got this plastic hull that you can replace and put a new one in so it's not contaminated, like a hull condom, I guess, kind of thing. Right?
Jon: Sure. That's an interesting way of putting it, but yeah, I get that. That makes sense, right? Because you hear, when you take your boat out of the lake and then you bring it back home, you should wash the hull because you're going to be carrying things, and they could be invasive things, to new wetlands or new water ecosystems. One of the fascinating things about this was that discovery of the Tiger Salamander and how rare that is. These are cute little beasties. I saw one when I went for a walk down by Fort Saskatchewan and they're amazing looking little guys. I don't know much about them. I wouldn't let my son touch them just because I don't know why. But what other sorts of animals are you guys finding that are unique and maybe seldom seen? Any Yetis, unicorns?
Brian Eaton: Hard to get a primer for those, you need tissue samples.
Jenet Dooley: That's right.
Brian Eaton: If you've got a preserved unicorn somewhere, we might be able to do something.
Katie: This brings me back to the dinosaur question, right?
Jon: Full circle.
Brian Eaton: Interestingly enough, early on in the whole eDNA thing, one of the first applications was to look at reconstructing what they call paleocommunities. They were looking at Ice Age mammal communities using cores through glaciers or permafrost to collect information. They were actually able to find or demonstrate that Wooly Mammoths, for example, existed, I think it was 10,000 years later in the cycle or 5,000 years later in the cycle than they thought. They thought they'd gone extinct before that. That's one application. I don't think dinosaurs work because I don't think DNA was preserved from back then. But if you have things that are preserved deep in glaciers or permafrost, you can actually reconstruct some of that information.
Katie: Well, and it has me thinking about our-
Katie: ... the animals that are going extinct right now. Right? How can we use the DNA, this eDNA, to maybe preserve those species?
Brian Eaton: eDNA is an application related to genetic information, but it's more about detecting species that we have now. It's not about genetically engineering to bring species that are extinct back. I mean, there is some work that's been done like that I believe. Right? Trying to bring back some species that have been more recently exacerbated or extinct, but that's not what the point of eDNA is.
Jenet Dooley: But it could be very helpful in those situations where you do have a rare species that you're not sure if it's present or not.
Jon: Oh, okay.
Jenet Dooley: When you're getting to the point where a species is almost extinct, it's never black and white. It takes a while to decide, okay, it's officially extinct, because you're not sure if it's there or not.
Jon: Well, now that raises an interesting ... I'm sorry, go ahead, Brian.
Brian Eaton: Sorry. I was going to say it could help you identify habitats or areas where that species is still existing and protect those too. Right?
Jenet Dooley: Right.
Brian Eaton: You could use it in that kind of management.
Jon: That was going to be my question. Right? Can you determine concentrations of specific animals based on the sample you take?
Brian Eaton: People are working on that, relating the genetic signal to relative abundance of the organisms that left that signal behind kind of thing. I would say there are large error bars right now.
Brian Eaton: You might get some kind of very gross ... I don't mean gross, coarse estimate of relative abundance, so there's more here than here. We're actually doing some work with ABMI looking at whether we can use information we collect by collecting macroinvertebrates and turning them into a milkshake and then counting how many fragments of DNA we can attribute to each organism and seeing if that relates back to relative biomass. It's a little different.
Brian Eaton: Yeah. It's cool.
Jenet Dooley: To be clear-
Katie: Bug milkshake?
Jenet Dooley: No milk involved.
Jon: Okay. This is just a metaphor then?
Katie: Just ground up?
Jenet Dooley: Yeah.
Brian Eaton: This is a little different than ... anyway. It's not taking an environmental sample. It's taking a sample of the actual animals, but it does allow you to use high throughput to say what species are in here. There might be 20 or 30 or 40 different species. Right now somebody's got to sit down and try and identify them down as far as they can, in terms of kingdom, phylum, class, order, family, genus, species. Often it's hard to get down to species, for example. If an organism is young or damaged, you often can't get down that far anyway. I've been told they can only identify maybe 30%, 40% of a sample down as far as they want to go. Whereas if we can use high throughput and we have good genetic information about the different species in question, then we may be able to identify a much larger proportion of that sample using high-
Jon: High throughput is the milkshake metaphor?
Brian Eaton: Yes.
Jon: Ah, okay.
Brian Eaton: Yes.
Brian Eaton: But you can also do it with environmental samples. We could take a sample of water, run it through a high throughput system and if we use one of those universal primers, we might be able to pull out all fish, for example.
Katie: What other things can eDNA be used for? Something that just popped into my mind is land reclamation, is there potential?
Jon: Can I also add to that? Land reclamation is one. One thing that crossed my mind too is just, I don't know ... is it correct to say the potability of water, the drinkability of it? Would it be easy enough to do a test and then determine, yeah, there's no pathogens in this water, it's good to drink?
Brian Eaton: Well, let's talk about the reclamation piece first, right? This is actually something we've been thinking about. We've got an idea for a project to look at that. It being that if we could look at multiple taxonomic groups using high throughput, and if we could determine which ones we would expect to occur in a natural wetland of that type, can we then compare over time the recovery of, say, a constructed wetland, say a borrow pit, can we compare over time how well that is doing compared to a reference wetland to determine how close it is to recovery? Can we also, by looking at a sequence of these habitats over time, can we figure out what a recovery trajectory should look like and when we've departed from that?
We don't know that, but this is something we're trying to work on now, by comparing what we get from our eDNA sampling to some traditional sampling that's been going on in those same places. Then by having these recovered wetlands and reference wetlands in the same area, we can compare those as well. Right? The idea that you can try and get these trajectories is not new, but I think using eDNA in this way is fairly new. I've only seen it with some microbial soil community stuff work. I don't know if you've seen anything else.
Jenet Dooley: I know there's general interests around the province.
Brian Eaton: Yeah.
Jenet Dooley: People are looking to eDNA whenever monitoring is used. It is used, in this example, for reclamation and trying to figure out where a system is on the spectrum of healthy, thriving reference to not.
Jon: Right. When you see that work in conjunction with other work in terms of reclamation, it's fascinating. Simply speaking, replanting trees and replanting areas so they can then develop a thriving ecosystem. You might know if you're using eDNA and you refine it to that point where you can start to figure out what those trajectories are in terms of going from not so healthy to healthy, when do you plant, when would be the appropriate time to plant so it would take.
Jenet Dooley: Yeah and that's-
Jon: It seems conceivable in my mind.
Jenet Dooley: Yeah. That's the thing with the eDNA. It has a lot of potential to make monitoring efforts more efficient, right? With amphibians, like we were talking about, usually your going out at night to actually see or listen for amphibians. It's dark, it's raining, you're trudging around. It's a lot of effort and work.
Brian Eaton: There's wolves.
Jenet Dooley: There's wolves.
Jenet Dooley: There's a lot of time and effort invested in monitoring. When you have a method like eDNA, that helps make that more efficient, where you're just going out and filtering a water sample. You're in and out a lot quicker. It's cheaper, takes less time, then you can monitor safer. You can monitor more often, get more data and start refining those curves like you're talking about, right?
Jon: Yeah. I get ... I think my question talking about water and testing the potability and all that, it's leaning into that. Where do you see eDNA being used beyond what you guys are doing? Is it something that can be commercialized and used by an entrepreneur? An innovator to go and do, Hey, I want to try eDNA to test these water samples for drinkability or to test ... we were talking about Copperstone Technologies somehow collaborating. Is there commercial viability to this?
Jenet Dooley: I just saw a study, I think it was in Toronto. They're using eDNA in their storm water samples to figure out the source of fecal contamination.
Jenet Dooley: Traditional water quality testing, you know you have fecal coliforms present. There's some source in your water, a fecal source, that you don't want, but with eDNA, you can then figure out what kind is there. Is it cows? Is it human? So then that helps point you to solving the issue. If it's human, it might be septic tanks that are coming into the water so then you can start to solve the problem. I see a DNA ... I mean, I think the applications, anytime identifying the source of something, identifying anything with a genetic code that you want to identify, you probably could use it. That's just one example that I saw recently.
Katie: This is incredible. I keep going back to Jurassic Park, and when Jon was talking about the commercialization, I was like, oh, this is a bad idea. But Jenet, when you're talking about this, it makes so much sense. But do you think it would ever be commercialized like Jon is saying? To me, it doesn't seem likely, or that it would be necessary.
Jon: Do you guys ever have people reaching out and saying, Hey, this is interesting. I'd like to learn more about this?
Brian Eaton: Yeah. We did a presentation about two and a half years ago on AEA, online virtual thing about genomics and sampling. A bunch of people reached out to us afterwards. Some of them were consultants, for example, that wanted to be able to sample water from stormwater ponds in Edmonton and Calgary and determine if there were goldfish. Because if there are goldfish, it triggers a management response in which you Rotenone. Rotenone is a piscivorous ... it kills fish. Rotenone. So you would go in and you would blast that pond to make sure that that invasive species is controlled in that site. Right? There are commercial companies that will provide certain levels of eDNA analysis. Right? For specific species. I think it's useful in situations like this, where you're looking for one species, it's an invasive, it's of management concern. You know what you do if you're going to find it.
Where we're different is we work with our clients or whatever agencies are engaging with us, help them design an actual sampling program. We actually develop experiments and we customize them to their needs. Right? We're always happy to ... we go out in the field with our clients. We interact with them all the time. We talk about next steps, how we can develop a better approach, blah, blah, blah. Right? It's very important to have that engagement, which is different than sort of some of the, just, yes, they're going to tell you a yes, no, if it's there or not kind of thing. Sorry. One of the challenges around the whole system is that there are things in the environment that can inhibit the PCR reaction, the molecular reaction. You have to know about those, you have to understand what kind of impact it can have on your answers. You have to have a better ... you have to have an understanding of the ecology of the system you're working in.
It is an opportunity for very multi ... ah, I can't say it.
Brian Eaton: Multidisciplinary teams to work together where we often engage with ... there'll be an ecologist, there'll be a molecular biologist. There might be some field staff that understand how to do the sampling better than other folks. One thing we've done with our work in eDNA stuff is to try and develop better sampling approaches, for example. We have changed the way we do things over the years. Going from, initially we did bulk samples and then we've developed different filtering systems that we can use in the field to get that filter that Jenet was talking about. Then we can preserve it in the field so it's actually stable. Then we can bring it back to the lab. Sample preservation is a very important step. Right?
Jon: Oh, I'm sure. Yeah.
Brian Eaton: Because if your sample, if it gets degraded coming back to lab, then what good is it? Right?
Jon: Right, right. What's conceivable then that an entrepreneur and innovator who's listening to this podcast and going, Hmm, eDNA could potentially do this. If they get to that point and they have that little epiphany or thought they could reach out?
Brian Eaton: Yep.
Jon: To you, Brian?
Brian Eaton: For sure.
Jon: Would they reach out to you, too, Jenet? Or is it more you're focused on what the ABMI is doing with the biodiversity monitoring?
Jenet Dooley: Yeah. I would probably point them towards Brian anyway.
Jenet Dooley: But then I feel like if it was a biodiversity question, we might just be pulled right back in. I feel like we have a lot of things going on, and this collaboration's been really reciprocal.
Jon: What's next for eDNA and ABMI and InnoTech in this collaboration?
Jenet Dooley: Well, I was going to actually build off of what Brian was saying and bring it back to our project that started it all, I guess. In that project, we were wanting to compare the autonomous recording units, or the ARUs, and eDNA. Because of the potential eDNA has for increasing efficiency of monitoring and the potential down the road, ABMI incorporating eDNA into our monitoring methods. I think from the beginning, it was only four ponds. We knew we weren't going to have statistically robust results. But I think the big thing was the collaboration establishing this relationship with Brian's lab and knowing that we were a part of how eDNA is being developed in the province, part of the conversation, aware of the innovations and what was happening so that when we can pull it in and use it, we'll be able to.
But some of the results from that study, the Tiger Salamanders that you brought up, that was ... everyone was very excited that we picked up on Tiger Salamanders. I should be clear, they're not super rare, but they can be elusive. They spend a lot of their time underground in borrows. You tend to only see them when they're migrating to their breeding ponds. That's when people see them on the move, but they're not a good species for monitoring with ARUs. Right? They don't make broadcast calls. We can't pick them up on our recorders.
Jon: Just to clarify, a broadcast call is a Tiger Salamander saying, Hey, Hey you?
Jenet Dooley: Yeah.
Jon: Calling out to another Tiger Salamander? Is that-
Brian Eaton: More like a Tiger Salamander in a bar going, Hey.
Jenet Dooley: Yeah. [crosstalk 00:39:46]. It's a breeding call, yeah.
Jon: I get you. Okay. Okay. Broadcast call is synonymous to breeding call. Okay.
Jenet Dooley: Yeah, broadcasting a breeding call. There you go. That's probably a better way to put it.
Jon: I get you.
Jenet Dooley: So, it's not something we can rely on to be able to identify them with the ARUs. That's why the eDNA ... for a species like that, using eDNA is a solution to that problem. In our pilot study, we did pick up on Tiger Salamanders in two of our ponds, which we didn't with the ARUs, of course. That was the exciting part and what got picked up and a lot of people are excited about. But on the flip side, we heard one Western Toad with an ARU at one pond, a solitary Western Toad. We didn't pick it up with the eDNA.
This is a long way of getting to your question of what's next, but Brian's team and us have been talking a lot about what's next. I think one of the things that those results got us thinking about is species behavior and how that impacts which tool you use to identify them. That's what eDNA is, it's another tool in the toolbox. In the appropriate situation, it's going to do a better job, more efficiently than other tools, so getting to know when to use it and where it's going to be helpful.
Jon: Yeah. That makes sense. It's not like this, the eDNA, is replacing the ARUs, it's ... yeah, the tool is-
Brian Eaton: We'll get there.
Jenet Dooley: It could. I think it could. It has potential, but right now it clearly replaces ARUs for things like tiger Salamanders.
Jon: Right, but not for those frogs.
Brian Eaton: I just wanted to build on Jenet's comment. It also helps us understand how we would deploy the tool most effectively. We know, for example, in a pond where the water's not mixing very well laterally, that if we do get pockets of amphibians that are only in a specific spot and don't move around, that means we have to move around where we're we're sampling. One thing we did look at with the ABMI was what is the relative ... what kind of information, sorry, do we get if we take three samples versus nine samples in a pond, for example? With nine samples, we would cover a bigger spatial area. Right?
We also looked at sampling the same pond three times during the summer to understand if there are better periods when we should be sampling so that we capture as many species as possible using eDNA or if it doesn't matter. Right? That's an operational piece too, for the ABMI, because they go out at certain times to select their ARUs or whatever. If they can just collect the water sample then, it's only one trip. Right? There are multiple different questions around the operational application of this approach as well that we can explore.
Jon: Okay. Those are things that you're looking at?
Jenet Dooley: Brian's a great person to work with about those. I'll vouch for Brian said, he'll work with whoever's coming to him with the question, it's a very collaborative process. His team trained our team how to sample for eDNA. He mentioned sampling in nine places versus three places. That was something that came out of us talking about how they've been developing methods and maybe one of the things that they were thinking about trying and us saying, yeah, let's try it. It was definitely a collaborative process. I think-
Jon: That's cool.
Jenet Dooley: ... a real benefit of working with Brian.
Katie: Well, something that I love learning, every time I talk to someone at InnoTech, I just learn so much more about the work that InnoTech is doing. Right? I mean before talking to, or learning about eDNA and our salamanders, I didn't know that this was something that InnoTech offered as a service. Right? So it's just really interesting to know and actually I can also vouch for Brian. He is excellent to work with. On that note, I think that we should wrap this up. This was a really great conversation and I can't wait to see what you guys do next with eDNA and your collaboration.
Jon: Shift can be found online at shift.albertainnovates.ca or email us at [email protected] On behalf of everyone here, I'm Jon, until next time, have a great day.