By Ashleigh Papp
Living organisms everywhere are leaving behind clues of their presence. Known as environmental DNA, or eDNA for short, this genetic information is being used by conservation ecologists to pinpoint species in a way that they never have been able to before.
California researchers are testing out new tools that can offer up answers to our questions in a matter of minutes. With a potential to revolutionize how we do conservation science, eDNA technology presents many opportunities for us to better understand the dynamics and health of our California Bay and Delta ecosystems.
Science-in-Short is a quarterly podcast introducing scientists working on emerging topics in the San Francisco Estuary watershed. The podcast is written and produced by Ashleigh Papp with editing support from Ariel Rubissow Okamoto and the Estuary News Group, and music created by Peter Rubissow. Science in Short is funded by the Delta Stewardship Council.
TRANSCRIPT
You’re listening to Science in Short, a quarterly podcast introducing you to scientists working on emerging topics in the San Francisco estuary watershed. I’m Ashleigh Papp.
Interviewer Ashleigh Papp: When I mention deoxyribonucleic acid, or DNA for short, what comes to mind? … Crossing chromosomes, spiral staircase diagrams, maybe even crime scenes.
In every swath of land, every river, and even in the ocean as it ebbs in and out, are living organisms filled with this genetic information, DNA. It does everything from determining physical appearance and sex to influencing behavioral patterns and lifespan. This information, which originates as DNA and is expressed as proteins, also gets passed on to offspring and future generations.
So DNA is inside of us and all living organisms. And it’s specific ordering of nucleotides, the A’s, T’s, C’s, and G’s, is what makes each of us unique. In the last few decades, researchers have begun using DNA taken from an environment, called eDNA, to pinpoint species in a way that they never have been able to before. Beyond this being an easier and faster way to identify species, eDNA presents a fantastic opportunity to better understand and ultimately, manage an ecosystem.
Ecologist Andrea Schreier: My name is Andrea Schreier, and I am an Adjunct Associate Professor in the Department of Animal Science at University of California Davis. My lab uses genetic and genomic tools to answer ecological questions about fish and wildlife populations, usually with direct applications to the management or conservation of those populations.
Papp: Schreier’s lab group spans the gamut from undergraduate students to PhD level studies. The students focus on various projects, some of which are directly tied to California’s water supply and the Delta. But all of her students are using new tools to answer old, and new, questions about conservation-related science.
Schreier: The field of conservation biology is studying how we can best protect unique species or unique populations. And the field of genetics has allowed us to much better understand how populations are related to each other [and] how different they are from each other. And it also allow us to better understand the ecology of populations. We can use things like parentage analysis to understand reproductive dynamics, for example, and all of those things, help conservation practitioners make decisions that allow for better protection.
Papp: Bringing genetics into conservation began in the 1970s, when a group of researchers identified alloenzymes, also known as allozymes, as a tracking tool. This group of enzymes all do the same thing, but their shape varies because their genetic information is different. The researchers realized that by tracking allozymes, they could better understand genetic differences among species.
Another big breakthrough in this field was PCR, which stands for polymerase chain reaction.
Schreier: PCR basically allows you to isolate a piece of DNA and make a billion copies of it. And when you have that much DNA, you could separate different versions of sequence of DNA on a gel, or you could determine the sequence of particular regions of DNA. And that also helped scientists to be able to look at the relationships between populations with higher resolution than with the allozyme data. And we were able to start looking at areas of the genome that were highly variable. And just, I guess dial in the patterns of gene flow between populations that helped people better manage the populations.
Papp: There have been a lot of other advancements in this field of work over the years. But most relevant to Schreier’s work is a study that was published in 1999. Researchers extracted DNA from an ice core that was taken in Greenland. They were able to separate all of the genetic information that was in the ice and ultimately, got a sweeping look at which organisms were there. This type of DNA is known as environmental DNA, or eDNA for short.
Schreier: One way I like to introduce eDNA is to say this — we and every other living organism is shedding little bits of ourselves into the environment. We’re shedding cells and hairs and all of these things. And these little bits of ourselves can be a source of DNA to answer ecological or public health related questions. So in the field of environmental DNA and how it’s applied in ecology, we get cells that are shed by wild animals or by plants in the environment, and we isolate them and then we extract the DNA. And then we can do different tests to figure out what species are present at a location.
Papp: Before eDNA came into the picture, ecologists and field researchers like Schreier had to go to great lengths to learn about the species that they were studying. Think things like applying for permits to be in a specific area, setting out on a boat and trawling with nets in the water, capturing and releasing for hours on end … All to try and confirm the presence of a single, endangered species.
This route, a more traditional way to conduct field research, requires time, money, and a whole lot of patience. The chance to grab a water sample and quickly test it for eDNA to determine what’s present, however, opens up an exponential amount of new data points in a fraction of the time.
So let’s get into how one goes about sampling for eDNA in the field …
Schreier: My lab studies fish. And so we’re looking for DNA that comes from scales that fall off of fish or mucus that comes off of fish, or from sperm or from feces or urine, just different things that are coming off of the fish that we are trying to detect.
And what we do is we go out into the field, and we sample some water. And either in the field or back at the lab, we filter that water, with filters that have a very small pore size that will capture the cells that have the DNA in them on the filter. And then we take that filter, and we go into a clean lab or lab that is kept very sterile, and DNA free. And we extract the DNA from the filters. And then once you have the eDNA, there’s two different ways you can analyze it.
If you’re interested in detecting a single species, you could use something called quantitative PCR or qPCR, which is a technique that isolates a region of the genome. And we would choose a region that was specific to that species. So if that region of DNA is found in your sample, and is detected by the quantitative PCR, then you know that species is present in the area where you collected water.
Papp: Another approach to analyzing the DNA from the sample takes a more holistic view … It looks beyond a single species, at a bigger grouping of organisms, called “taxa.”
Schreier: If you’re interested and looking at a whole biological community, you can do something called meta barcoding. And in this case, we use regular old PCR to isolate a region of the genome that’s common in a wide array of taxa. If we were targeting fish, for example, we might pick a marker that focused on a region of mitochondrial DNA, that tends to be the same within species but different across species. So once we amplify our sample with PCR, so that region of DNA is isolated, we can then sequence it and look for all of the different versions of that gene. And then we use some analysis [and] some bioinformatics that will match those sequences to the species they come from. So you can get sort of a snapshot of all of the different species within that location.
Papp: In order to identify either a single or a group of organisms in the sample, Schreier first needs a library of known genomes to reference. And thanks to the work of many eDNA researchers around the world, public databases are becoming more and more accessible.
Schreier: So all of our new sequence data, we’ve put in a database called GenBank. So that any researcher can go and see what the sequence is of that species. And we compiled all of the sequences for all the species that we could detect in our region, and we made it publicly available on a website. So anyone who wants to do aquatic eDNA work in our region can download the database, and that database will help them better analyze their E DNA samples to know what species they have present in their sample.
Papp: Schreier’s lab has a lot of projects in this area underway. One project, in partnership with the state Fish Restoration Program, is working to understand how effective this new sampling method is compared to the traditional route. And they’re looking specifically at endangered and threatened species, like the Delta and longfin smelt and Chinook salmon.
Schreier: They’re looking at whether the same species are detected with eDNA as with the field sampling. Also, they want to see what the fish communities look like in the newly-restored sites versus the sites that have been restored for several decades. And they’re also really interested in seeing if eDNA detection can be used in the summer, because in the summer, the Fish Restoration Program can’t go out and access a lot of those sites, it becomes too difficult to access it with the boat. But you can do eDNA sampling during that time. And so the idea is seeing whether or not eDNA represents a community as well or better than the conventional field sampling, and whether or not this program could then start sampling in all seasons.
Papp: Another area where eDNA is proving super useful, is detecting trace amounts of something before we notice it with the naked eye. For example, before an invasive species becomes an issue across an entire ecosystem, it may first infiltrate a single organism … Which means it’s DNA is available for environmental testing long before it grows into a visibly widespread problem.
Schreier: You can detect an invasive species getting into an organism perhaps earlier than you would be able to detect it through capture. And so that early invasion stage is a really critical stage for the potential to actually eradicate an invasive organism. Once an invasive species is established, it’s very difficult to get rid of, but if you catch it in that very early stage, different activities can be taken to try to protect the native biodiversity at a location.
Papp: In addition to tracing eDNA, Shreier and her team are trying out new tools. One project involves tracking tiger salamander tadpoles, an endangered species that lives in temporary patches of water, known as vernal pools. The researchers are using a hot new tool on the market, called SHERLOCK. And it kind of works like a COVID or pregnancy test.
Schreier: The CRISPR based genetic detection platform SHERLOCK has the added advantage that the analysis can be done in the field. So if you need an answer quickly, you can get an answer in potentially 30 minutes … The molecular biology is a little bit different. But the idea that you add some solution to this piece of paper, and then you get a line or no line, depending on if the DNA of your target is present or not.
Papp: Consider the potential power of this type of tool in the field … Instead of taking your water sample from a far flung pool in the mountains back to the lab for analysis, you could know in 30 minutes or less, while still at the pool, what’s in the water. And the good news is, this technology is user-friendly, so you don’t need to be an expert to use it.
Schreier: The SHERLOCK platform is something that can be used by non-genetics experts. And so a field biologist who knows a ton about the organism, but maybe hasn’t had a genetics class in a decade or two can still perform this very simple test and interpret the results and get an answer in a short space of time.
Papp: But, this eDNA toolkit is relatively new. So there are limitations that Schreier and other conservation scientists are still working to figure out.
Schreier: eDNA detection is not a magic bullet. Like any other kind of sampling method, there’s going to be some biases. The amplification reaction may work more efficiently for some species than others just due to the nature of the DNA that surrounds the area you’re targeting. And so you may get lots of sequence reads from one species and very little from another. But that doesn’t mean there’s lots of species A and not a lot of species B, it’s because of the efficiency of the PCR that creates that difference.
Also another limitation is that you can’t get data about individuals other than presence or absence. You can tell if a species was present or absent at a site, [but] you can’t tell what sex it is, what size it is … Those things might be actually important for the type of study that you’re doing. And so you would need to do additional types of sampling, to capture individuals to determine that.
Papp: And of course, there’s also the very important element of timing.
Schreier: Another limitation is that DNA can stick around in the environment, especially if it’s in the sediment, for up to a couple months. So, if you accidentally disturbed the sediment when you’re collecting water, you could detect a species that isn’t there currently, but could have been there a couple months ago, which maybe is fine for your question, but maybe that’s not what you’re looking for. And if you are trying to sample in a system that has flowing water, so in a river, DNA can be carried from upstream to downstream. Or in the San Francisco estuary, where I work, tides move DNA back and forth, so it’s actually a very challenging system to work in to do eDNA detection.
Papp: Despite the current limitations and challenges, eDNA and the SHERLOCK technology are two really powerful new tools added to the conservation scientist’s toolbelt.
Schreier: So there’s still a lot for us to learn about what the best methods are for isolating eDNA … Where’s the eDNA coming from? How does it move in a system? Can you infer things like abundance, or biomass from the amount of eDNA from the species that you’re detecting in the location. Those are very active areas of research, still, but it [eDNA research] has a lot of advantages for conservation. You’re able to detect the presence of a threatened or endangered species without having to capture it. As an academic researcher, it might be hard for me to get the permits and the clearances to be able to handle a threatened or endangered species. But I could go out and sample some eDNA, and learn whether it’s present on location without getting near that species. Also, you can detect very rare species that might be very difficult to detect through camera traps, or through trawling, or trapping. And you could detect their DNA more easily than you could ever trap them through a conventional method. So these are all really great advantages for using eDNA in conservation.
I’m hoping that with the eDNA expertise my lab has developed and with all of the advances in research going on at other institutions, that we will be able to improve the way that we monitor biodiversity … Improve the accuracy of it and also maybe reduce the invasiveness of our monitoring activities.
Papp: Science in Short is a quarterly podcast written and produced by me, Ashleigh Papp! With editing support from Ariel Rubissow Okamoto and the Estuary News Group, and with funding from the Delta Stewardship Council. For Maven’s Notebook, I’m Ashleigh Papp. Thanks for listening!
