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New Aquatic DNA Database Could Transform Water, Wildlife Management

The U.S. Forest Service plans to unveil a genetic database of all streams and lakes in the western United States. Dan Isaak explains the new sampling techniques he calls the “holy grail” of biology.

Written by Matt Weiser Published on Read time Approx. 7 minutes
Kellie Carim samples water for DNA to be brought to the National Genomics Center for Wildlife and Fish Conservation to detect if both threatened bull trout and invasive brook trout are present in Rattlesnake Creek, Missoula, Mont.Michael K. Schwartz/US Forest Service via Associated Press

Water projects necessarily have impacts on fish and other aquatic species. Water, after all, is habitat. So when a new dam or diversion is proposed, we need to find out what fish, frogs and other species will be affected, how many and how significantly.

Trouble is, those questions have always been answered based on limited data. It’s virtually impossible to survey a stream and know every creature that lives there. The stream is too big and the survey tools too crude.

Until now. The U.S. Forest Service is on the verge of unveiling a comprehensive genetic database of every stream and lake in the western United States. Within a few years, it will be possible to quickly analyze a water sample for DNA traces of every species living in that waterway. And that information will be available to anyone with an internet connection.

Dan Isaak, a research fisheries scientist at the Forest Service Aquatic Sciences Lab in Boise, Idaho, calls this the “holy grail” of biology. Isaak is overseeing the project, known as the Aquatic eDNA Atlas. It’s expected to go live on the internet late in 2017, and Isaak recently spoke with Water Deeply about how it works.

Water Deeply: Tell me how this environmental DNA (eDNA) project came into being.

Dan Isaak: It originally grew out of some soil sampling that people were doing. There are all kinds of nematodes and weird things that live in the dirt that people can’t identify. So they figured out a way to process those soil samples using different techniques to discern what species are there without having to go through a microscope and stare at things. That also translates well to waterways.

That water medium is transporting DNA from species that live there all the way downstream. So everything that lives is metabolizing things as they go about their daily lives. Fish are sloughing off cells from their gills and they’re pooping and peeing, and all of that is concentrated in waterways. All you’ve got to do is go in and take a water sample and use a pump to suck it out of whatever water body you’re sampling. It goes through a special piece of filter paper that has a pore size small enough that it can retain the DNA that’s floating in the water column.

That filter gets sent to the lab. The one we’re working with on this atlas project is up in Missoula – a Forest Service research facility called the National Genomics Center for Fisheries and Wildlife Conservation. Then it’s a fairly straightforward genetic query at that point. They search through the DNA copies and match that up to the different critters they’ve already got in their library.

If you get a positive match, then you know definitely that species is either right in that reach of stream you sampled, or it’s somewhere upstream of there. It’s actually incredibly sensitive. They literally can detect one fish in, like, 100m [325ft] of stream. If you were to take a DNA sample downstream of that, they would detect that fish being there about 90 percent of the time. The sensitivity is just hard to believe. It’s a lot more black and white than a lot of our traditional sampling techniques that are based on electrofishing or nets. Some species are hard to capture, or there’s not very many of them, so there’s always uncertainty. A lot of that goes away with the eDNA.

Water Deeply: It sounds like it’s a lot easier on the critters, too.

Isaak: Exactly. You don’t ever have to see or touch them. It’s all based on things they’re releasing into the environment. The sampling is actually a lot cheaper than traditional sampling techniques. Literally, you’re just taking a water sample. So the equipment you need to do the sampling is something you can load into a daypack.

One person can hike around and take dozens of samples in a day. It takes 10–15 minutes at a site to capture the water sample and record the data. Then you’re just carrying around a little piece of filter paper. It’s really opening the doors now in terms of democratizing the data collection process. You don’t have to have a permit to go collect these samples – it’s not like you have to go and touch an ESA-listed fish or something like that.

We’re seeing all these different groups rapidly starting to use this technique. Our hope through this atlas project is that we can get ahead of that to a certain degree and provide some level of coordination amongst these groups just by building this shared database and creating a website and having digital maps where people can see where samples do and don’t exist. Over time, that map of the western U.S. will just fill in with thousands of sites where people collect the samples.

Water Deeply: What is the geographic extent of this new atlas?

Isaak: What we’re funded to do right now is the 12 western states, including Alaska and California, through a grant from the National Fish and Wildlife Foundation. All rivers and streams and lakes within that will be part of the master sampling template. We’re building it off of nationally available geospatial datasets, and we’ll build a website that tunes off of that.

We’ve got one website up already that focuses on bull trout in the Pacific Northwest. That is a microcosm of what were proposing to do with the atlas. That project focuses on bull trout because they are ESA (Endangered Species Act)-listed and they’re important in regards to what people can and can’t do around streams. We’re in the process now of designing an online tool that will be kind of like Google Maps that allows people to see that dataset and query it dynamically.

Water Deeply: You’ve described this project as the “holy grail” of biology. What do you mean by that?

Isaak: It’s literally like magic in terms of what we can discern from a water sample about the critters that live there. A lot of that sampling technology is pretty well developed now. The atlas project is essentially just combining that with digital information technology so that we’ll have a website and a database that’s publicly accessible so they can coordinate and be more effective going forward.

Most of the questions we have about conserving species or managing species or the regulatory frameworks we have built around trying to conserve species, they all really boil down to knowing the distribution and abundance of different species with enough spatial precision to make decisions. Right now, we just don’t have that for most (aquatic) species, other than the few charismatic ones that have adipose fins and that people like to fish for. So we have quite a bit of distribution information on trout species and salmon species. But they’re just one small part of the aquatic community.

Water Deeply: Do you plan to expand this to the rest of the nation?

Isaak: Yeah, probably. If we get it up and running next year, then our experience with projects like this in the past is they just kind of grow organically from there. So at this point, we’re contemplating that being a logical thing we plan on doing a year from now. We’ll probably go back to the National Fish and Wildlife Foundation for year two of the grant to do the eastern half or eastern third of the country.

Water Deeply: How will these tools help assess new water development projects, stream diversions and the like?

Isaak: The biggest thing is it can get a person pretty comprehensive baseline data for what is there, before the project begins, for a low cost. Then you go in and do that project, you can repeat that set of surveys and that’ll give you an assessment of the change that happened. Or if they’re planning a project and it’s controversial because they think it could be habitat for sensitive species, they can go in and do the eDNA survey and quickly determine whether or not that species actually occurs or not. That can either eliminate the controversy or show, yeah, the species is there and you have to plan around it.

The biggest thing is, the quality of information that everyone has common access to is going to be fundamentally better than it was before.

Water Deeply: I understand you can only analyze each DNA sample for a single species. Do you expect that to change?

Isaak: That’s kind of the cutting edge of eDNA work now. Labs are figuring out how to reliably analyze a sample for dozens of species at a time. That is developing rapidly, so in the next year or two that will probably become a fairly standard way that samples get processed.

Part of the beauty of the DNA stuff and building this big integrated database is the samples that people collect can be stored indefinitely. When a sample gets processed, say this year for bull trout, they don’t destroy the whole sample. Most of that sample still sits in the archive in the lab, so that a year from now or five years from now, they can rerun the sample and ask whether or not a dozen or 100 different species occurred there. So every time somebody collects a sample, they just contribute to that long-term biodiversity archive.

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