Thursday, January 18, 2018

Environmental DNA: Frontiers of Adirondack Science

Filtering Stream WaterConserving our native fish is a major goal of the Ausable River Association (AsRA). We know the Ausable River watershed, particularly the high elevation tributaries to the East Branch, is one of the most likely places to retain Brook Trout under future climate warming scenarios across their native range. We also know that much of that habitat is fragmented by undersized culverts that serve as barriers to fish passage. Finally, we know that introduced non-native species, such as Brown Trout and Rainbow Trout, threaten our native fish populations. These facts are well documented in the scientific literature and summarized in reports produced by the Eastern Brook Trout Joint Venture.

When developing conservation strategies to protect our native fish, one of the first things we need to understand is where fish are. Surprisingly, we know very little about where Brook Trout and other native fish are found in the Ausable River watershed. We have a broad sense of their distribution, but when we walk up to a particular reach of a small tributary we are often making “best guesses.” Before doing stream or habitat restoration work, we take the time, with our partners at the U.S. Fish and Wildlife Service, to survey the fish population.

The problem with this approach is we are left without a big picture understanding of where Brook Trout are, how that relates to barriers that fragment their population, and where non-native invasive species are. Surveying large areas of the Ausable watershed using traditional backpack electrofishing techniques would take thousands of person-hours and a lot of money. Luckily, emerging science is offering a much quicker and more cost-effective approach.

Filtering Lake Water Detection of a species with environmental DNA, or eDNA, relies on finding a small fragment of their DNA in an environmental sample – in this case 6 liters of stream water. When looking at an organism such as a fish, the DNA is most likely captured in the form of shed skin and gut cells. The use of eDNA to detect aquatic species, other than bacteria, is relatively new. The first paper published using this technique was a 2008 study looking for American bullfrogs in streams. The technique drew much wider attention when it was used in 2011 to detect Silver and Bighead Asian Carp that are threatening to make their way into the Great Lakes Basin.

Previous work on detecting fish in streams similar to those in the Ausable River watershed have documented that eDNA is more sensitive to the detection of rare species than traditional sampling techniques. AsRA and others believe there is great potential to learn about the presence of Brook Trout and other fish species at the limits of their ranges.

Only in the last few years has the cost come down enough to make it affordable and practical for an organization like AsRA to employ this technology. Through a partnership with Dr. Lee Ann Sporn at the Adirondack Watershed Institute (AWI) we are able to utilize lab space and equipment for a reasonable cost. Lee Ann also serves as an advisor and collaborator on this work.

AsRA staff are collaborating with Lee Ann on several projects utilizing eDNA. We are assessing its effectiveness for early detection of aquatic invasive species, such as the spiny waterflea (Bythotrephes longimanus). In collaboration with Dr. Curt Stager at Paul Smith’s College, we have been exploring and refining the use of eDNA to detect historical fish presence in lakes by analyzing sediment cores retrieved from the lake bottom. Finally, AsRA is leading a pilot project to map the distribution of trout species in a subwatershed within the Ausable River watershed.

Preparing to Collect Sediment Cores This summer we launched our pilot project in the Otis Brook subwatershed, a tributary to the East Branch. We chose this watershed for several reasons; 1) it is one of few tributaries to the East Branch where non-native Brown Trout are stocked, 2) the entire stream system in the watershed is fragment by culverts that serve as moderate to severe barriers to aquatic organism passage, and 3) we have electrofished several reaches of the stream with the U.S. Fish and Wildlife Service over the past two years.

The goals of this project were to map the spatial distribution of Brook Trout, Brown Trout, and Rainbow Trout at a 1-km stream resolution throughout the entire watershed, as well as assess the differences in these species distributions above and below barriers. This resulted in nearly 30 sampling sites within this subwatershed. Additionally, we looked at the seasonal change in these distributions, by sampling each site in the late spring, summer, and fall. Finally, we carefully tracked the time and expense associated with this project so we could accurately estimate the cost of doing this work on a much larger scale.

At the time of publication, we are still working in the lab to analyze our samples for each fish species. We have completed the work for Brook Trout, and the results are promising. We were able to detect Brook Trout at all locations where they were identified using backpack electrofishing. Additionally, we detected their presence in locations where traditional techniques had not: mainly at low abundances in the lower reaches of Otis Brook. We also detected them in a small tributary to Otis Brook that is seasonally isolated due to the middle portion of the stream drying up in the summer. This small isolated population of Brook Trout has interesting implications for Brook Trout resilience and the potential for genetically distinct strains to evolve over short distances.

The results of this work thus far are very promising. The ability for us to create detailed maps of the distributions of these fish species is within our reach. We also have the ability to rapidly monitor stream sites for fish presence, something that is invaluable to our conservation efforts. We are currently seeking financial support to expand this work.

Perhaps the most exciting part of this work is where it could lead in the future. Each sample we collect serves as an archive of the species living in that stream at that time. In the future, as we grow and refine these genetic tools, we can return to these samples to ask new questions. For instance, we are considering working on an eDNA assay capable of detecting spring salamanders (Gyrinophilus porphyriticus), a species that is particularly hard to survey. With archived samples in hand, our effort is reduced even as we take on further queries. We are excited to be applying cutting edge science to the conservation of our freshwater ecosystems in the Adirondacks.

Photos from above: Filtering Stream Water; Filtering Lake Water; and Preparing to Collect Sediment Cores (courtesy Brendan Wiltse).

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Brendan Wiltse

Brendan Wiltse is the Science & Stewardship Director for the Ausable River Association and a professional conservation photographer. He holds a Ph.D. in Biology from Queen's University in Canada. While not out on the water studying Adirondack lakes and streams, he is often roaming the Wilderness with his camera and dog. You can view is photography at

6 Responses

  1. Boreas says:


    Interesting article, fascinating technology!

    I have just one question – when testing segments of a stream, what keeps eDNA from upstream fish from contaminating the results of the section you are testing? Wouldn’t any given sample include any and all upstream fish as well?

    • DNA rapidly degrades in the stream environment. Without going into too much detail, for streams this size we expect the DNA to persist for about 1km downstream. This is why we spaced our sample sites that distance apart. Each site is then an integration of the 1km of upstream environment. eDNA doesn’t give us as much information as traditional fish survey techniques, but it does allow us to acquire data much quicker, at a lower cost, and in a completely non-invasive way (fish are never handled or disturbed). Depending on the specific question we are trying to answer, followup surveys using other techniques may be necessary.

  2. Charlie S says:

    “Detection of a species with environmental DNA, or eDNA, relies on finding a small fragment of their DNA in an environmental sample – in this case 6 liters of stream water.”

    Amazing! What next? I wonder if this new technology has its roots in Area 51 out there in Nevada!

    • .Paul says:

      No this technology, like other similar technology, has its roots in academic research labs. In this case with the 2008 Royal Society paper it came from French and Italian university labs. All the underlying technology that led to it basically came from other academic labs. The DNA amplification technology that underlies this was invented by a US scientist who was working at Cetus (a biotech company in Berkley) something that earned him the Nobel Prize in chemistry. BUT the real underlying science came from the University of Wisconsin where an Indian American scientist and a few others (who also won the Nobel Prize) was working!

      Nothing at Area 51 as I understand it

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