DNA: Tool for Freshwater Biodiversity Conservation

By Johanna Mitra, at Stony Brook University.
All Photos © Alison M. Jones, unless otherwise noted.

This is the latest post to our NWNL NEXTGEN BLOG series. Since 2007, NWNL has supported watershed education with college internships and blogging opportunities. This NWNL NEXTGEN BLOG series posts student essays; sponsors a forum for our student contributors; and invites upper-level students to propose work focused on watershed values, threats and solutions.

Johanna Mitra is currently an undergraduate student at Stony Brook University. She is majoring in Ecosystems and Human Impact, with a focus on wildlife conservation and minoring in geospatial science. Read Johanna’s earlier posts here.

Around the world, freshwater ecosystems are experiencing a rapid loss of biodiversity. Freshwater species – of which there are a known 140,000 – are disappearing faster than any species on land or in our oceans.[mfn]IUCN[/mfn] The main causes of this decline include habitat fragmentation by dams and other water-related infrastructure; habitat degradation by pollution; and the introduction of invasive species.[mfn]IUCN Freshwater Fish Specialist Group[/mfn] Aquatic Invasive Species (AIS) are one of the biggest threats to native freshwater fish. They can crowd out and outcompete native species; carry diseases and pathogens; and even cause the local extinction of other species in the area.[mfn]U.S. Fish and Wildlife Service[/mfn] It is estimated that as many as one third of all freshwater fish species face extinction because of invasive species and human activity. To combat these issues, scientists and conservationists are employing advances in genetic research to prevent the spread of AIS and better protect native and endangered fish.

What is Environmental DNA?

Environmental DNA (hereafter, eDNA) is the genetic material left behind in an environment by an organism. Found in the form of shed skin or hair, feces, or the organism’s carcass, researchers can use eDNA to determine which species are present or absent in an environment.[mfn]U.S. Geological Survey[/mfn] This is especially useful in aquatic ecosystems, where it can be difficult to catalog the diversity of species over a large area or to locate where a single species might exist. Traditional methods of surveying and sampling fish include trapping, netting fish and electrofishing – all of which can be time consuming, labor intensive and costly. This makes the collection of eDNA an appealing route for many researchers and citizen scientists. After collecting and filtering a water sample, researchers can extract the genetic material from the sample; and then either screen for a single fish species in what is known as a “targeted” approach, or for a number of different species in a “non-targeted” approach.[mfn]Miller, Sue[/mfn] This process is relatively quick, efficient, and much more cost-effective. Analyzing multiple samples across a watershed can also help researchers get a better sense of the geographical distribution of a fish species and whether its population is localized in one area.

Extracting total DNA from eDNA water filter samples collected in the field, courtesy of Yellowstone National Park on Creative Commons

Preventing Invasive Species

One of the most useful applications of eDNA in freshwater biodiversity conservation is its ability to detect the presence of invasive species before their populations begin to grow out of control. This “early detection” method of invasive species prevention has already proven to be successful in several watersheds across the United States. For example, Asian carp are incredibly harmful to the Mississippi River Basin, dominating native species and threatening to damage the Great Lakes’ fishing industry, which brings in about $7 billion each year.[mfn]National Park Service[/mfn] Despite their large size, Asian carp are reportedly very difficult to capture, making it complicated to determine where their populations might be located within the Mississippi River and its tributaries. The U.S. Geological Survey therefore developed portable eDNA “detection kits” that allow citizen scientists to screen water samples for types of Asian carp.[mfn]U.S. Geological Survey[/mfn] Within just an hour, it’s possible to tell whether Asian carp are present in the area, alerting natural resource managers of the need to step in with preventative measures while their population is still small.[mfn]U.S. Geological Survey[/mfn]

Asian Carp eDNA process, courtesy of U.S. Army Corps of Engineers Chicago District on Creative Commons

In the Columbia River Basin, eDNA analysis is being used to prevent the spread of the invasive Northern Pike. This AIS has only been observed upstream of the Columbia River’s Grand Coulee Dam, but conservationists fear that it will eventually spread further downstream, where populations of endangered salmon live.[mfn]Miller, Sue[/mfn] The use of eDNA analysis allows for the continuous monitoring of the waters below the Grand Coulee Dam for signs of Northern Pike and helps to ensure that a breeding population cannot establish itself elsewhere.

Aerial view from helicopter of Grand Coulee Dam and its reservoir, Lake Roosevelt

Conserving Native and Endangered Species

Because eDNA analysis can determine a species’ presence in a habitat, it also has applications in conserving native, endangered and threatened species whose populations may be too small or rare to observe during regular surveys. In the Raritan River Basin, dams have contributed to the sharp decline of the Raritan’s native and migratory river herring (including alewife and blueback herring) to the point where they are considered “Species of Special Concern” by the National Marine Fisheries Service.[mfn]Rutgers[/mfn] A number of these dams have been removed in recent years, prompting researchers to “track” progress in the return of these river herring using eDNA analysis as they make their way back into old habitats, previously blocked off by dams.[mfn]Rutgers[/mfn]

Raritan River Basin, New Jersey

The Columbia River Basin also contains many dams and other hydroelectric infrastructure [albeit on a much larger scale than the Raritan River Basin] which disrupt migration routes and life stages of salmon species and a number of other freshwater species. The native Pacific lamprey, once widespread across the Columbia River Basin, can no longer be found upstream of most of today’s hydrodams due to lack of passage.[mfn]U.S. Fish and Wildlife Service[/mfn] IN this watershed, eDNA is being used to determine the best locations in which to reintroduce native Pacific Lamprey back into their habitat, as well as find where existing populations are currently situated.

The Future of Freshwater Biodiversity

Use of eDNA analysis is becoming increasingly accessible to community science programs around the world. One initiative led by the International Union for Conservation of Nature (IUCN) and NatureMetrics is providing water-sampling kits to citizen scientists “in areas of critical freshwater conservation importance, including the Amazon, Ganges, Mekong Delta and the Niger Delta.”[mfn]The Freshwater Blog[/mfn] The project, titled eBioAtlas, will collect more than 30,000 water samples in these target areas to provide a comprehensive database of global freshwater biodiversity.[mfn]The Freshwater Blog[/mfn] This research will offer invaluable insight into which freshwater habitats and species should be prioritized for conservation efforts and will help inform conservationists and natural resource managers on the best ways to ensure their long-term survival.

Seagull and terns at sunrise on India’s Ganges River

Given the fact that freshwater species are disappearing at such an alarming rate, it is more important than ever to understand how invasive species spread and to detect their presence early on. While it may be difficult to get a sense of a species’ numbers solely from an eDNA analysis, simply detecting the presence of an invasive species or the absence of an endangered species offers a wealth of information to conservationists. As genetics research continues to advance and the use of eDNA analysis becomes more commonplace in fisheries management, we should continue to see success in curbing the loss of freshwater biodiversity due to this valuable tool.

“An eBioAtlas of Global Freshwater Biodiversity.” The Freshwater Blog, July 1, 2021. Accessed on August 12, 2021

Aquatic Invasive Species.” U.S. Fish and Wildlife Service, May 18, 2021. Accessed on August 12, 2021 by JM. https://www.fws.gov/fisheries/aquatic-invasive-species.html

“Asian Carp Early Detection.” U.S. Geological Survey, n.d.  Accessed on August 12, 2021. https://www.usgs.gov/special-topic/glrist/science/asian-carp-early-detection?qt-science_center_objects=0#qt-science_center_objects

“Asian Carp Overview.” National Park Service, June 24, 2019. Accessed on August 12, 2021 by JM.  https://www.nps.gov/miss/learn/nature/ascarpover.htm

“Environmental DNA (eDNA).” U.S. Geological Survey, n.d. Accessed on August 12, 2021 by JM. https://www.usgs.gov/special-topic/water-science-school/science/environmental-dna-edna?qt-science_center_objects=0#

“Environmental DNA (eDNA) Assay for Monitoring Recovery of River Herring.” Rutgers – Raritan River Initiatives, n.d. Accessed on August 12, 2021 by JM.  http://raritan.rutgers.edu/environmental-dna-edna-assay-for-monitoring-recovery-of-river-herring/

“Freshwater Biodiversity.” IUCN, n.d. Accessed on August 12, 2021 by JM. https://www.iucn.org/theme/species/our-work/freshwater-biodiversity

Help to Answer Your Species Questions.” United States Department of Agriculture, May/June 2020. Accessed on August 12, 2021 by JM. https://www.fs.fed.us/rm/pubs_journals/2020/rmrs_2020_miller_s001.pdf

“Major Threats.” IUCN Freshwater Fish Specialist Group, n.d. Accessed on August 12, 2021 by JM. https://www.iucnffsg.org/freshwater-fishes/major-threats/

Miller, Sue. “Black and White and Shed All Over: How eDNA Analysis Can

“Pacific Lamprey.” U.S. Fish and Wildlife Service, April 2021. Accessed on August 12, 2021 by JM. https://www.fws.gov/oregonfwo/articles.cfm?id=149489457

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