The Use of eDNA to Test for Invasive and Endangered Species

Project ID: 2447
Principal Investigator: Jacque Keele
Research Topic: Invasive Species
Funded Fiscal Years: 2016
Keywords: None

Research Question

Over the last decade the field of environmental DNA (eDNA) analysis has grown. The use of environmental DNA
(eDNA) for the identification of rare, endangered, and invasive species in aquatic environments represents a new
tool that can assist in management of these organisms. eDNA encompasses both free floating DNA (extracelluar)
and DNA that is present in cells that an organism leaves behind in the environment (intracellular). Current analysis
methods do not differentiate between extracellular and intracellular DNA. eDNA is being used for the monitoring
of invasive, endangered, and threatened species. One of the important aspects of eDNA analysis is that the
collection methods do not impact the environment. For example, when eDNA is used to monitor for endangered
salamanders, researchers are able to filter water at the site and analyze the filter paper for the presence of the
organism. The traditional survey method involved turning over rocks and disturbing the environment to look for
the salamander. eDNA is a much less destructive survey tool for determining the presence of an organism. The
sample collection methods for eDNA has been explored for small streams and lakes, but not in a large reservoir.
Determining the best sample collection method in a large body of water is key because the bodies of water that
Reclamation manages are large, and it is important to increase our understanding of the behavior of eDNA in
these large reservoirs. Understanding the behavior of eDNA in a large body of water is important if Reclamation is
going to make use of this testing method. eDNA analysis can be used to make management decisions for
construction when exotic species are present. The field of eDNA is rapidly changing and keeping current with the
literature is key to making sure that the best methods are being used for the detection, analysis, and decision
making with eDNA is being studied.

Need and Benefit

RDLES is the leader in early detection of quagga mussels and needs to continue optimizing testing methods for
invasive mussels. eDNA testing is a very useful way to identify target organisms in raw water. RDLES needs to
expand its understanding of this process and how eDNA is transferred from location to location. This method of
testing will be vital to identify forthcoming invasive species that may be detrimental to Reclamation waters and
facilities. It can also be used to test for the presence of rare or engendered species.
Invasive species represent at costly problem both for the economy and the environment. Invasive species cost the
Unites States more than $120 billion in damages each year (Pimental et al. 2005). Invasive species displace,
compete, and are predators on native species. In the case of quagga mussels, boating is the number one vector
for moving this organism to new bodies of water. According to the Fish and Wildlife Service more than 400 of the
over 1,300 species currently protected by the Endangered Species Act are considered at risk because of an
invasive species. In addition, invasive species are the leading factor in freshwater fish extinction and
endangerments. Aquatic invasive species can alter the food chain, habitat, water quality, and impact the water
industry. Thus, there is a link between the arrival of an invasive species and native species becoming endangered.
Understanding the methods (such as eDNA) for detecting potential organisms of concern is important if RDLES is
going to stay a leading laboratory in the field of early detection. As people continue to utilize Reclamation waters
for recreation the possibility of an introduction of an invasive species rises. Also, eDNA analysis can improve the
management of construction projects where exotic species may be present by enabling the builders to know that
an organism is present and may be impacted. In addition, as the climate continues to change in the West,
organisms that were previously hindered by cold weather, can find more areas to invade. Both human and
environmental factors contribute to the spread of invasive species. As invasive species emerge, native species are
impacted, and can become endangered. Monitoring for both invasive and endangered species by the presence of
eDNA offers a unique method for detection. eDNA allows for a sample to be collected, and analyzed for the
presence of the DNA of the organism of interest. Collecting the DNA that is left behind by organisms in the
environment can enable researchers at Reclamation to have less of an impact on the environment. Traditional
survey methods can be destructive to the environment. eDNA can simplify sample collection and identification.
Sample collection is made easier because a water sample is filtered and the filter paper is then sent to the
laboratory for analysis. Identification is simplified because standardized genetic markers are used. Instead of
having an intensive monitoring program it would be possible to collect water samples and then analyze for the
presence of the organism of interest.

Contributing Partners

Contact the Principal Investigator for information about partners.

Research Products

Bureau of Reclamation Review

The following documents were reviewed by experts in fields relating to this project's study and findings. The results were determined to be achieved using valid means.

The Use of eDNA to Test for Invasive and Endangered Species (final, PDF, 634KB)
By Jacque Keele
Publication completed on September 30, 2016

The analysis of eDNA for the detection of invasive and endangered species is continuing to grow in the coming years. There are both advantages and disadvantages to performing eDNA analysis. This scooping project had several goals. First, to perform a literature search on current eDNA methods and techniques. Second to perform a time course study of the impact of inhibitors on PCR outcome. Inhibitors are a major issue for eDNA studies. Finally, to attend and present at the first annual eDNA workshop. While the impact of eDNA on environmental studies is growing as researchers realize the advantages of this method, it is also important to understand that there is still many areas of research that need to be addressed if this method is going to reach its full potential.


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Last Updated: 4/4/17