Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens Active
Using DNA, USGS researchers are able to detect the presence of invasive species in aquatic ecosystems. The DNA they use is literally floating around in the environment and is called environmental DNA (eDNA) and is a powerful tool for the early detection of invasive species and pathogens, which can cause serious ecological and economic damage. USGS researchers are also combining the use of eDNA with robotic technology and have deployed automated, robotic eDNA samplers that can detect invasive species in aquatic systems. By combining biology and technology, USGS science can help resource managers detect invasive species and other biological hazards early or monitor their spread, which may provide managers with adequate time and flexibility in developing management strategies, including invasive species control.
Background
Nonnative species can be ecologically disruptive and economically damaging, and early detection is important for developing robust monitoring and control strategies. However, trying to find a handful of individuals invading new habitat can be nearly impossible, especially if those individuals are small or well-hidden as is commonly the case in aquatic systems.
To address this issue, scientists use biology and the aquatic habitat the invasive species live in and turn those factors into a tool they can use. Organisms shed and excrete DNA into the environment, and this DNA, termed environmental DNA (eDNA), can be found suspended in the water, making it accessible to researchers who have the means to extract it from water samples. Using eDNA can be a more effective approach to detect difficult-to-find invasive species than using nets, electro shocking, visual surveys, or other traditional means of detecting aquatic invasive species.
Using eDNA can be part of an early warning system letting resource managers know that invasive species are now present in a habitat that they were previously not. Early detection of invasive species may provide managers flexibility in how they develop their management strategies and could increase the chances of successful control efforts because the invasive species’ population numbers might be relatively low at the time of detection. Once an invasive species gets well established in a habitat, controlling that species can become very difficult and expensive.
NOROCK Research
Using eDNA: Testing water samples from rivers in Oregon, Colorado, Idaho, Montana, Wyoming, and Minnesota, we have successfully used eDNA to detect invasive species. Specifically, we have been able to detect the DNA of nonnative fish, aquatic weeds, and aquatic invertebrates, such as mussel and snail species, and a microscopic parasite that causes proliferative kidney disease in fish, which can cause fish kills in the salmon family (salmon, trout, char, etc.). We have repeatedly used eDNA sampling to detect dreissenid mussel (zebra and quagga mussels) DNA from rivers, lakes and reservoirs. This is particularly exciting because zebra and quagga mussels are a notoriously ecologically and economically harmful group of invasive species that grow on hard surfaces and can damage water pipes and other infrastructure, recreational vehicles, and even other organisms like turtles. They can also outcompete native mussels, disrupt native aquatic communities, and alter how aquatic ecosystems function. Once dreissenid mussels become well established, they are extremely difficult to manage, so having an early detection system that warns managers these mussels have started to occupy a new habitat could be very valuable in controlling these invaders before their numbers become overwhelming.
eDNA and Robots: We, along with our collaborators from other USGS Science Centers and the Monterey Bay Aquarium Research Institute, deployed robotic eDNA samplers to test if they could provide as reliable, timely eDNA samples as those collected by humans. Our results indicate that the robotic sampler could provide samples of similar quality as those taken by humans. In contrast to humans, the robotic samplers can be programed to take samples at a higher frequency than a human could take them, which could be a serious advantage when trying to detect potentially harmful invasive species as early as possible.
Below are other science projects associated with this project.
READI-Net: Providing Tools for the Early Detection and Management of Aquatic Invasive Species
Using Robots in the River: Biosurveillance at USGS streamgages
Below are data or web applications associated with this project.
Environmental DNA robotic and manual sampling data, Yellowstone and Snake Rivers, 2017-2019
PCR results from dreissenid mussel round robin assay analyses, 2018-2019
Below are publications associated with this project.
Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health
Robotic environmental DNA bio-surveillance of freshwater health
A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels
Adding invasive species bio-surveillance to the U.S. Geological Survey streamgage network
Improved detection of rare, endangered and invasive trout using a new large-volume sampling method for eDNA capture
Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
Improved conventional PCR assay for detecting Tetracapsuloides bryosalmonae DNA in fish tissues
Adding value to monitoring efforts with environmental DNA
A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
Potential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: An experimental test and case study
Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
Potential utility of environmental DNA for early detection of Eurasian watermilfoil (Myriophyllum spicatum)
Below are news stories associated with this project.
Below are partners associated with this project.
- Overview
Using DNA, USGS researchers are able to detect the presence of invasive species in aquatic ecosystems. The DNA they use is literally floating around in the environment and is called environmental DNA (eDNA) and is a powerful tool for the early detection of invasive species and pathogens, which can cause serious ecological and economic damage. USGS researchers are also combining the use of eDNA with robotic technology and have deployed automated, robotic eDNA samplers that can detect invasive species in aquatic systems. By combining biology and technology, USGS science can help resource managers detect invasive species and other biological hazards early or monitor their spread, which may provide managers with adequate time and flexibility in developing management strategies, including invasive species control.
Background
Nonnative species can be ecologically disruptive and economically damaging, and early detection is important for developing robust monitoring and control strategies. However, trying to find a handful of individuals invading new habitat can be nearly impossible, especially if those individuals are small or well-hidden as is commonly the case in aquatic systems.
To address this issue, scientists use biology and the aquatic habitat the invasive species live in and turn those factors into a tool they can use. Organisms shed and excrete DNA into the environment, and this DNA, termed environmental DNA (eDNA), can be found suspended in the water, making it accessible to researchers who have the means to extract it from water samples. Using eDNA can be a more effective approach to detect difficult-to-find invasive species than using nets, electro shocking, visual surveys, or other traditional means of detecting aquatic invasive species.
Using eDNA can be part of an early warning system letting resource managers know that invasive species are now present in a habitat that they were previously not. Early detection of invasive species may provide managers flexibility in how they develop their management strategies and could increase the chances of successful control efforts because the invasive species’ population numbers might be relatively low at the time of detection. Once an invasive species gets well established in a habitat, controlling that species can become very difficult and expensive.
NOROCK Research
Using eDNA: Testing water samples from rivers in Oregon, Colorado, Idaho, Montana, Wyoming, and Minnesota, we have successfully used eDNA to detect invasive species. Specifically, we have been able to detect the DNA of nonnative fish, aquatic weeds, and aquatic invertebrates, such as mussel and snail species, and a microscopic parasite that causes proliferative kidney disease in fish, which can cause fish kills in the salmon family (salmon, trout, char, etc.). We have repeatedly used eDNA sampling to detect dreissenid mussel (zebra and quagga mussels) DNA from rivers, lakes and reservoirs. This is particularly exciting because zebra and quagga mussels are a notoriously ecologically and economically harmful group of invasive species that grow on hard surfaces and can damage water pipes and other infrastructure, recreational vehicles, and even other organisms like turtles. They can also outcompete native mussels, disrupt native aquatic communities, and alter how aquatic ecosystems function. Once dreissenid mussels become well established, they are extremely difficult to manage, so having an early detection system that warns managers these mussels have started to occupy a new habitat could be very valuable in controlling these invaders before their numbers become overwhelming.
eDNA and Robots: We, along with our collaborators from other USGS Science Centers and the Monterey Bay Aquarium Research Institute, deployed robotic eDNA samplers to test if they could provide as reliable, timely eDNA samples as those collected by humans. Our results indicate that the robotic sampler could provide samples of similar quality as those taken by humans. In contrast to humans, the robotic samplers can be programed to take samples at a higher frequency than a human could take them, which could be a serious advantage when trying to detect potentially harmful invasive species as early as possible.
- Science
Below are other science projects associated with this project.
READI-Net: Providing Tools for the Early Detection and Management of Aquatic Invasive Species
The USGS has developed the Rapid environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) to accelerate the implementation of environmental DNA (eDNA) analysis as a best practice for the early detection of aquatic biological threats. READI-Net provides tools and a strategy to collect and deliver early detection data for natural resource managers and public health protection...ByEcosystems Mission Area, Biological Threats and Invasive Species Research Program, Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, New York Water Science Center, Northern Rocky Mountain Science Center, Upper Midwest Environmental Sciences Center, Wetland and Aquatic Research Center , Wyoming-Montana Water Science Center, Pacific Northwest Environmental DNA LaboratoryUsing Robots in the River: Biosurveillance at USGS streamgages
For more than a decade, researchers around the world have shown that sampling a water body and analyzing for DNA (a method known as eDNA) is an effective method to detect an organism in the water. The challenge is that finding organisms that are not very abundant requires a lot of samples to locate this needle in a haystack. Enter the "lab in a can", the water quality sampling and processing robot... - Data
Below are data or web applications associated with this project.
Environmental DNA robotic and manual sampling data, Yellowstone and Snake Rivers, 2017-2019
Environmental DNA detection results from samples collected using autonomous water sampling robots and manual approaches. Samples were collected in the Upper Yellowstone River (Montana) and Upper Snake River (Idaho/Wyoming) in 2018 and 2019. Samples were tested for the DNA of the following species: the waterborne protozoa Naegleria spp., the fish pathogen Tetracapsuloides bryosalmonae, Scomber japoPCR results from dreissenid mussel round robin assay analyses, 2018-2019
Real-time PCR results of a round robin evaluation of 5 assays that target dreissenid mussel DNA. Water samples collected from waters with and without dreissenid mussels were analyzed using these five assays in four USGS laboratories. Samples from waters without dreissenid mussels were spiked with known amounts of dreissend DNA. - Publications
Below are publications associated with this project.
Filter Total Items: 13Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health
Autonomous, robotic environmental (e)DNA samplers now make it possible for biological observations to match the scale and quality of abiotic measurements collected by automated sensor networks. Merging these automated data streams may allow for improved insight into biotic responses to environmental change and stressors. Here, we merged eDNA data collected by robotic samplers installed at three U.AuthorsAdam J. Sepulveda, Andrew B. Hoegh, Joshua A. Gage, Sara L. Caldwell Eldridge, James M. Birch, Christian Stratton, Patrick R. Hutchins, Elliott BarnhartRobotic environmental DNA bio-surveillance of freshwater health
Autonomous water sampling technologies may help to overcome the human resource challenges of monitoring biological threats to rivers over long time periods and large geographic areas. The Monterey Bay Aquarium Research Institute has pioneered a robotic Environmental Sample Processor (ESP) that overcomes some of the constraints associated with traditional sampling since it can automate water sampleAuthorsAdam J. Sepulveda, Jim M. Birch, Elliott Barnhart, Christopher M. Merkes, Kevan Yamahara, Roman III Marin, Stacy Kinsey, Peter R. Wright, Christian SchmidtA round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels
Resource managers may be hesitant to make decisions based on environmental (e)DNA results alone since eDNA is an indirect method of species detection. One way to reduce the uncertainty of eDNA is to identify laboratory‐based protocols that ensure repeatable and reproducible results. We conducted a double‐blind round‐robin analysis of probe‐based assays for DNA of dreissenid (Dreissena spp.) musselAuthorsAdam J. Sepulveda, Patrick R. Hutchins, Craig Jackson, Carl Ostberg, Matthew Laramie, Jon Amberg, Timothy Counihan, Andrew B. Hoegh, David PilliodAdding invasive species bio-surveillance to the U.S. Geological Survey streamgage network
The costs of invasive species in the United States alone are estimated to exceed US$100 billion per year so a critical tactic in minimizing the costs of invasive species is the development of effective, early-detection systems. To this end, we evaluated the efficacy of adding environmental (e)DNA surveillance to the U.S. Geological Survey (USGS) streamgage network, which consists of > 8,200 streamAuthorsAdam J. Sepulveda, Christian Schmidt, Jon Amberg, Patrick R. Hutchins, Christian Stratton, Christopher A. Mebane, Matthew Laramie, David PilliodImproved detection of rare, endangered and invasive trout using a new large-volume sampling method for eDNA capture
Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may be to collect fewer, large volume water samples usAuthorsAdam J. Sepulveda, Jenna Schabacker, Seth Smith, Robert Al-Chokhachy, Gordon Luikart, Stephen J. AmishTradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
Environmental DNA (eDNA) has improved detection probabilities of aquatic invasive species but lab-based analyticalplatforms for eDNA analyses slow opportunities for rapid response. Effective approaches that address this analyticalbottleneck and improve capacity for rapid response are urgently needed. We tested the sensitivity of a portable, field-basedeDNA platform relative to widely used lab-baseAuthorsAdam J. Sepulveda, Patrick R. Hutchins, Robert L. Massengill, Kristine J. DunkerImproved conventional PCR assay for detecting Tetracapsuloides bryosalmonae DNA in fish tissues
Conventional PCR is an established method to detect Tetracapsuloides bryosalmonaeDNA in fish tissues and to confirm diagnosis of proliferative kidney disease (PKD) caused by T. bryosalmonae. However, the commonly used PKX5f‐6r primers were designed with the intention of obtaining sequence information and are suboptimal for determining parasite DNA presence. A new PCR assay to detect T. bryosalmonaAuthorsPatrick R. Hutchins, Adam J. Sepulveda, Renee M. Martin, Lacey R. HopperAdding value to monitoring efforts with environmental DNA
No abstract available.AuthorsAdam J. Sepulveda, Andrew M. Ray, Anna M. McKeeA probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples
A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA saAuthorsPatrick R. Hutchins, Adam J. Sepulveda, Renee Martin, Lacey HopperPotential of environmental DNA to evaluate Northern pike (Esox lucius) eradication efforts: An experimental test and case study
Determining the success of invasive species eradication efforts is challenging because populations at very low abundance are difficult to detect. Environmental DNA (eDNA) sampling has recently emerged as a powerful tool for detecting rare aquatic animals; however, detectable fragments of DNA can persist over time despite absence of the targeted taxa and can therefore complicate eDNA sampling afterAuthorsKristine J. Dunker, Adam J. Sepulveda, Robert L. Massengill, Jeffrey B. Olsen, Ora L. Russ, John K. Wenburg, Anton AntonovichUnderstanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production ratAuthorsTaylor Wilcox, Kevin S. Mckelvey, Michael K. Young, Adam J. Sepulveda, Bradley B. Shepard, Stephen F Jane, Andrew R. Whiteley, Winsor H. Lowe, Michael K. SchwartzPotential utility of environmental DNA for early detection of Eurasian watermilfoil (Myriophyllum spicatum)
Considering the harmful and irreversible consequences of many biological invasions, early detection of an invasive species is an important step toward protecting ecosystems (Sepulveda et al. 2012). Early detection increases the probability that suppression or eradication efforts will be successful because invasive populations are small and localized (Vander Zanden et al. 2010). However, most invasAuthorsJeremy Newton, Adam J. Sepulveda, K Sylvester, Ryan Thum - News
Below are news stories associated with this project.
- Partners
Below are partners associated with this project.