USGS researchers are working with the Monterey Bay Aquarium Research Institute to optimize autonomous, robotic samplers for detection of DNA fragments shed by biological threats (BT; invasive species, parasites, pathogens) in our nation’s waters. Finding DNA fragments (a method known as environmental DNA sampling) produced by an emerging BT in water is akin to finding a needle in a haystack—many samples must be collected at the right time and place to find evidence of the BT. Robotic samplers have an advantage over humans because they can be programmed to sample any time of day or night, can sample more frequently (hourly or daily, for example), and can sample during hazardous conditions.
Working with our collaborators, we will develop field sampling and lab analyses protocols and provide the products and framework to manage, organize, analyze, and distribute the large amounts of data a network of robotic samplers is expected to generate. Ultimately, this project should enhance the ability of resource managers to develop an early detection and rapid response strategy to biological threats in our freshwater aquatic systems before they become overly difficult and expensive problems.
Biological Threats
Biological threats like invasive species and pathogens or parasites that can infect fish, wildlife, or humans, can disrupt biological communities, alter how ecosystems function, cause local extinctions of native species, and be economically costly. Early detection of biological threats can provide resource managers flexibility on how to address the threats before they become too large to manage. For example, invasive dreissenid mussels have caused economic and ecological damage to waterways in much of the United States and when adult dreissenid mussels become established, there is often no way to remove them. If adult dreissenid mussels become established in Montana, it is predicted that it will cost Montana an estimated $234 million/year in repairs and lost revenue. Dreissenid mussels are just one example of a particularly destructive biological threat. There are many others that, once established, will be difficult and expensive to control.
Environmental DNA
One approach for early detection of biological threats is to detect their DNA in the environment.
When organisms shed and excrete their DNA into the environment, termed environmental DNA (eDNA), it can be found suspended in the water and can be sampled by scientists. eDNA can be a more effective detection tool for difficult-to-find species than using nets, electro shocking, visual surveys, or other traditional means. Using eDNA can be part of an early warning system, letting resource managers know that biological threats are now present in a habitat where they were previously not.
READI-Net: rapid eDNA assessment and deployment initiative and network
Currently, we, along with our collaborators from other USGS Science Centers and the Monterey Bay Aquarium Research Institute (MBARI), have been deploying autonomous, robotic DNA samplers that can be programmed to take and preserve eDNA samples at a higher frequency than what humans are capable of. The higher frequency of sampling is an obvious advantage for an early detection and rapid response strategy when monitoring for biological threats in aquatic systems.
However, the current robotic eDNA samplers are large, heavy, and expensive and are deployed at a limited number of sites. What is needed are smaller, less expensive robotic eDNA samplers that can be deployed in streams and lakes as a network across the nation. This approach will generate a lot of data that must be quality-assured, managed, organized, analyzed, and distributed.
Goals of READI-Net
- Develop new robotic eDNA samplers that will be mobile, cheaper, and easy to use
- Develop appropriate guidance to inform when and where to deploy the new eDNA robotic to optimize surveillance capabilities
- Develop appropriate statistical tools to optimize early detection probabilities and reduce uncertainty in the results
- Provide standard operating procedures to ensure high-quality, rapid results
- Develop a database and data visualization products to provide READI-Net data to decision-makers and the public
- Engage with DOI partners and interest groups to review and make recommendations about READI-Net, including how to prioritize critical infrastructure and waters for biothreat surveillance with eDNA samplers
The overall goal of READI-Net is to enhance early detection and rapid response capacities for effectively containing and controlling biological threats by resource managers.
National Early Detection Rapid Response (EDRR) Information System
Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
Using Robots in the River: Biosurveillance at USGS streamgages
Environmental DNA water sample analyses for smallmouth bass surveillance, Gardner River, Montana, March 2022
Environmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada
T. bryosalmonae detection in fish and water, DNA sequence, and simple sequence repeat data collected in the Inter-Mountain West from 2011 to 2019
Environmental DNA robotic and manual sampling data, Yellowstone and Snake Rivers, 2017-2019
PCR results from dreissenid mussel round robin assay analyses, 2018-2019
A framework to integrate innovations in invasion science for proactive management
Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies
Integrating environmental DNA results with diverse data sets to improve biosurveillance of river health
Eastward expansion of Round Goby in New York: Assessment of detection methods and current range
Robotic environmental DNA bio-surveillance of freshwater health
A round-robin evaluation of the repeatability and reproducibility of environmental DNA assays for dreissenid mussels
Integration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network
Reporting the limits of detection and quantification for environmental DNA assays
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
Sampling designs for landscape-level eDNA monitoring programs using three-level occurrence models
Tradeoffs of a portable, field-based environmental DNA platform for detecting invasive northern pike (Esox lucius) in Alaska
- Overview
USGS researchers are working with the Monterey Bay Aquarium Research Institute to optimize autonomous, robotic samplers for detection of DNA fragments shed by biological threats (BT; invasive species, parasites, pathogens) in our nation’s waters. Finding DNA fragments (a method known as environmental DNA sampling) produced by an emerging BT in water is akin to finding a needle in a haystack—many samples must be collected at the right time and place to find evidence of the BT. Robotic samplers have an advantage over humans because they can be programmed to sample any time of day or night, can sample more frequently (hourly or daily, for example), and can sample during hazardous conditions.
Working with our collaborators, we will develop field sampling and lab analyses protocols and provide the products and framework to manage, organize, analyze, and distribute the large amounts of data a network of robotic samplers is expected to generate. Ultimately, this project should enhance the ability of resource managers to develop an early detection and rapid response strategy to biological threats in our freshwater aquatic systems before they become overly difficult and expensive problems.
Invasive dreissenid mussels, a common biological threat in our nation's waters. Biological Threats
Biological threats like invasive species and pathogens or parasites that can infect fish, wildlife, or humans, can disrupt biological communities, alter how ecosystems function, cause local extinctions of native species, and be economically costly. Early detection of biological threats can provide resource managers flexibility on how to address the threats before they become too large to manage. For example, invasive dreissenid mussels have caused economic and ecological damage to waterways in much of the United States and when adult dreissenid mussels become established, there is often no way to remove them. If adult dreissenid mussels become established in Montana, it is predicted that it will cost Montana an estimated $234 million/year in repairs and lost revenue. Dreissenid mussels are just one example of a particularly destructive biological threat. There are many others that, once established, will be difficult and expensive to control.
Environmental DNA
One approach for early detection of biological threats is to detect their DNA in the environment.
An inside look at an MBARI environmental DNA (eDNA) sampler. This version weighs about 400 pounds, but future, READI-Net versions will be more portable. When organisms shed and excrete their DNA into the environment, termed environmental DNA (eDNA), it can be found suspended in the water and can be sampled by scientists. eDNA can be a more effective detection tool for difficult-to-find species than using nets, electro shocking, visual surveys, or other traditional means. Using eDNA can be part of an early warning system, letting resource managers know that biological threats are now present in a habitat where they were previously not.
READI-Net: rapid eDNA assessment and deployment initiative and network
Currently, we, along with our collaborators from other USGS Science Centers and the Monterey Bay Aquarium Research Institute (MBARI), have been deploying autonomous, robotic DNA samplers that can be programmed to take and preserve eDNA samples at a higher frequency than what humans are capable of. The higher frequency of sampling is an obvious advantage for an early detection and rapid response strategy when monitoring for biological threats in aquatic systems.
However, the current robotic eDNA samplers are large, heavy, and expensive and are deployed at a limited number of sites. What is needed are smaller, less expensive robotic eDNA samplers that can be deployed in streams and lakes as a network across the nation. This approach will generate a lot of data that must be quality-assured, managed, organized, analyzed, and distributed.
Goals of READI-Net
- Develop new robotic eDNA samplers that will be mobile, cheaper, and easy to use
- Develop appropriate guidance to inform when and where to deploy the new eDNA robotic to optimize surveillance capabilities
- Develop appropriate statistical tools to optimize early detection probabilities and reduce uncertainty in the results
- Provide standard operating procedures to ensure high-quality, rapid results
- Develop a database and data visualization products to provide READI-Net data to decision-makers and the public
- Engage with DOI partners and interest groups to review and make recommendations about READI-Net, including how to prioritize critical infrastructure and waters for biothreat surveillance with eDNA samplers
The overall goal of READI-Net is to enhance early detection and rapid response capacities for effectively containing and controlling biological threats by resource managers.
Detecting the DNA of a new aquatic invader can be difficult. Having robotic samplers that can sample at any time, day or night, provides advantages over humans conducting the sampling. (A stretch of Fall River in Wyoming, outside of Yellowstone National Park) - Science
National Early Detection Rapid Response (EDRR) Information System
The National Early Detection Rapid Response (EDRR) Information System is an emerging online resource for invasive species information sharing and collaboration that serves as the information hub of the National EDRR Framework. This centralized network will improve access to existing and emerging information resources and expand collaboration to facilitate early detection and rapid response to...Environmental DNA (eDNA): Combining Technology and Biology to Detect Aquatic Invasive Species and Pathogens
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...Using 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
Environmental DNA water sample analyses for smallmouth bass surveillance, Gardner River, Montana, March 2022
Environmental DNA results for March 2022 smallmouth bass surveillance in the Gardner River, MontanaEnvironmental DNA data, fish abundance data, and stream habitat data from northwest Montana and northeast Washington and southern British Columbia, Canada
Field estimates of the abundance of two trout species (bull trout and westslope cutthroat trout) in Montana and rainbow trout in Washington and British Columbia were collected in concert with environmental DNA samples (eDNA) to evaluate if eDNA copy numbers correlated with abundance of trout. In addition, stream habitat data including channel units (pools, riffles), substrate, large woody debris,T. bryosalmonae detection in fish and water, DNA sequence, and simple sequence repeat data collected in the Inter-Mountain West from 2011 to 2019
This data release contains molecular diagnostic results and molecular detection of the myxozoan parasite Tetracapsuloides byrosalmonae in fish tissue and environmental DNA samples collected from the inter-mountain West, USA.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
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A framework to integrate innovations in invasion science for proactive management
Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches haAuthorsCharles B. van Rees, Brian K. Hand, Sean C. Carter, Charles Bargeron, Timothy Joseph Cline, Wesley Daniel, Jason A. Ferrante, Keith Gaddis, Margaret E. Hunter, Catherine S. Jarnevich, Melodie A. McGeoch, Jeffrey T. Morisette, Matthew E. Neilson, Helen E. Roy, Mary Ann Rozance, Adam J. Sepulveda, Rebekah D. Wallace, Diane Whited, Taylor Wilcox, John S. Kimball, Gordon LuikartTime to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies
Environmental (e)DNA methods have enabled rapid, sensitive and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision-making has been impeded by uncertainties associated with false positive tests putatively caused by sporadic or systemic contamination. Sporadic contamination is a process that is inconsistent across samples andAuthorsPatrick Ross Hutchins, Leah Nicole Simantel, Adam J. SepulvedaIntegrating 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 BarnhartEastward expansion of Round Goby in New York: Assessment of detection methods and current range
The Round Goby Neogobius melanostomus has spread rapidly around the Great Lakes region since its introduction to North America in 1990. In 2014, a specimen was captured in the New York State Canal System west of Utica, prompting concerns that Round Goby would soon reach the ecologically and economically valuable watersheds of Lake Champlain and the Hudson River estuary. The establishment of RoundAuthorsScott D. George, Barry P. Baldigo, Christopher B. Rees, Meredith L. Bartron, Dylan R. WinterhalterRobotic 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 PilliodIntegration of eDNA-based biological monitoring within the US Geological Survey’s national streamgage network
This study explores the feasibility and utility of integrating environmental DNA (eDNA) assessments of species occurrences into the United States (U.S.) Geological Survey’s national streamgage network. We used an existing network of five gages in southwest Idaho to explore the type of information that could be gained as well as the associated costs and limitations. Hydrologic technicians were traiAuthorsDavid Pilliod, Matthew Laramie, Dorene McCoy, Scott MacleanReporting the limits of detection and quantification for environmental DNA assays
BackgroundEnvironmental DNA (eDNA) analysis is increasingly being used to detect the presence and relative abundance of rare species, especially invasive or imperiled aquatic species. The rapid progress in the eDNA field has resulted in numerous studies impacting conservation and management actions. However, standardization of eDNA methods and reporting across the field is yet to be fully establisAuthorsKaty E. Klymus, Christopher M. Merkes, Michael J. Allison, Caren S. Goldberg, Caren C. Helbing, Margaret Hunter, Craig Jackson, Richard F. Lance, Anna M. Mangan, Emy M. Monroe, Antoinette J. Piaggio, Joel P. Stokdyk, Chris C. Wilson, Catherine A. RichterAdding 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. AmishSampling designs for landscape-level eDNA monitoring programs using three-level occurrence models
Resource managers conduct landscape-level monitoring using environmental DNA (eDNA). These managers must contend with imperfect detection in samples and sub-samples (i.e., molecular analyses). This imperfect detection impacts their ability to both detect species and estimate occurrence. Although occurrence (synonymously occupancy) models can estimate these probabilities, most models and guidance fAuthorsRichard A. Erickson, Christopher M. Merkes, Erica L. MizeTradeoffs 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. Dunker - News