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
- 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.
Sources/Usage: Public Domain.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.
Sources/Usage: Public Domain.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.
Sources/Usage: Public Domain.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
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