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. Designed with stakeholder input, READI-Net maximizes the power and cost effectiveness of eDNA sampling for detecting biological threats by using autonomous robotic sample collection, multi-species analysis tools, strategic sample design, standardized and accountable lab analysis, and a communication framework for eDNA detection results. For users interested in implementing or continuing eDNA surveillance of aquatic biological threats, READI-Net provides support from start to finish, creating a network of standardized data which informs science, management, and policy.
READI-Net: A National Plan using eDNA for the Early Detection of Aquatic Invasive Species
The Department of Interior (DOI) and its partners have created the National Early Detection and Rapid Response (EDRR) Framework to reduce the impacts of biological threats. A focus of this strategy is developing and implementing an environmental DNA-based (eDNA) species detection and assessment framework.
This eDNA-based effort, known as the USGS Rapid environmental DNA Assessment and Deployment Initiative & Network (READI-Net), puts eDNA technology into the hands of USGS partners and stakeholders to support early detection of and rapid response to aquatic biological threats such as invasive species, and human or wildlife pathogens and parasites.
Similar to the USGS Streamgaging Network, READI-Net provides a national framework to standardize eDNA methods and data management, creating a clearinghouse of data to protect resources and economies through invasive species management.
Learn more: Toward a national eDNA strategy for the United States
What is eDNA?
eDNA is DNA shed or excreted from living organisms into the environment, which makes it available to be sampled and monitored using new molecular methods. Using methods that rely on physically locating the few, often well-hidden individuals that comprise the first wave of an invasion into a new habitat can be difficult and costly. In contrast, sampling for the DNA of biological threats can be more effective and cost efficient.
Learn More:
What is eDNA? (video)
Environmental DNA: An Emerging Tool for Understanding Aquatic Biodiversity
Early Detection is Key to Managing Biological Threats
Biological threats are a serious concern for the United States as they can threaten native species, disrupt recreation, damage critical infrastructure, and impose millions of dollars of costs toward management and mitigation. The annual global cost imposed by biological threats is greater than $423 billion dollars and has quadrupled every decade since 1970 (IPBES, 2023). Biological threats are easily introduced and can have severe repercussions (case study).
Early detection is the process of surveying for, reporting, and verifying the presence of a biological threats, such as non-native species, before the founding population becomes established or spreads so widely that eradication is no longer feasible (DOI, 2016).
Second only to prevention, the National EDRR Framework considers early detection to be a cornerstone of biological threat management because it is critical in accomplishing three goals:
- Limit the ability of the biological threat to become established in the new habitat, spread to additional areas, and become ecologically and economically destructive
- Increase the chance that eradication or control efforts will be successful
- Ensure management efforts will be cost effective, especially compared to scenarios when the biological threat has become well established
eDNA Enables Early Detection of Invasive Species
eDNA analysis is extremely sensitive to species presence and has become a rapid, cost-effective tool for species detection and monitoring, particularly in aquatic environments (Sepulveda et al., 2020). DNA from environmental samples (e.g., water, air, soil) can provide indirect evidence of a species’ presence in a given environment, even when its numbers are low or the species is difficult to differentiate from close relatives (Marshall and Stepien, 2019). In comparison with traditional collection and identification methods in aquatic environments, such as netting, electrofishing, and visual surveys, eDNA techniques can be more sensitive, cost-effective, and targeted to the identification of species of interest; safer for wildlife and field staff; and less harmful to the ecosystem (Darling, 2019). By implementing eDNA techniques, resource managers can now reliably detect new aquatic biological threats before they have a chance to become well established, costly to manage, and ecologically or economically disruptive.
Learn more:
- Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool
- Demystifying eDNA validation
- When are environmental DNA early detections of invasive species actionable?
READI-Net MAXIMIZES eDNA’s EARLY DETECTION CAPABILITIES
READI-Net is a set of tools designed with input from scientists and end-users to help new or current users of eDNA technology leverage tested protocols and best practices to collect, analyze, and share eDNA data that can assist managers, stakeholders, and decision-makers with their aquatic biological threat monitoring and research needs.
READI-Net’s Components
READI-Net components (see polygons in READI-Net graphic) can be accessed individually or as the full suite, providing practical and financial flexibility and meeting stakeholders and partners where they are.
Autonomous (robotic) eDNA Samplers
Portable robotic eDNA samplers can be placed in the right place at the right time, programmed to sample any time of day or night, sample frequently (hourly or daily, for example), and can sample during hazardous conditions. READI-Net is collaborating with Monterey Bay Research Institute (MBARI) and Smith-Root to design and test robotic eDNA samplers that collect high quality samples and are affordable, scalable, and mobile. Designed with easy-to-use computer interfaces and wireless connectivity, researchers can control sampling remotely and safely.
- Benefits of Autonomous eDNA samplers
- Increase the odds of being at the right time and right place to document a new invasion or other unique/rare events
- Cost effective eDNA surveillance, especially at remote or hard to access sites
- Track changes in relative species abundance over time
- Able to collect up to 144 samples at a time, which increases the odds to detect rare target species
- Standardized field sampling methods
Two robotic sampler options provide different sampling capabilities to meet a variety of user sampling strategies:
- The Smith-Root eDNA Autosampler is designed to be a portable robotic sampler that can collect up to 8 samples. The lower sample capacity works well for those that need to frequently collect samples or where the worksite is nearby.
- The MBARI Environmental Sample Processor is being developed as a portable robotic sampler that will allow multiple-instrument interface, networked deployments, and the ability to take 144 samples to accommodate frequent or long sampling deployments.
Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Multi-species Analysis
Any number of species have the potential to invade a single site, therefore READI-Net is collaborating with partners to develop eDNA tools (e.g., high-throughput qPCR) that rapidly and simultaneously test a single sample for the DNA of many biological threats, rather than just a single species.
- Simultaneously detects the DNA of multiple species across a range of taxa (harmful algae, mussels, and fish, for example) from a single sample
- Provides greater detection efficiency at lower cost
- Retains the sensitivity and specificity found in single-species analyses
- Provides more data per sample and a lower cost to facilitate early detection of invasive species
Sampling Guidance
READI-Net provides users with initial guidance to create sampling strategies that optimize detection of target species.
- Research-based guidance on where and when to sample
- Statistical tools to inform number and frequency of samples
- Improved chances of detecting target species
- Optimized use of limited resources
Laboratory Standards
READI-Net protocols recognize that it is imperative to process samples efficiently and provide data that are grounded in repeatable and reproducible lab workflows that meet critical quality management criteria.
- Unique barcoding of all samples for efficiency and tracking
- Tested and cross-validated lab techniques for processing eDNA samples developed in collaboration with iTRACKDNA.
- Consistent workflow and analysis across READI-Net labs
- Standards and proficiency testing performed to evaluate READI-Net labs quality
Sample Tracking and Data Delivery
Among the READI-Net laboratories, a single eDNA database tracking system is employed that utilizes a variety of software to track samples, automate workflows, and check for errors throughout the process. This sample tracking system provides individual sample tracking from initial collection, through analysis and reporting, and finally, to long-term storage.
- Allows for the sharing of the sample status, data, and metadata to partners through automation, mapping, and reporting
- ArcGIS-based workflows enhance and simplify workflow and communication among labs and partners
- Provides data in formats designed for specific user groups
- Integrates with established networks (e.g., USGS Streamgaging Network) for additional analytical power
- Provides a communication framework that quickly distributes results and invasive risk assessments to a wide variety of users (resource managers, policymakers, municipalities, public, scientists)
Building READI-Net Partnerships
Creation of READI-Net has been informed by stakeholders and subject matter experts to create a program that has wide user applicability. Outreach with a variety of users continues to expand the READI-Net project.
- Communicate the value of READI-Net to biological threat management partners and stakeholders
- Inform user groups as READI-Net expands protocols and workflows to include eDNA from air and terrestrial samples
Who are READI-Net Users?
If you’re currently using eDNA, or contemplating using eDNA for species detection, READI-Net is already designed for you. READI-Net complements traditional techniques to describe species distributions with the sensitivity, speed, and accuracy inherent in eDNA methodology. Using eDNA is especially effective in providing timely warning of potential invasion events to reduce downstream economic and environmental impacts. By compiling best practices across the many stages of eDNA surveillance, READI-Net removes guesswork for designing and implementing eDNA techniques to support early detection of invasive species.
Potential READI-Net Users
- Federal and State Management Agencies
- Tribal Management Agencies
- Protected Area Managers
- Resource Managers, Policymakers
- Dam Operators
- Fisheries Managers
- Scientists, Municipalities
- Fishing & Recreation Enthusiasts…
Related Links:
- READI-Net Fact Sheet
- READI-Net Podcast
- Toward a national eDNA strategy for the United States
- Application of Environmental DNA for Inventory and Monitoring of Aquatic Species
- Safeguarding America’s Lands and Waters from Invasive Species: A National Framework for Early Detection and Rapid Response
FOR MORE INFORMATION:
Adam Sepulveda, PhD, USGS Biologist, Lead READI-Net Investigator
Northern Rocky Mountain Science Center
406-404-9155
READI-Net Collaborators (non-government)
Monterey Bay Aquarium Research Institute (MBARI)
iTRACKDNA (University of Victoria and Institut National de La Recherche Scientifique)
Participating USGS Mission Areas:
Participating USGS Science Centers:
Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, Great Lakes 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
Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Siren: The National Early Detection and Rapid Response 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
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. Designed with stakeholder input, READI-Net maximizes the power and cost effectiveness of eDNA sampling for detecting biological threats by using autonomous robotic sample collection, multi-species analysis tools, strategic sample design, standardized and accountable lab analysis, and a communication framework for eDNA detection results. For users interested in implementing or continuing eDNA surveillance of aquatic biological threats, READI-Net provides support from start to finish, creating a network of standardized data which informs science, management, and policy.
READI-Net: A National Plan using eDNA for the Early Detection of Aquatic Invasive Species
The Department of Interior (DOI) and its partners have created the National Early Detection and Rapid Response (EDRR) Framework to reduce the impacts of biological threats. A focus of this strategy is developing and implementing an environmental DNA-based (eDNA) species detection and assessment framework.
This eDNA-based effort, known as the USGS Rapid environmental DNA Assessment and Deployment Initiative & Network (READI-Net), puts eDNA technology into the hands of USGS partners and stakeholders to support early detection of and rapid response to aquatic biological threats such as invasive species, and human or wildlife pathogens and parasites.
Similar to the USGS Streamgaging Network, READI-Net provides a national framework to standardize eDNA methods and data management, creating a clearinghouse of data to protect resources and economies through invasive species management.
Learn more: Toward a national eDNA strategy for the United States
What is eDNA?
eDNA is DNA shed or excreted from living organisms into the environment, which makes it available to be sampled and monitored using new molecular methods. Using methods that rely on physically locating the few, often well-hidden individuals that comprise the first wave of an invasion into a new habitat can be difficult and costly. In contrast, sampling for the DNA of biological threats can be more effective and cost efficient.
Learn More:
What is eDNA? (video)
Environmental DNA: An Emerging Tool for Understanding Aquatic Biodiversity
Early Detection is Key to Managing Biological Threats
Biological threats are a serious concern for the United States as they can threaten native species, disrupt recreation, damage critical infrastructure, and impose millions of dollars of costs toward management and mitigation. The annual global cost imposed by biological threats is greater than $423 billion dollars and has quadrupled every decade since 1970 (IPBES, 2023). Biological threats are easily introduced and can have severe repercussions (case study).
Early detection is the process of surveying for, reporting, and verifying the presence of a biological threats, such as non-native species, before the founding population becomes established or spreads so widely that eradication is no longer feasible (DOI, 2016).
Second only to prevention, the National EDRR Framework considers early detection to be a cornerstone of biological threat management because it is critical in accomplishing three goals:
- Limit the ability of the biological threat to become established in the new habitat, spread to additional areas, and become ecologically and economically destructive
- Increase the chance that eradication or control efforts will be successful
- Ensure management efforts will be cost effective, especially compared to scenarios when the biological threat has become well established
eDNA Enables Early Detection of Invasive Species
eDNA analysis is extremely sensitive to species presence and has become a rapid, cost-effective tool for species detection and monitoring, particularly in aquatic environments (Sepulveda et al., 2020). DNA from environmental samples (e.g., water, air, soil) can provide indirect evidence of a species’ presence in a given environment, even when its numbers are low or the species is difficult to differentiate from close relatives (Marshall and Stepien, 2019). In comparison with traditional collection and identification methods in aquatic environments, such as netting, electrofishing, and visual surveys, eDNA techniques can be more sensitive, cost-effective, and targeted to the identification of species of interest; safer for wildlife and field staff; and less harmful to the ecosystem (Darling, 2019). By implementing eDNA techniques, resource managers can now reliably detect new aquatic biological threats before they have a chance to become well established, costly to manage, and ecologically or economically disruptive.
Learn more:
- Strategic considerations for invasive species managers in the utilization of environmental DNA (eDNA): steps for incorporating this powerful surveillance tool
- Demystifying eDNA validation
- When are environmental DNA early detections of invasive species actionable?
READI-Net MAXIMIZES eDNA’s EARLY DETECTION CAPABILITIES
READI-Net is a set of tools designed with input from scientists and end-users to help new or current users of eDNA technology leverage tested protocols and best practices to collect, analyze, and share eDNA data that can assist managers, stakeholders, and decision-makers with their aquatic biological threat monitoring and research needs.
READI-Net’s Components
READI-Net components (see polygons in READI-Net graphic) can be accessed individually or as the full suite, providing practical and financial flexibility and meeting stakeholders and partners where they are.
Autonomous (robotic) eDNA Samplers
Portable robotic eDNA samplers can be placed in the right place at the right time, programmed to sample any time of day or night, sample frequently (hourly or daily, for example), and can sample during hazardous conditions. READI-Net is collaborating with Monterey Bay Research Institute (MBARI) and Smith-Root to design and test robotic eDNA samplers that collect high quality samples and are affordable, scalable, and mobile. Designed with easy-to-use computer interfaces and wireless connectivity, researchers can control sampling remotely and safely.
- Benefits of Autonomous eDNA samplers
- Increase the odds of being at the right time and right place to document a new invasion or other unique/rare events
- Cost effective eDNA surveillance, especially at remote or hard to access sites
- Track changes in relative species abundance over time
- Able to collect up to 144 samples at a time, which increases the odds to detect rare target species
- Standardized field sampling methods
Two robotic sampler options provide different sampling capabilities to meet a variety of user sampling strategies:
- The Smith-Root eDNA Autosampler is designed to be a portable robotic sampler that can collect up to 8 samples. The lower sample capacity works well for those that need to frequently collect samples or where the worksite is nearby.
- The MBARI Environmental Sample Processor is being developed as a portable robotic sampler that will allow multiple-instrument interface, networked deployments, and the ability to take 144 samples to accommodate frequent or long sampling deployments.
Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Multi-species Analysis
Any number of species have the potential to invade a single site, therefore READI-Net is collaborating with partners to develop eDNA tools (e.g., high-throughput qPCR) that rapidly and simultaneously test a single sample for the DNA of many biological threats, rather than just a single species.
- Simultaneously detects the DNA of multiple species across a range of taxa (harmful algae, mussels, and fish, for example) from a single sample
- Provides greater detection efficiency at lower cost
- Retains the sensitivity and specificity found in single-species analyses
- Provides more data per sample and a lower cost to facilitate early detection of invasive species
Sampling Guidance
READI-Net provides users with initial guidance to create sampling strategies that optimize detection of target species.
- Research-based guidance on where and when to sample
- Statistical tools to inform number and frequency of samples
- Improved chances of detecting target species
- Optimized use of limited resources
Laboratory Standards
READI-Net protocols recognize that it is imperative to process samples efficiently and provide data that are grounded in repeatable and reproducible lab workflows that meet critical quality management criteria.
- Unique barcoding of all samples for efficiency and tracking
- Tested and cross-validated lab techniques for processing eDNA samples developed in collaboration with iTRACKDNA.
- Consistent workflow and analysis across READI-Net labs
- Standards and proficiency testing performed to evaluate READI-Net labs quality
Sample Tracking and Data Delivery
Among the READI-Net laboratories, a single eDNA database tracking system is employed that utilizes a variety of software to track samples, automate workflows, and check for errors throughout the process. This sample tracking system provides individual sample tracking from initial collection, through analysis and reporting, and finally, to long-term storage.
- Allows for the sharing of the sample status, data, and metadata to partners through automation, mapping, and reporting
- ArcGIS-based workflows enhance and simplify workflow and communication among labs and partners
- Provides data in formats designed for specific user groups
- Integrates with established networks (e.g., USGS Streamgaging Network) for additional analytical power
- Provides a communication framework that quickly distributes results and invasive risk assessments to a wide variety of users (resource managers, policymakers, municipalities, public, scientists)
Building READI-Net Partnerships
Creation of READI-Net has been informed by stakeholders and subject matter experts to create a program that has wide user applicability. Outreach with a variety of users continues to expand the READI-Net project.
- Communicate the value of READI-Net to biological threat management partners and stakeholders
- Inform user groups as READI-Net expands protocols and workflows to include eDNA from air and terrestrial samples
Who are READI-Net Users?
If you’re currently using eDNA, or contemplating using eDNA for species detection, READI-Net is already designed for you. READI-Net complements traditional techniques to describe species distributions with the sensitivity, speed, and accuracy inherent in eDNA methodology. Using eDNA is especially effective in providing timely warning of potential invasion events to reduce downstream economic and environmental impacts. By compiling best practices across the many stages of eDNA surveillance, READI-Net removes guesswork for designing and implementing eDNA techniques to support early detection of invasive species.
Potential READI-Net Users
- Federal and State Management Agencies
- Tribal Management Agencies
- Protected Area Managers
- Resource Managers, Policymakers
- Dam Operators
- Fisheries Managers
- Scientists, Municipalities
- Fishing & Recreation Enthusiasts…
Related Links:
- READI-Net Fact Sheet
- READI-Net Podcast
- Toward a national eDNA strategy for the United States
- Application of Environmental DNA for Inventory and Monitoring of Aquatic Species
- Safeguarding America’s Lands and Waters from Invasive Species: A National Framework for Early Detection and Rapid Response
FOR MORE INFORMATION:
Adam Sepulveda, PhD, USGS Biologist, Lead READI-Net Investigator
Northern Rocky Mountain Science Center
406-404-9155
READI-Net Collaborators (non-government)
Monterey Bay Aquarium Research Institute (MBARI)
iTRACKDNA (University of Victoria and Institut National de La Recherche Scientifique)
Participating USGS Mission Areas:
Participating USGS Science Centers:
Columbia Environmental Research Center, Eastern Ecological Science Center, Forest and Rangeland Ecosystem Science Center, Fort Collins Science Center, Great Lakes 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
Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.