Environmental DNA as a Tool for Inventory and Monitoring of Aquatic Vertebrates
RC-201204
Objective
Six threatened or endangered amphibian species and 23 threatened or endangered fish species are known to occur on Department of Defense (DoD) lands, creating potential constraints on training and resource management. These species pose unique challenges for inventory and monitoring due to the difficulty of thoroughly surveying aquatic environments. An efficient alternative to traditional field surveys is the use of environmental DNA (eDNA) to detect species presence. The objective of this project is to develop the methods and protocols necessary for widespread application of eDNA as a monitoring tool – sampling design guidelines, laboratory requirements and protocols – and quantify the cost-efficiency of the eDNA method compared with standard field surveys. The aim is to produce an efficient, broadly applicable set of protocols for the use of eDNA techniques for monitoring listed and at-risk aquatic vertebrate species and their invasive species threats at DoD installations.
Technology Description
Animals shed cells with their DNA into the environment regularly through the shedding of skin, mucous, and excrement. Although this eDNA is subject to a number of degrading forces (ultraviolet light, heat, and hydrolyzation), recent studies have shown that enough DNA remains suspended in natural water bodies to detect the presence of individual aquatic species, even at low densities. While this technology is mature and has been demonstrated across a range of systems, applications for inventory and monitoring of specific species remain limited. This project will expand and transfer the application of the eDNA method to resource management on DoD lands by developing general and installation-specific protocols for eDNA monitoring of aquatic vertebrate species through DNA analysis of water samples. The team will develop and apply eDNA protocols at three DoD installations that cover a range of ecoregions and hydrologic systems (Fort Huachuca, Arizona; Fort McCoy, Wisconsin; and Yakima Training Center, Washington). At each site, a codified list of species of management concern (target species) will be selected and water samples taken across a range of environmental conditions within the potential habitat of the target species. Repeated samples (through time and space) will be taken to determine recommendations for sampling designs (locations and numbers of replicates) across each installation and measure potential correlates of eDNA breakdown (heat, light, acidity) for further analysis. In the laboratory, standard modern molecular genetic materials and equipment will be used to determine whether samples contain DNA of the target species. The detectability of eDNA for target species will be modeled using the program PRESENCE, which analyzes a series of detections and non-detections to create models of the probability of occupancy at a site, given that occupancy cannot always be detected. These models as well as controlled laboratory DNA degradation experiments will be used to investigate the relationships between potential DNA stressors and detection to produce recommendations for optimal sampling design. Finally, the relative cost and survey efficiency of eDNA protocols compared with standard field survey protocols will be quantified.
Benefits
The application of eDNA techniques for monitoring aquatic species is expected to be more cost-efficient and more effective and to have lower ecological impact compared with current field protocols. These techniques will help inform ongoing natural resource management activities, including (1) development of species-specific endangered species management plans, (2) Section 7 consultations with the U.S. Fish and Wildlife Service, and (3) early detection and control of invasive aquatic species that may prey on or hybridize with native species. To support technical transfer, managers at each site will receive full reporting of occupancy results for target native and non-native amphibian and fish species, a comparison of costs and sensitivity for eDNA methods and field observation methods, and a detailed, site-specific protocol for continued eDNA inventorying and monitoring of target species. (Anticipated Project Completion - 2015)
Symposium & Workshop
FY 2013 New Start Project Selections
Points of Contact
Principal Investigator
Dr. Alexander Fremier
University of Idaho
Phone: 208-885-6405
Fax: 208-885-9080
Program Manager
Resource Conservation and Climate Change
SERDP and ESTCP
Document Types
- Fact Sheet - Brief project summary with links to related documents and points of contact.
- Final Report - Comprehensive report for every completed SERDP and ESTCP project that contains all technical results.
- Cost & Performance Report - Overview of ESTCP demonstration activities, results, and conclusions, standardized to facilitate implementation decisions.
- Technical Report - Additional interim reports, laboratory reports, demonstration reports, and technology survey reports.
- Guidance - Instructional information on technical topics such as protocols and user’s guides.
- Workshop Report - Summary of workshop discussion and findings.
- Multimedia - On demand videos, animations, and webcasts highlighting featured initiatives or technologies.
- Model/Software - Computer programs and applications available for download.
- Database - Digitally organized collection of data available to search and access.