Aquatic Species Surveillance Using Environmental DNA

Project ID: 2105
Principal Investigator: Kevin Kelly
Research Topic: Ecosystem Needs
Funded Fiscal Years: 2014
Keywords: enviromental dna, edna, aquatic species

Research Question

Is it possible to perform environmental DNA (eDNA) survey to test for the presence and distribution of aquatic species (including endangered species) that requires our attention as they relate to the operations and maintenance of Reclamation facilities?

Is it possible for eDNA to serve as a more sensitive and representative sampling for rare and elusive targets that are impossible or difficult to find using traditional surveillance methods?

Need and Benefit

Although eDNA surveillance tools developed here would benefit all five regions, depending on target aquatic species, initial efforts of this research project will be done in collaboration with the Lower Colorado River Multi-Species Conservation Program (LCR MSCP). LCR MSCP has developed the Habitat Conservation Plan (HCP), which described general and species-specific conservation measures for twenty-six covered species and five evaluation species on the lower Colorado River ( Reclamation, through the Lower Colorado Regional Office, is the lead implementing agency for LCR MSCP.

Major components of the HCP include native fish population augmentation, research and monitoring of LCR MSCP species and their habitats, maintenance of existing covered species habitat, creation and long-term management of new habitat, and adaptive management. The plan includes conservation measures to raise and stock over 1.2 million native fish into the lower Colorado River and to create and manage over 8,100 acres of riparian, marsh, and backwater habitats for native species.

One component of the LCR MSCP program is committed to the conservation of federally endangered fish along the lower Colorado River. Parts of this activity include monitoring of the existing populations of endangered fish species (i.e., razorback sucker, bonytail, humpback chub, flannelmouth sucker) that will lead to the development of a management plan, and ongoing research on LCR MSCP fish species that will allow for more efficient rearing and monitoring tools, which will also provide the basis for future management actions. Current monitoring includes a variety of traditional survey techniques such as netting, electrofishing, and remote sensing taking place at pre-determined intervals for fish population estimates from Lake Mead, Lake Mohave, Lake Havasu, and other areas along the lower Colorado River. However, rare target species such as threatened or endangered fish species are difficult to detect, especially in certain locations, during particular time periods or development stages, potentially causing a bias in study outcomes that may lead to harmful or inadequate management actions. Since fish species leave a molecular imprint in the water, where there is an expanding cloud of eDNA to detect even when the target fish species is elusive or rare, is it possible to performed sensitive aquatic eDNA surveillance.

Another component of the LCR MSCP program is the Wildlife Program which focus on the conservation, monitoring, and management of 27 covered and evaluation terrestrial species. Included are semi-aquatic amphibians (Colorado River Toad, Lowland Leopard Frog, and Relict Leopard Frog), species which may also be monitored using eDNA. Similar work has been successfully accomplished in tracking the American bullfrog (Rana=Lithobates catesbeiana), an invasive aquatic amphibian from western North America introduced into ecosystems around the world, using eDNA. Another non-native species that may also need to be monitored is the Rio Grande Leopard Frog (Rana berlandien), which is currently only known to exist in the Yuma, AZ area as far north as Imperial Dam on the lower Colorado River. This species is believed to be contributing to the population decline of the Lowland Leopard frog, a LCR MCSP targeted species. We proposed to adapt the same eDNA surveillance tools here for LCR MSCP amphibians as well as the American bullfrog and Rio Grande Leopard frog since they are responsible for the decline of native amphibians. Similar to the challenges of surveying endangered fish species described, frog and toad species are also difficult to detect in some locations. The Wildlife Program has a need to assess species distribution using eDNA to support habitat management activities.

Contributing Partners

Contact the Principal Investigator for information about partners.

Research Products

Bureau of Reclamation Review

The following documents were reviewed by experts in fields relating to this project's study and findings. The results were determined to be achieved using valid means.

Aquatic Species Survelliance Using Environmental DNA (eDNA) (final, PDF, 422KB)
By Kevin Kelly
Research Product completed on May 18, 2015

Environmental DNA or eDNA has been defined as genetic material obtained directly from environmental samples (soil, sediment, water, etc.) without any obvious signs of biological source material. The concept originated from the study of micro-organisms (e.g., metagenomics) in environmental samples, but has developed to include eDNA analysis of environmental samples for the detection of rare or elusive macro-organisms. Due to the difficulty of monitoring rare or elusive aquatic species by tradi

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Last Updated: 6/22/20