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Katie Zarn collects an eDNA sample from Fossil Creek in Arizona. Photo by Matthew R. Jones.Keeping tabs on the whereabouts of invasive or endangered species is an important job for managers, but it can be a nearly impossible task to accomplish across a vast landscape. Traditionally, species monitoring has relied on physical observations of organisms in the field. These surveys can be labor-intensive, particularly when surveying in remote areas or for organisms that are rare or difficult to find. Today, there is a powerful new approach that can determine the presence of a species simply by sampling a cup of water: environmental DNA (eDNA).
Organisms continually shed cells containing their DNA into their surroundings. For example, DNA in skin cells sloughed from a fish can be found in water, or DNA in plant pollen can be found in the air. That DNA persists in the environment, where it can be collected in an air, soil, or water sample and analyzed for species of interest.
Environmental DNA is major breakthrough in wildlife and fish monitoring. It ties traditional field-based ecology to advanced computational tools and exacting molecular methods, such as quantitative polymerase chain reaction (qPCR), which is able to detect DNA from just a couple cells in an environmental sample. It can reveal important information about species presence or absence more quickly and cost-effectively than traditional sampling techniques. It is particularly useful for detecting organisms in low abundance, like threatened and endangered species or individuals at the leading edge of an invasion. For example, scientists used filtered water samples to detect the spread of invasive feral pigs in the Southwestern United States and Burmese python in Florida. Scientists are using similar techniques in the Rocky Mountains to determine the distribution of endangered bull trout, invasive brook trout, Canada lynx, and wolverine.
This technology has been used primarily to survey for fishes and amphibians. However, samples collected from water, air, and soil all contain DNA of many species, and applications are expanding to other aquatic taxa, such as mollusks and insects, as well as semi-aquatic mammals like river otter and beaver. Environmental DNA is also found in snow tracks allowing reliable species identification of carnivores such as wolverine, fisher, and Canada lynx.
Lab techniques for eDNA analysis vary depending on the specific research question. For example, targeted analysis designed to detect a particular species may be used to detect the presence or absence of a rare species. Nontargeted approaches are less sensitive for individual species, but can be used to answer questions about community diversity or reveal previously unknown members of ecological communities. The National Genomics center is also pioneering a third option, high-throughput qPCR, which completes multiple targeted analyses simultaneously. For example, identifying which species is responsible for a track in snow is one of the many potential application for high-throughput qPCR.
The eDNAtlas is an open-access database developed through crowd-sourced field surveys that provides precise spatial information on the occurrence locations of aquatic species in the United States. The eDNA samples constituting the database are collected using a standardized field sampling protocol by numerous natural resource agencies and non-governmental organizations partnered with the National Genomics Center for Wildlife and Fish Conservation. The eDNAtlas database contains results from thousands of sites and dozens of species and is updated annually with additional results for a growing list of species. Funding to develop the eDNAtlas database was provided by the National Fish and Wildlife Foundation Bring Back the Natives Program. Additional information can be found here: project background, eDNA sampling grid map, & eDNAtlas interactive results map.
We have designed and validated over 75 qPCR assays for eDNA applications including both aquatic and terrestrial species. Assays are typically designed on a project-need basis then published in a peer-reviewed journal. We are continually designing and validating new assays and would love to work with you on your species of interest. If you do not see the species you are interested in listed on the Assay List, please contact Tommy Franklin (thomas.franklin@usda.gov) or Mike Young (michael.k.young@usda.gov).
If you do not see the species listed below that you are interested in working with, please do not hesitate to contact Tommy Franklin (thomas.franklin@usda.gov) or Jennifer Hernandez (jennifer.hernandez@usda.gov).
The bull trout is an Endangerd Species Act-listed species with a historical range that encompasses many waters across the Northwest. Though once abundant, bull trout have declined in many locations and are at risk from a changing climate, nonnative species, and habitat degradation. Informed conservation planning relies on sound and precise information about the distribution of bull trout in thousands of streams, but gathering this information is a daunting and expensive task. To overcome this problem, we coupled 1) predictions from the range-wide, spatially precise Climate Shield model on the location of natal habitats of bull trout with 2) a sampling template for every 8-digit hydrologic unit in the historical range of bull trout, based on the probability of detecting bull trout presence using environmental DNA (eDNA) sampling (McKelvey et al. 2016). The template consists of a master set of geospatially referenced sampling locations at 1-km intervals within each cold-water habitat. We also identified sampling locations at this same interval based on the U.S. Fish and Wildlife Service's designation of critical spawning and rearing habitat. Based on field tests of eDNA detection probabilities conducted by the National Genomics Center for Wildlife and Fish Conservation, this sampling approach will reliably determine the presence of populations of bull trout, as well as provide insights on non-spawning habitats used by adult and subadult fish. The result will be a rapid, robust, and repeatable range-wide assessment of natal habitats of this species. Additional information can be found here: project background & interactive map of bull trout eDNA survey results.
A guide for using eDNA methods to assist invasive fish eradication in streams. From Carim et al, 2020.The documents listed here provide necessary information for collecting environmental DNA samples from streams and snow tracks while avoiding sample contamination.
A full list of searchable NGC publications can be found here.
The NGC provides a variety of services to facilitate eDNA sampling. These include:
Sample analysis. Samples that have been collected using established protocols may be processed at the NGC for species that have quantitative PCR (qPCR) assays developed at the NGC or that have been developed elsewhere and used by the NGC previously. For aquatic species, our standard service includes assistance in determining an appropriate sampling design to meet your information needs, providing sampling materials (e. g. “kits”, pumps, and batteries) sufficient to complete the design, qPCR based species analysis for one or more species, uploading of results to the eDNAtlas, and sample archiving. We offer similar services for collection of carnivore DNA from snow tracks.
Assay development. Assay development is often required prior to qPCR-based eDNA analysis because species of interest are often local endemic species for which no assays have previously been developed. While fairly standard, assay development is a collaborative process between the investigator and the NGC: tissue samples must be obtained for the target species to facilitate in vitro testing, and environmental samples must be taken in both known positive and known negative locations to test field efficacy.
Training. We will travel to locations to provide hands-on training for field crews on how to use specific field protocols.
If you are interested in eDNA services through the NGC and pricing estimates please contact ngc@usda.gov.
If you would like to propose a project using eDNA, please contact Tommy Franklin (thomas.franklin@usda.gov) or Mike Young (michael.k.young@usda.gov).
If you would like to borrow equipment for eDNA sampling, please contact Jennifer Hernandez (jennifer.hernandez@usda.gov).
