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U.S. Geological Survey - Great Lakes Science Center

Environmental DNA and genomics: novel approaches to species assessment

Processing eDNA samples

Environmental DNA (eDNA) is quickly becoming a revolutionary tool for the rapid detection and quantification of invasive or imperiled native species. If new invasive species are introduced and begin to spread, it is critical for environmental managers to be able to monitor the species’ progress in order to stave off expansion and minimize ecological and economic costs. Managers monitor and inventory native species to ensure conservation goals are met, but monitoring programs can be challenged by constraints to time and budget. Environmental DNA sampling techniques offer cost-effective and timely solutions for both invasive and native species monitoring.

Genomic, or gene-based, techniques involve collecting samples, isolating DNA suspended in the sample (shed from skin, defecation, or biofilm), and identifying the DNA to the species level by matching it to known DNA sequences from a public database. Some newer methods even allow for estimating not just the presence or absence of a species, but the actual abundance of the species in that area.

Scientists at the USGS Great Lakes Science Center (GLSC) are at the forefront of exploring eDNA and other genomic tools for detecting and quantifying species, from microbes to fish. Presently, GLSC scientists are targeting the round goby, rusty crayfish, and New Zealand mudsnail. Scientists have tested and validated several DNA markers for use in direct monitoring applications for the invasive species itself. Other research focuses on characterization microbial communities in the soil associated with certain invasive plants. In the future, GLSC scientists will compare eDNA results with results from more costly traditional methods to highlight the accuracy and usefulness of this technology.

The techniques developed through this research will enable environmental managers at multiple scales to easily assess the threat of a potential invader or to understand the spread and abundance of species already living in an ecosystem.

Round goby: Detection and abundance

In initial field results, scientists consistently detected round goby eDNA marker in high quantities alongside visual surveys and minnow trapping of gobies. The round goby is an invasive species that has successfully established itself throughout the Great Lakes and has become an important part of the lake food web. Because the goby utilizes rocky habitats that are hard to sample with traditional trawl nets, scientists wonder whether their assessments of the biomass of gobies are accurate. They have sought new methods to corroborate or calibrate the estimates.

Initial experiments in the lab suggest that the strength of the eDNA signal for fish may be dependent on the biomass of the fish population. This means that eDNA quantities correlate to the number and size of round goby present. Findings also suggest that the eDNA signal can still be detected in a controlled aquatic environment at early summer water temperatures of 19°C for at least 72 hours after the organism leaves the system. This may mean that the presence or abundance of organisms in their natural habitat could be detected days after they leave the area.

Oriental bittersweet: Assessing bacterial communities

Invasive lianas, or woody climbing plants, like Oriental bittersweet, are a significant threat to public and private lands across North America. Lianas can impact tree mortality and therefore successive stages of forests. In addition, they can directly compete with native vegetation for resources in the soil. National parks and national wildlife refuges in eastern North America are especially threatened by Oriental bittersweet and a few other lianas. Managers currently use traditional, labor-intensive techniques, such as physically cutting them down or applying herbicide, to deal with these invaders.

Scientists use microbial genomics to characterize differences in bacterial communities within the soil zone of invasive and native species of woody vines, including invasive Oriental bittersweet and American bittersweet, which is native. The soil zone is the small area around a plant’s roots that is directly influenced by root secretions and associated microorganisms. There is evidence that certain soil microbes are stimulated by secretions from invasive plants, in turn promoting the plant’s growth. At this point, it is not clear whether similar plant-microbe interactions occur in the highly successful Oriental bittersweet. Scientists at the GLSC are attempting to characterize the differences among soil communities and describe associations between soil communities and certain plants in order to develop tools for controlling invasive species. 

Photo Credit: 
USGS. Processing eDNA samples.

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