Snapshots of Biodiversity: eDNA as a methodology for species detection

Nicole Conner wrote this post as a project for Stacy Krueger-Hadfield’s Conservation Genetics course at the University of Alabama at Birmingham.  She is a Master’s student in Dr. Thane Wibbels’ lab where she is developing new protocol to detect diamondback terrapins off the coast of Alabama using eDNA. This will allow for an accurate and streamlined process for evaluating the distribution of the species in Alabama. Nicole completed a B.S. in Marine Science and Biology at the University of Alabama and participated in an REU internship through the Duke University Marine Lab in 2017. Throughout her life she has been passionate about the conservation of marine species and hopes to continue participating in research that improves conservation management approaches.

How do we detect an organism that can’t be seen? Or how can we reliably identify a species’ geographic range if it spends its life underwater?

The answer is actually pretty simple: environmental DNA, or eDNA. Implementation of eDNA methods, however, is not quite as simple. Particularly when dealing with aquatic environments, eDNA study results can be confounded by factors such as degradation, dispersal through tides and currents, and turbidity.

DNA can be found in the excrement, saliva, hair, sloughed off tissues, feathers, or even egg shells (Waits and Paetkau, 2005). Often times it ends up dispersed throughout the environment where it can be collected in soil, water, air, or fecal samples. Using PCR to amplify target sequences in DNA, researchers can determine whether a sample contains eDNA from a certain species and even quantify the amount of target sequences in each sample to estimate the abundance of that organism. 

When eDNA was first being applied in ecological studies, Ficetola and co-authors used it to detect the presence of the American bullfrog, Rana catesbeiana (Ficetola et al., 2008). Since then, it has been widely applied to a variety of studies including the detection of the presence of rare or cryptic species, the identification of diet items, and even population structures (Waits and Paetkau, 2005). I’m currently working on developing a PCR method that will detect the presence of Diamondback terrapin eDNA on the coast of Alabama in order to map their distribution. 

With the potential for widespread application of eDNA technology, though, comes the need for a complete understanding of how exactly it works. How reliable is it? Can we apply it to every organism? What does the detection of eDNA really tell us?

A shoal of juvenile Silver Trevally (Pseudocaranx dentex). © Fairy Bower, Manly, NSW

In a recent study, Murakami et al. (2019)investigated how dispersion and degradation processes affect the collection of eDNA at sea and evaluated whether eDNA is a useful tool in the ocean. They set up a cage of 49 hatchery-reared striped jack juveniles in the water off a floating pier at the Maizuru Fisheries Research Station in Maizuru Bay, the Sea of Japan.  Due to the pier’s position on a southern edge of the bay, sampling locations were selected northeast and northwest of the cage. Then they collected water from 1m away all the way out to 1000m away in either direction at varying depths (1-8m).  These samples were collected at regular intervals over a 24-hour period after submerging the fish, and then again over 24 hours after removing the cage. After sampling, the researchers filtered out the eDNA from the samples and used species-specific primers and a probe to amplify striped jack DNA in qPCR.

Murakami et al. (2019) noted several trends in their analyses. They saw that about 72% of the positive water samples were collected within 30 m of the cage and that eDNA concentration decreased exponentially with distance from the source. They also noticed that at a given station, the eDNA concentration decreased 63.5% in an hour. In addition, two hours after removing the cage, no target DNA was detectable; so there was a clear decrease in eDNA concentration with time. 

Murakami et al. (2019) were able to make several inferences about eDNA collection in an oceanic environment based on these results. They suggested that eDNA retention time was shorter in ocean water than in freshwater. This was attributed to a combination of biological decay and physical dispersion seen in the sea water, as well as higher water temperatures which are known to accelerate DNA degradation. In regards to depth, they noted that eDNA was most frequently found at the surface, which was either because it was staying in the layer in which it was released or due to buoyancy of the material. Overall, they concluded that in oceanic environments, eDNA can accurately reveal the presence and abundance of an organism within brief time periods and over small areas. (Murakami et al., 2019).

So what does eDNA tell us? According to this study, eDNA in a marine setting gives us a snapshot of the diversity found in specific location during a short time frame. Moving forward, this information can better inform the design of studies based in marine environments. As we continue to learn more about the robustness of eDNA methodology from studies such as this one, the hope is that results produced will become increasingly more reliable.

References

Ficetola, G. F., Miaud, C., Pompanon, F., and Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters 4, 423–425.

Murakami, H., Yoon, S., Kasai, A., Minamoto, T., Yamamoto, S., Sakata, M. K., … & Masuda, R. (2019). Dispersion and degradation of environmental DNA from caged fish in a marine environment. Fisheries Science, 1-11.

Waits, L. P., & Paetkau, D. (2005). Noninvasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. The Journal of Wildlife Management, 69(4), 1419-1433

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About Stacy Krueger-Hadfield

I am a marine evolutionary ecologist interested in the impacts of seascapes and complex life cycles on marine population dynamics. I use natural history, manipulative field experiments and population genetic and genomic approaches with algal and invertebrate models in temperate rocky shores,estuaries and the open ocean.
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