Fisheries CSI: DNA in the Water

By Brandon Peoples

Fisheries managers often must monitor rare species.  Regardless of the sampling gear being used, detecting numerically rare fishes can be difficult.  With traditional fisheries gears, increasing detectability often means increasing sampling effort—which costs more money.

Recently, researchers have found a new way to monitor rare species: environmental DNA (eDNA). Like any animal, fishes leave minute traces of themselves in their environment.  For fishes, this is usually in the form of sloughed-off mucus, feces, or bits of scales.  Detecting fish species using eDNA is fairly straightforward: just collect a water sample and screen it for the appropriate signature at the right genetic locus.

Sampling water for (fish) eDNA. (Source)

Recent research suggests that eDNA may be a more efficient and inexpensive way of detecting rare fishes than more traditional methods.  Below, I briefly summarize two recent papers in which eDNA has been used to monitor rare fishes.

Jerde, C.L., A.R. Mahon, W.L. Chadderton, and D.M. Lodge. 2011. “Sight-unseen” detection of rare aquatic species using environmental DNA. Conservation letters 4:150–157

In 2009, Asian carps (silver and bighead) were poised to invade Lake Michigan from a series of canals in Chicago, IL.  The only thing stopping them was a system of electric barriers placed across the Des Plaines River.  To identify the “invasion front” where carp were moving upstream, agencies conducted 62 days of electrofishing.  Over the course of that year, the authors were collecting water samples for an eDNA survey.  For analysis, detections were standardized by effort (catch-per-unit-effort, CPUE) in units of person hours. CPUE was considerably higher for the eDNA survey than for the electrofishing survey.  In fact, the eDNA survey detected carp in locations where none were found with electrofishing—very close to Lake Michigan, beyond the electric barrier.

Exotic species, such as these Asian carp, can be monitored using eDNA. (Source)

Minamoto, T., H. Yamanaka, T. Takahara, M.N. Honjo, and Z. Kawabata. 2011. Surveillance of fish species composition using environmental DNA. Limnology 13:193–197

Minamoto and co-authors sought to extend the work of Jerde et al. by using eDNA to survey for multiple fish species at once.  First, they kept fish of 5 species in aquaria.  After 48 hours, the authors ran water samples from the aquaria to demonstrate that eDNA could be extracted.  Then, they took water samples from 3 sites on the Yura River in Japan.  The authors detected 6 fish species in the samples. Some fish seemed more detectable, probably because of differences in body size and mucus excretion.  Although the eDNA sampling did not detect all species found in the Yura River, the authors believe that increasing sampling effort is feasible.

The Yura River in Japan has undergone eDNA testing to count fish species. (Source)

We still have a lot to learn before eDNA becomes mainstream.  How long does a piece of DNA persist in the environment after it leaves a fish?  What is the relationship between a species’ abundance in a site and its detectability with eDNA?  Scientists are currently working on those questions.   Until then, keep an eye out for new studies on how the use of eDNA is revolutionizing fisheries science.