Scientists use DNA sequencing to identify marine animals from only seawater

“There are plenty of fish in the sea.” But which kinds of fish are where, and when? It’s a big question that scientists are now one step closer to answering.

Scientists at the Center for Oceans Solutions at Stanford University and at the University of Washington are helping to usher in a new era of ocean monitoring using bold new tools based on cutting-edge DNA sequencing technology.  

Visitors to the Monterey Bay Aquarium’s Open Sea tank exhibit observe a sea turtle, sardines, tuna, and other fish. Scientists used this controlled environment to test new DNA sequencing technology to identify marine animals. Credit: Randy Wilder, Monterey Bay Aquarium.

Tracking the presence and abundance of fishes and other ocean wildlife is a critical aspect of understanding marine ecosystems and applying science-based policy. Traditional methods of ocean monitoring can be time-consuming, expensive, and error-prone because they often involve boat-based scuba divers counting individual animals. In some cases, these methods can be invasive, as trawling or other fishing techniques are used to collect animals.

The new technology is based on environmental DNA, or “eDNA”, found in seawater. As animals go about their lives, they slough off tissue and dead skin cells, just as pets shed hair on the couch. These cells break down and leak their naked, free-floating DNA into the surrounding seawater. Scientists can now collect this seawater, extract eDNA from it, and sequence it to reveal the identity of the animals present.

With the advent of faster and cheaper DNA sequencing, researchers have increasingly explored these methods to study microbes or, more recently, fish in freshwater lakes.  

Now, as detailed in a new article just published in the journal PLoS ONE, Center for Ocean Solutions scientists have successfully tested this technology in the ocean for marine fish. The study’s authors were Ryan Kelly, formerly an Early Career Fellow at the Center for Ocean Solutions and now faculty at University of Washington, joined by Center Early Career Fellows Jesse Port and Kevan Yamahara and Center Science Director Larry Crowder.

The group sought a ‘closed’ environment so that they could compare the results of the eDNA sequencing with the identities of the animals known to be present. What better place to test than the 1.2 million gallon Open Sea tank exhibit at the Center’s partner, the Monterey Bay Aquarium?

Kelly and colleagues collected water from the Open Sea tank itself, from the food added to it, and from the seawater pipes that supply it with water. They detected the majority of the bony fish residents – tuna, sardines – from their eDNA. The relative abundances of eDNA roughly matched the abundances of animals in the tank, suggesting that in the future these tools will provide a window into not just which animals are there, but also how many.

Left: Jon Hoech, Director of Husbandry Operations at the Monterey Bay Aquarium (left) and Center for Ocean Solutions Early Career Fellow Kevan Yamahara (right) collect seawater from the supply pipe feeding the aquarium’s Open Sea tank exhibit. Right: Center Early Career Fellow Jesse Port collects seawater in a bottle from the top of the Open Sea tank exhibit while Jon Hoech assists. Credit: Jesse Port, Center for Ocean Solutions.

The technology is so sensitive that Kelly and his colleagues were even able to detect eDNA from non-tank residents like other fishes and even humans. These eDNA sources appear to have come from the fish food and the tank’s seawater supply pipe, drawn from the Monterey Bay. The Bay itself receives terrestrial input from agricultural run-off, human use, and other sources.

Some of the tank residents, such as a sea turtle and giant sunfish, were not detected in the test. This may be because of technological bias in the current tools, sample size, or that these organisms shed DNA differently than their neighbors.

“To really make this approach relevant to monitoring, further enhancement and refinement of the technology will be needed, including more molecular work, a better understanding of eDNA fate and transport in the ocean, and broader species detection”, adds Jesse Port.

Interestingly, the test detected sea otter eDNA from the tank’s seawater supply pipe, originating either from nearby exhibits housing otters or from wild otters living in Monterey Bay near the pipe’s intake. This demonstrates that these methods may be applicable to marine mammal monitoring in Monterey Bay, a key priority for the management of this important ecosystem.

This project demonstrated the ability of eDNA sequencing technology to allow scientists to monitor fish populations from the comfort of dry land. The test in the aquarium’s Open Sea tank exhibit was a crucial proof-of-principle, showing that while a few refinements are needed, this technology is poised to complement and strengthen ocean monitoring in the wild. First stop: the Open Sea tank exhibit at the Monterey Bay Aquarium. Next stop: the open sea!

by Liz Hambleton, Science Communications Early Career Fellow at the Center for Ocean Solutions. The research article “Using Environmental DNA to Census Marine Fishes in a Large Mesocosm” by Kelly et al. is freely available online from the journal PLoS ONE.