Sampling Ocean Waters for Species’ DNA Shows Promise in Ecosystem Management

Cost-effective method for measuring biodiversity could improve monitoring and oversight of fisheries, protected areas, and more


Sampling Ocean Waters for Species’ DNA Shows Promise in Ecosystem Management
Pipetting sample into tray for DNA testing
Even tiny water samples, like this droplet, often contain DNA of the fish and other species that live in an area. Using new eDNA sampling and analysis, scientists can help improve management of marine protected areas.
Andrew Brookes Getty Images

Effectively managing marine ecosystems—by preserving biodiversity, protecting ocean-based livelihoods, and ensuring sustainable fisheries—requires a lot of information about threats, and about species location, abundance, and food and habitat needs. Regularly collecting this data as part of a monitoring program allows for informed and adaptive decision making on how best to promote ecosystem-based management as well as the design, implementation, and assessment of marine protected areas (MPAs).


Traditional and new approaches

Traditional methods for measuring the breadth and abundance of marine biodiversity can be expensive, time-intensive, and challenging to conduct. This is particularly true when assessing rare or cryptic species—those that appear identical to another but are genetically distinct—or when operating in remote areas. In particular, the lack of high-quality data on biodiversity in isolated locations has limited researchers’ ability to track changes over time, which in turn has made it harder to estimate the effectiveness of MPAs and other fisheries management measures.

Fortunately, scientists and managers have an exciting new alternative to assess marine conditions: environmental DNA (eDNA) analysis, which involves collecting and testing water samples for DNA traces of organisms. This saves researchers from having to observe or capture individual species and, because of this, eDNA is better at identifying a wide diversity of marine life, including rare and endangered species. Scientists can use the method to survey community biodiversity and relative abundance in a rapid, repeatable, and more affordable manner.

This emerging genetic analysis does have limitations. For example, it can’t yet reveal the age and size of species. However, especially when used in conjunction with traditional methods such as scuba or net-based surveys and emerging technologies such as the use of underwater cameras that record species activity, eDNA could streamline and standardize data collection to the benefit of marine managers around the globe.

Putting eDNA to use

One place that’s happening is Ascension Island, a remote U.K. overseas territory in the South Atlantic Ocean. With support from the Pew Bertarelli Ocean Legacy Project and Pew’s conservation science program, managers of the Ascension Island MPA are establishing an eDNA laboratory and applying next generation sequencing technology, initially for two purposes: to monitor for the presence of key species using the MPA, and to detect non-native species—in near-real time—that pose biosecurity threats, including those species that may have arrived via visiting vessels.

Such data will help Ascension’s MPA managers evaluate whether protections are effectively preserving marine life. If successful, Ascension Island’s pilot program may serve as a case study in effective, low-cost monitoring protocols that can be replicated in other remote MPAs.

Pew’s past support for the use of eDNA in conservation and fisheries management has already shown promise in other marine ecosystems. For example, researchers funded by Pew were recently able to use eDNA techniques to identify distinct deep-sea communities in seamounts and abyssal plains in the Clarion-Clipperton Zone of the Pacific Ocean, highlighting the need to protect biodiversity in regions targeted for deep sea mining. Similarly, Pew-funded research has shown that eDNA surveys are better able to detect the wide diversity of shark species than both scuba- and video-camera based methods. A lead researcher on this project, the marine ecologist Stefano Mariani, said, “eDNA has great potential for complementing traditional survey methods and improving species detection. It could definitely lead to more efficient conservation strategies for threatened species.”

Pew’s grant to help establish the Ascension Island eDNA lab adds to our growing portfolio of initiatives assisting MPA managers around the world. For example, in Tristan da Cunha, the Pew Bertarelli Ocean Legacy Project is supporting the application of a new monitoring platform, Global Fishing Watch Marine Manager, which allows marine managers and researchers to combine numerous datasets on marine biology, oceanographic conditions, and human activity to make informed decisions to better manage the ocean. In the Pacific Ocean, the Pew Bertarelli Ocean Legacy Project worked with OceanMind, a U.K.-based nonprofit, to leverage satellite technology in real-time enforcement against illegal, unreported, and unregulated fishing within the Pitcairn Island Marine Reserve.

Without new, effective, and low-cost methods to detect species and determine their abundance, prey, and habitat needs, fisheries and MPA managers will have a hard time meeting their objectives. New biodiversity monitoring tools such as eDNA analysis can bolster the design and management of effective marine governance programs, including ecosystem-based fisheries management and MPAs, and inform ongoing policy discussions to ensure that the ocean is able to provide a diverse suite of ecosystem goods and services far into the future.

Jim Palardy is a project director with The Pew Charitable Trusts’ conservation science program and Johnny Briggs is a senior officer with the Pew Bertarelli Ocean Legacy Project.


DNA in Seawater Reveals Presence of Sharks—Even When They’re Unseen

Quick View

Marine scientists rely on traditional techniques, including underwater video surveys and visual observation, to keep track of migratory species such as sharks. But to do that effectively requires being in the right place at the right time, which is often hard to achieve.


How Scientists Use DNA to Find Sharks

Quick View

By analyzing environmental DNA (or eDNA), a relatively inexpensive and non-invasive technique, researchers can determine if a species is—or has recently been—in the area. The work, led by Professor Stefano Mariani and researcher Judith Bakker from the University of Salford, UK, is detailed in a study published Dec. 4 in Scientific Reports.