Expanding the toolkit for assessing marine biodiversity

Environmental DNA (eDNA), is a powerful tool for researchers seeking to understand aquatic ecosystems. As organisms live in and navigate their aquatic habitat, they leave behind a trail of shed cells, skin, waste, and mucus. Just a few drops of water can contain this cellular material, in addition to microscopic animals, algae, viruses, and free DNA. This pool of genetic material is like nature’s fingerprint. Researchers can use these genetic clues to identify this diverse cast of characters in oceans, lakes, and rivers long after they have moved on.

A special issue of Oceanography magazine highlights the Marine Biodiversity Observation Network (MBON). The cover of the special issue features Ray Troll’s rendition of life in the sea colorized by Grace Freeman that was originally featured in the 1994 book Planet Ocean: A Story of Life, the Sea and Dancing to the Fossil Record, by Bradford Matson and Ray Troll (Ten Speed Press, 133 pp.). Image: © 1994 Ray Troll/Grace Freeman

Marine biodiversity is a measure of the abundance of individuals and species in the ocean. This interconnected mosaic of organisms—from the smallest plankton to the largest whales—supports food webs, produces the air we breathe, and regulates our climate.

Measuring biodiversity is essential to monitoring ecosystem health. However, differences in the type, frequency, spatial scale, and channels for sharing biodiversity data have made this a difficult task.

eDNA is a relatively new field—but one that is growing rapidly. It has the potential to disrupt paradigms for studying biodiversity that were developed using traditional observation and sampling methods. eDNA can reveal the changing distribution of life in the sea over space (both horizontally and vertically) and time. eDNA analyses yield results similar to those obtained using traditional observation methods, are complementary to them, and because of the breadth of information provided, they have the potential to improve conservation and management practices.

MBARI is poised to bring novel eDNA analyses to broad applications through innovations in sampling methodology and autonomous platforms. Coupled with the development of new technology and standardized methods, eDNA offers a means to scale biological observations to a global level. On a global scale, eDNA analyses can ultimately result in a far better understanding of marine biodiversity and contribute to better management and sustainable use of the world ocean.

The Marine Biodiversity Observation Network (MBON) is helping realize a vision for a global eDNA observation network. Since 2014, MBON has been laying the foundation to enhance our understanding of life in the sea from local to global scales. Established by the US National Oceanographic Partnership Program, MBON spans the science to monitor life in the sea to the people and partnerships needed to build and operate a sustained monitoring system.

MBON launched with demonstration projects in the Florida Keys, Monterey Bay, Santa Barbara Channel, and the Chukchi Sea in the Arctic. Senior Scientist Francisco Chavez leads MBARI’s MBON effort to assess pelagic, or open-ocean, biodiversity within Monterey Bay National Marine Sanctuary.

It is not only about figuring out “who” and “how many” are present—MBON also seeks to understand how organisms use, move through, and interact with their environment from “birth” to death. MBON leverages various tools to better understand ocean health, coupling information from new and emerging technologies with models to advance ecological forecasting.

“Laying this foundation requires partnerships across government, academic, and private sector groups. This includes securing the required resources to develop and apply scalable methods that will provide the information required by decision makers to maintain a healthy and sustainable ‘Planet Ocean,’” —MBARI Senior Scientist Francisco Chavez

Chavez served as guest editor for a collection of papers published in a special edition of Oceanography that highlights the groundwork of MBON, from the development of monitoring methods and best practices to the importance of partnerships to advancing data and knowledge systems that are accessible and useful to a wide range of people.

Environmental DNA (eDNA) is the pool of genetic material that can be collected from an environmental sample. As organisms live in and navigate their aquatic habitat, they leave behind a trail of shed cells, skin, waste, and mucus. Just a few drops of water can contain this cellular material, in addition to microscopic animals, algae, viruses, and free DNA. Scientists use these genetic clues to identify this diverse cast of characters long after they’ve moved on.

eDNA has been a critical tool for MBARI researchers studying biodiversity in Monterey Bay. The MBON project has been developing best practices and standards for eDNA analyses, and resolving the myriad of methodological challenges associated with the new techniques.

A research diver lays out a transect to survey the abundance and diversity of organisms living in a kelp forest near Santa Barbara, California. Image: SBC LTER

In a paper published this year in Scientific Reports, Chavez and MBARI Senior Research Technician Kathleen Pitz joined researchers from the University of California, Santa Barbara—Robert Miller, Thomas Lamy (now at the University of Montpelier), and Christie Yorke—to illustrate how eDNA can help us understand the health of kelp forests and other important marine habitats off the California coast.

For the study—a collaboration with the Southern California Bight Marine Biodiversity Observation Network and Central and Northern California Ocean Observing System (CenCOOS) Central California Marine Biodiversity Observation Network—the researchers compared the results of eDNA samples taken from nine sites along the Santa Barbara coast and two off Santa Cruz Island to the results of underwater visual censuses taken at those same locations. Comparing the visual and eDNA-based data allowed the team to begin to answer questions around how well eDNA would detect different species known to be present in the area.

Using eDNA, researchers detected species like this leopard shark (Triakis semifasciata) not normally seen by divers in their visual surveys. Image: © Monterey Bay Aquarium

For almost 20 years, researchers at the Santa Barbara Coastal Long-Term Ecological Research (SBC LTER) site have conducted detailed censuses of the majestic kelp forests off Santa Barbara’s coast. While these visual surveys have provided critical long-term observations of the region, this method requires intensive time and resources to deploy divers or specialized equipment like cameras. Even then, species that are absent at certain times of day, cryptic or invisible to the naked eye, or rare may not be represented by the census.

The study revealed that eDNA could detect a higher number of species than the visual surveys because fish can secrete DNA through mucus or other waste that would otherwise be invisible. The higher resolution of eDNA results compared to the underwater survey data gave the researchers a clearer picture of the presence and distribution of the different fish species and fish families in the region.

In terms of abundance, the eDNA species detections align with the information taken by underwater visual censuses. But eDNA was more effective at identifying the rare and less commonly counted species such as leopard sharks (Triakis semifasciata) and bat rays (Myliobatis californica) in comparison to the diver surveys. It also, for the first time at the SBC LTER, detected species such as California lizardfish (Synodus lucioceps) and barred surfperch (Amphistichus argenteus)—fish that are known to live in nearby sandy bottom areas—and the highly mobile white shark (Carcharodon carcharias).

The study demonstrates that eDNA is a powerful tool for scaling up observations in support of coastal ecosystem management, especially when used in concert with additional data sources.

The MBON project is unique in the way that it has integrated data from the global scale to the microscopic scale. Satellite imagery reveals patterns at the ocean’s surface across entire hemispheres, animal tagging tracks movement across kilometers-wide swaths, and eDNA provides a snapshot of biodiversity in just a small sample of water.

Similar to what is done for weather observations, the vision for a fully operational MBON is to make routine observations of life in the sea to provide information about status, trends, and shifts over time. Articles presented in the special edition highlight results from the demonstration projects and emphasize the importance of utilizing the information gathered to solve real-life challenges—particularly how people and our changing climate are affecting marine life and their habitats—and how these changes impact society.

MBARI researchers are now looking to investigate the factors that influence the presence of eDNA in an environmental sample. How long does eDNA persist in the environment after an organism leaves it behind? How far does it drift in the dynamic ocean ecosystem? How can we account for animals that shed greater quantities of eDNA?

This work demonstrates how eDNA can expand ocean monitoring, especially for rare species or habitats that are hard to observe, like the deep sea. Detecting eDNA requires much less effort and cost than sending out divers or submersibles to survey marine environments.

As a co-lead of the Marine Life 2030 Program of the UN Decade of Ocean Science for Sustainable Development, MBON is developing an information management and forecasting system for sustainable development and conservation of life in the sea.

MBARI is leading MBON efforts to engage partner organizations to build capacity for ocean monitoring and share information that will enhance our ability to make informed coastal management decisions. Ultimately, eDNA and novel tracking tools will allow us to better understand and protect our blue planet and the millions of species who call it home.

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