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Environmental DNA is an effective tool for calculating marine biodiversity

New research from the University of California, Santa Barbara and MBARI demonstrated how environmental DNA (eDNA) could be a powerful tool for revealing marine biodiversity of fishes in Southern California kelp forests. Image: SBC LTER

Environmental DNA is an effective tool for calculating marine biodiversity

New research from the University of California, Santa Barbara and MBARI demonstrated how environmental DNA (eDNA) could be a powerful tool for revealing marine biodiversity of fishes in Southern California kelp forests. Image: SBC LTER

Assessing biodiversity—the abundance of individuals and species—is critical for understanding an ecosystem. But in the ocean, studying what lives beneath the surface presents several challenges. Now, researchers from the University of California, Santa Barbara (UCSB) and MBARI have shown that drifting bits of genetic material called environmental DNA, or eDNA, can be a valuable tool for monitoring coastal ecosystems. 

In a new paper in Scientific Reports, MBARI’s Francisco Chavez and Kathleen Pitz joined researchers from UCSB—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.

“This study demonstrates that eDNA performs as well, or better than, visual diver surveys in capturing biodiversity in kelp beds and provides a means to scale observations in support of improved coastal management,” said Francisco Chavez, a biological oceanographer at MBARI.

The lush kelp forests off the California coast teem with life. They provide shelter to a variety of fishes and invertebrates. 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. These towering underwater forests are highly productive aquatic environments, supporting not just the creatures living in the canopy and on the reefs, but also organisms on nearby beaches who feed on and live in the kelp wrack. Counting fish species and placing them in the context of their environmental conditions can reveal the effects of human activity and natural drivers on kelp and its ability to maintain the kelp forest communities.

But taking a census is more than just a matter of deploying divers to take a headcount. Researchers are also interested in beta diversity, which can be a somewhat convoluted concept for even seasoned ecologists.

“There are a lot of different ways to measure it, but the way I think of it is that it’s the turnover of species as you go from one place to another,” said Robert Miller, a coastal marine ecologist at UCSB who heads the research at the National Science Foundation-supported SBC LTER site. “How many new species are in a place compared to the last place you went to? And so that obviously increases the farther you go.”

Beta diversity is useful for measuring the overall state of biodiversity between given areas over time, which in turn provides some indication of those areas’ ecological health. A higher beta diversity number (more different species) could indicate robust systems that can support various, interconnected forms of life. A lower beta diversity number (fewer different species) might signal that conditions have become favorable to the survival of certain organisms, with effects that could reverberate into adjacent spaces.

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

Counting species at the SBC LTER can be tricky. Each census requires divers to conduct underwater visual surveys or to deploy and monitor special equipment, such as cameras. Even then, many fish species are mobile and often not represented during these surveys. “Some might be there outside the time you are sampling, say at night or at different times of day,” said Miller. Others, he added, are cryptic or too small to notice.

Enter eDNA.

“As organisms move through the water, they leave behind molecular traces of themselves through shed, excreted, or sloughed off material that contains their DNA,” explained Kathleen Pitz, a research associate at MBARI. “We now know it’s possible to detect this discarded DNA in seawater and identify which species it originated from.” 

Sampling the water and analyzing its DNA results in an inventory of the species that were in the vicinity during the time the sample was taken—a “Rosetta Stone” for biodiversity.

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 areas. “By comparing these two sources of data, both visual and eDNA-based, we could begin to answer some of the questions around how well eDNA would detect different fish species that we know are present in the area from this long visual time series,” explained Pitz.

“The eDNA was able to detect a lot more species than the diver counts, which is not particularly surprising because fish shed their DNA into the water, through their slime and breathing, et cetera,” said Miller. 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.

These Venn diagrams show the overlap of unique fish species, genera, and families detected by underwater visual census done by divers (blue) and eDNA (red). Illustration: Lamy et al. 2021 Scientific Reports via Creative Commons Attribution 4.0 International License.

In terms of abundance, the eDNA species detections align with the information taken by underwater visual censuses.

“They matched up pretty well with the diver surveys—the really abundant fish that were seen by the divers are really abundant in the eDNA samples as well,” said Miller. “The difference is really in the rarer species, or the commonly less counted species. We see these more consistently in the eDNA than in the diver surveys.” Species such as señorita (Oxyjulis californica), black surfperch (Embiotoca jacksoni), sheephead (Semicossyphus pulcher), and garibaldi (Hypsypops rubicundus) were found in higher relative abundance by both eDNA and visual surveys.

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

Meanwhile, eDNA succeeded in capturing the presence of leopard sharks (Triakis semifasciata) and bat rays (Myliobatis californica) where visual surveys did not. 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).

Is this the end of the diver survey, given eDNA’s powerful detection capabilities?

“The nice thing about eDNA is that it does provide that temporal integration, to give you a better idea of what might be there outside of the time you’re sampling,” said Miller. “But it can be hard to conclude whether they were really at the site.” The DNA may have traveled a long distance, and some fish may shed more than others. 

“We’re still learning about the different factors that control the presence of eDNA in seawater, such as how long DNA lasts in the water before degrading or how quickly a fish leaves behind enough material for us to detect its DNA within a sample,” added Pitz.

In addition, the fish DNA databases against which the metabarcoding results are referenced need to be improved. (Several DNA sequences detected could not be found in the library.) “More research,” Miller said, “will improve the confidence in interpreting eDNA data.”

“We don’t think it’s something that’s going to replace traditional methods, but it’s a really good additional data source that could be used to look at whether these fish communities and other communities are changing,” he added. 

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

This study complements several MBARI initiatives that leverage eDNA to examine the health of aquatic ecosystems. By deploying the Environmental Sample Processor (ESP)—a “lab in a can”—MBARI researchers can use eDNA like a fingerprint to monitor the health of diverse marine and freshwater environments.

MBARI’s Controlled, Agile, and Novel Ocean Network (CANON) experiment uses a variety of technologies, including eDNA, to understand ocean health. Image: Kelly Lance © 2019 MBARI

Chavez leads MBARI’s semiannual Controlled, Agile, and Novel Ocean Network (CANON) initiative. This interdisciplinary effort mobilizes a suite of technologies to collect oceanographic information about Monterey Bay. Past CANON experiments have deployed long-range autonomous underwater vehicles (LRAUVs) equipped with the ESP to sample eDNA. These samples—taken in conjunction with ROV dives, time-lapse video, and acoustic measurements for comparison and context—can provide important insight into Monterey Bay. Our hope is that with these new tools, researchers will be able to better predict what the future holds for ocean ecosystems. In addition, eDNA captured in a historical archive of samples from two of MBARI’s long-time monitoring projects promises to unlock the secrets of Monterey Bay over the past 30 years.

ESP technology provides vital data on freshwater environments too. 

The Sensors: Underwater Research of the Future (SURF) Center at MBARI and collaborators at Monterey Bay Aquarium, National Oceanic and Atmospheric Administration (NOAA), and the California State Polytechnic University, San Luis Obispo deployed the ESP at Scott Creek, just north of Santa Cruz, California, to improve sampling to detect endangered coho salmon (Oncorhynchus kisutch) and watch for non-native mud snails (Potamopyrgus antipodarum) and striped bass (Morone saxatilis). In 2019, in collaboration with NOAA, MBARI researchers launched autonomous robots equipped with the ESP to study toxic algal blooms in the Great Lakes

In the future, MBARI envisions eDNA and ESP technology offering a genomic “weather map”—a network of autonomous platforms providing a consistent and reliable stream of data for aquatic management and research.

Article adapted from a news release from the University of California, Santa Barbara. Read the full news release here.

Original journal article:

Lamy, T., K.J. Pitz, F.P. Chavez, C.E. Yorke, and R.J. Miller (2021). Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Scientific Reports, 11: 14439.

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