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eDNA Used to Track Marine Biodiversity Over Time in a Research First

Environmental DNA (eDNA) analysis is an emerging tool that holds promise for global biodiversity monitoring and conservation efforts

Written by Kristen Kusek, Communications Director for USF CMS

ST. PETERSBURG, FL – Just as the eyes are the window to the soul, a liter of seawater can be a window to all life in a region of the sea—revealing organisms from microbes to mammals. Or at least pretty darn close, says a team from the USF College of Marine Science (USF CMS) that recently reported a promising pilot study in Nature Communications.

It was the first time scientists used eDNA, or environmental DNA, to analyze the biodiversity of an entire marine system seasonally over time—from bacteria and diatoms at the base of the food web all the way up to fish and whales.

“No one’s ever done this before because we didn’t have the tools to make it happen,” said lead author Dr. Anni Djurhuus. Now an assistant professor at the University of the Faroe Islands, Djurhuus was a postdoctoral scholar working with USF CMS professor Dr. Mya Breitbart when the study took place. Breitbart is senior author on the publication.

Scientists traditionally perform field surveys – like counting whales through binoculars or trawling for fish – to assess biodiversity in a given region. But these surveys rely on what the eye can see, take lots of time and a bit of luck, and each is limited to a relatively small number of organisms. While surveys provide a snapshot of what lives in a slice of an ecosystem the day scientists sample it, it’s far from a full picture.

“There really isn’t a good way to monitor total biodiversity,” said Breitbart, and that’s a problem because many scientists worry that we are losing species quicker than we can even record what’s out there. A report released by the United Nations last year stated that one-third of marine mammals, and one million species in total face extinction–more than ever in human history.  

Genetic Sleuthing in a Soda-sized Bottle?

Enter eDNA, or environmental DNA, which is the genetic footprint left behind from all living things, barnacles to barracuda, plankton to porpoises. Organisms leave traces of their DNA behind when they excrete, shed skin cells, or die.

Monitoring eDNA in the ocean, a relatively new tool, is akin to performing marine detective work. Scientists take a water sample equivalent to volume of liquid in a lunch-time soda bottle – not much – and extract the DNA back in the lab to establish a record of who’s there. The technique doesn’t require that scientists physically see any living thing in the flesh, just the DNA it left behind.

This figure demonstrates the kinds of relationships that scientists can make using the new methods described in the publication. The blue represents the autumn season, and grey represents winter. The peaks indicate the relative abundance of species across the food web that were evident in the eDNA samples taken from Monterey Bay in 2015 and 2016.
This figure demonstrates the kinds of relationships that scientists can make using the new methods described in the publication. The blue represents the autumn season, and grey represents winter. The peaks indicate the relative abundance of species across the food web that were evident in the eDNA samples taken from Monterey Bay in 2015 and 2016.

 

For the pilot study the team collected samples from Monterey Bay, California over an 18-month period in 2015-2016. They wound up with a genetic dataset including 663 taxonomic groups, from microbes to mammals. A hefty dose of statistical analyses allowed them to group the organisms into clusters that displayed similar patterns over time, providing insight into changing biodiversity across various levels of the food chain and by seasons.

A lot of what they found was expected, and matched known relationships between predators and prey. For example, the results showed that jack mackerel, which hadn’t been physically seen in Monterey Bay for years, are strongly correlated with copepods. That’s no surprise because jacks eat copepods. Also not shocking was the strong relationship between jacks and sea lions, which enjoy jacks as a prized menu item.

But other results were surprising.  For instance, species across the entire trophic system in the autumn appear to be highly sensitive to temperature change – and humpback whales top the list as the most sensitive. The researchers also identified highly connected organisms that may serve as keystone species or early indicators of biodiversity change.

No one has ever made observations like these before, and they could be useful for conservation efforts.

“This method allows us to generate new hypotheses on relationships between species,” Djurhuus said. “It’s powerful to be able to measure the whole trophic system over time, all at once, from one water sample.”

The eDNA technique is also a new tool in the kit for a global initiative called the Marine Biodiversity Observation Network (MBON). The MBON goal is to understand changes and connections among different types of organisms and with the ecosystems they inhabit.

“We are excited about the potential in eDNA to revolutionize the way we monitor biodiversity around the globe,” said Dr. Frank Muller-Karger, a professor at the USF CMS and one of the leaders of the U.S. MBON program. “As the climate changes and ecosystems shift, expanding in geographic range or shrinking, we need to measure biodiversity as quickly and efficiently as we can.”

The team looks forward to a day when eDNA analyses inform monitoring and management decisions. On deck is a project to analyze similar eDNA data from other marine sanctuary sites, including the Florida Keys National Marine Sanctuary, which offers an ideal platform to forge conversations between policymakers, scientists, and other stakeholder groups.

Challenges on Deck

Breitbart and Djurhuus are quick to register that the method is not without challenges. “We have to be careful not to overstate or make false correlations,” Breitbart said. 

In addition, the method does not allow scientists to determine the actual number of organisms of any one species in an area. “Whales likely shed millions of cells but that doesn’t mean we have millions of whales in the area,” Djurhuus said. The DNA picked up in the water sample may reflect multiple copies of the same gene, and may represent one whale, five or ten–nobody knows. 

The method also fails to shed light on the age of a given animal. In fact, DNA is even shed when an organism dies so it may not even be around anymore.

“Our next step is to validate the interactions we’ve suggested in the analyses to see if they are in fact correct,” Djurhuus said.

Nevertheless hope—in this case eDNA—floats.

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