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Shinnecock Bay restoration is a model for ocean conservation, UN leaders say

Ocean conservation scientist Ellen Pikitch explains how Stony Brook University examines the environmental DNA, or eDNA, of the Shinnecock Bay to track the health of species over time.
John Griffin
Stony Brook University
Ocean conservation scientist Ellen Pikitch explains how Stony Brook University examines the environmental DNA, or eDNA, of the Shinnecock Bay to track the health of species over time.

For decades, the Shinnecock Bay was nearly uninhabitable. Algal blooms covered the water’s surface with a thick, overgrown film of scum.

Last June, the tides changed. The Shinnecock Bay was designated as a global “Hope Spot” by Mission Blue, an international organization that identifies ocean regions with vital ecosystems and supports their protection.

Once on the verge of collapse, habitats in the bay are thriving today.

This week, during World Oceans Week, members of the U.N. General Assembly recognized the hard clam restoration in the bay — 9,000 acres of open water salt marsh on eastern Long Island — as a prime example of mixing scientific advancements and natural solutions to help assist global ocean conservation efforts.

J.D. Allen

Ellen Pikitch, endowed professor of ocean conservation science at the School of Marine and Atmospheric Sciences at Stony Brook University, presented her work on Tuesday in front of the United Nations, joining “a world-renowned group of environmental marine scientists and other leaders to discuss environmental and related issues concerning the safety of the oceans, and new scientific work aimed at preserving our oceans and mitigating climate change.”

“The problems that we're facing in our environment today, people are going to have to come up with solutions. And the more that we can work together and understand one another, and be on the same page and accept different philosophies and different approaches, the better off we'll be,” Pikitch said during the hearing on new maritime technologies.

Friday officially inaugurates the bay as a Hope Spot, according to Mission Blue, recognizing its ecological and cultural importance to Long Island and the region.

Happy as a clam

Long Island’s South Shore has long been known for its shellfish. In the 1970s, more than half of the hard clams eaten in the U.S. came from the Great South Bay system.

By 1985, overharvesting of clams, oysters and scallops, which naturally filter the water, led to the deterioration in the water quality. Every year since, the water turned shades of brown and red with a harmful algal bloom.

J.D. Allen

The problem with opaque water is that sunlight can't penetrate through to the ocean floor where sea grasses grow, which are critical marine habitat. The water was starved of oxygen from the overgrowth, leading to fish kills and shellfish die-offs.

“It just led to what I would call a death spiral."
Ellen Pikitch

In 2012, the Stony Brook researchers began “hard clam sanctuaries” in an effort to restore Shinnecock Bay.

Native hard clam species were planted in high densities with the goal of boosting the bay’s spawning stock. “These sanctuaries would not only keep the clams within them alive, but those clams would reproduce and create new clams and those young clams within a couple of years would start reproducing,” she said.

It took 10 years for the team to increase the filtration capacity of the bay to eliminate some of these harmful algal blooms; there hasn’t been a brown tide in five years, and the red tide is nearly eradicated.

“It's now considered to be a beacon of hope that shows the world that we can undo some of the damage that's been done. If we use science, if we work hard, and if we're persistent, some of the things that we have done can be undone,” Pikitch said.

Gail Davis, who works on climate financing for the Development Committee of the United Nations System, called for the scientists to consider how their research can support the goal of protecting 30% of the ocean by 2030. “As citizens who are on, by the oceans, or near the oceans, Is there anything that we can do, everyday actions that we can take, that can help this move forward?” Davis asked.

“I think that one of the important things that you can do that everyone can do is to try to hold the United Nations and the countries that we live in accountable for actually living up to the commitments that they made,” Pikitch replied.

She acknowledged several challenges. Like today, Pikitch was involved in UN discussions in 2016 between scientists, decision makers and diplomats to explain the importance of the commitment to protect 10% of the ocean by the year 2020, which “depending on who you talk to still hasn't really been met,” she said.

Muhammad Abdul Muhith, the delegate from Bangladesh, said part of the trouble for world leaders is that marine life “doesn't have any political boundary like we do.”

“So it is very pertinent that areas beyond national jurisdictions ecosystems must be protected. Your identification and the concept of ecologically and biologically significant marine areas are quite precious and important,” he told Pikitch.

Other obstacles include resources to help them live up to the commitment, because conservation methods can be expensive, and ensuring the right people are in the room. For example, a relationship that has grown in the last decade of research in Shinnecock Bay is collaborating with the Shinnecock Indian Nation, who have called the bay home for thousands of years.

Pikitch, who is known in her field for ecosystem-based fishery management, has devoted much of her career to getting marine stakeholders to move beyond administration “species by species without really recognizing that species interact with one another.” This is an approach the Shinnecock Indian Nation finds “second nature."

“We're now involved in a partnership with them,” Pikitch said, celebrating a combined database of the latest advancements in collecting genetic information, a decade of trawling and centuries of observational history.

She also noted the success of an independent nonprofit formed by a group of six Indigenous women who worked to revitalize their historic waters through a kelp restoration farm, which feeds on nitrogen pollution and becomes habitat for marine life.

“This is an ideal testbed,” she added. “Now we are sharing knowledge and working together to do DNA analysis in Shinnecock Bay.”

Pikitch said she believes that “accelerating the power and reach of eDNA research for ocean observation” can outperform other marine animal survey methods, which can be leveraged for conservation.

DNA as a blueprint

Pikitch’s research is in eDNA, or environmental DNA. She said distilling the genetic make-up from a sample of the bay has helped scientists identify fish species present in the bay.

“Organisms that swim or live in the ocean in water leave behind pieces of DNA in that aquatic environment that they secrete or sloughed off skin cells or fish scales,” Pikitch said, which is much like taking a swab inside of a person’s cheek — or the dandruff left by someone.

“From a simple analysis of the DNA and water, we can learn a lot about the species that are there,” she added.

In 2018, a study Pikitch published in Science showed how eDNA could be used as a tool for finding rare and common marine species. Her research shows that using genetic material is a safer methodology for surveying biodiversity in the ocean, without mortality of species or damage of habitats, opposed to trawling the ocean floor with a net — commonly used in commercial fisheries around the world.

Pikitch said compared to other non-invasive methods, including baiting remote underwater video cameras, eDNA allows for a wider selection of species that might be missed. Plus, scientists who rely on visual observations also need to be actually able to identify fish. “With eDNA, you actually don't have to because the DNA tells the story and tells you who's who,” she said.

“We take a water bottle, put it over the side, and collect the water. We keep it on ice, rush it to the lab, filter the water, then rush to then take the filters and extract the DNA from those filters. And then we send it out to a lab to be sequenced,” Pikitch said. “We come back, and what comes back is a lot of data, and we figure out what species were there.”

Ellen Pikitch
Stony Brook University

Over the last few years, eDNA samples have brought new information about sharks, skates and ray species in Shinnecock waters. In fact, in one year, scientists found seven species in the restoration areas that were found nowhere else in Shinnecock Bay — and corrected misidentified species from a decade of trawling that were entered into the restoration database.

Since 2012, when eDNA “was very, very young,” Pikitch said the cost and time of sample processing has significantly declined. “eDNA sampling is more cost effective, less labor intensive and has a smaller carbon footprint than trawling,” she added.

Pikitch throws a battery-powered device propels itself through the Shinnecock Bay, checking for water quality and contaminants.
John Griffin
Stony Brook University
Pikitch throws a battery-powered device propels itself through the Shinnecock Bay, checking for water quality and contaminants.

Other methods scientists use in Shinnecock Bay include an instrument that can predict extreme weather and tides for the bay, and a robotic device that can assess sea water quality.

“You can't go trawling in a hard clam sanctuary,” Pikitch said “We've learned that DNA can be used in very sensitive habitats, where other methodologies cannot be employed.”

This story has been updated to clarify the operations of the Shinnecock kelp restoration project, which is an independent nonprofit formed by six Indigenous women — not the tribe.

A native Long Islander, J.D. is WSHU's managing editor. He also hosts the climate podcast Higher Ground. J.D. reports for public radio stations across the Northeast, is a journalism educator and proud SPJ member.