BRUNSWICK, Maine — There was a time when the waters of Casco Bay were thick with meadows of eelgrass.

Not anymore.

According to aerial photography taken by the Maine Department of Environmental Protection in 2013, seagrass covers just 44 percent of the area it covered in 2001.

And the upper reaches of Casco Bay, including Brunswick, show a nearly complete loss of the underwater vegetation.

But a group of scientists is trying to change that, starting with a small test plot in the shallow waters off Simpson’s Point.

Hilary Neckles, an ecologist with the U.S. Geological Survey, is leading a team that includes representatives from DEP, The Nature Conservancy of Maine, and U.S. Fish & Wildlife Service to identify the best ways to restore eelgrass beds.

“If there’s any silver lining to the loss of so much eelgrass, it’s that so many organizations have come together in this partnership to facilitate eelgrass recovery,” Neckles said.

Into the mud

Just before 8 a.m. on Tuesday, a group of about 15 scientists, volunteers and students descended on Simpson’s Point to help in the restoration effort.

On shore, University of New Hampshire seagrass scientist Fred Short walked the team through four different planting methods. Eelgrass shoots, collected the previous day in Cumberland, were either anchored by clam shells or bamboo skewers, tied into a wood-and-twine grid, or weaved into a burlap sack called a “tortilla.”

It was the group’s job to secure the shoots into the mud by hand.

Dan Devereaux, Brunswick’s marine resources officer, ferried people across the low tide line to the test sites in a Police Department airboat.

Calf-deep and slowly sinking in the thick mud, Neckles’ team members had to work quickly before the tide changed.

“I used to have nightmares about being stuck in the mud and the tide coming up and taking me out,” said Jeremy Bell, aquatic habitat restoration manager with the Nature Conservancy.

Serena Doose, a fish and wildlife biologist with USFW, described planting the eelgrass in the mud as “kind of (feeling) like being on a rice plantation, or kind of like gardening out in your backyard.”

As common terns dive-bombed the water for little silver fish, Bell described how eelgrass meadows are a safe haven for many juvenile fish, including alewife and striped bass.

Eelgrass provides structure for many species of invertebrates and algae, which young fish then prey on in the shelter of the grass’s blades, he said. In turn, larger, more commercially important deep-water fish like cod and bluefish, as well as birds like blue herons and terns, feed on the smaller species.

“Eelgrass is a link in habitat,” Bell said. “If you have a break in that link you have less productivity. … (This restoration) is trying to make sure all habitat pieces are intact along the way.”

Neckles described the ecological importance of eelgrass in similar terms.

“Eelgrass is one of the most productive plants on the planet,” she said. “It forms the base of many different food webs, it’s a rich source of invertebrates, … it baffles waves and currents, and its roots bind sediments.”

She said one of the telltale signs of eelgrass loss is the increased murkiness of the water in Brunswick’s bays. The disappearance of eelgrass is also linked with increased coastal erosion, she said.

Neckles stressed that a lot is known about the habitat benefits of eelgrass, but much remains unknown about its future.

Green crab link

The strongest working hypothesis for why so much eelgrass has disappeared is because the spike in invasive European green crabs; as the crabs dig into bay sediment in search of food, they uproot the eelgrass.

A recent paper by Neckles, set to be published in Northeastern Naturalist, linked green crab disturbance to eelgrass loss by using control groups of eelgrass in and outside of crab exclosures.

Half of the test sites at Simpson’s Point will be equipped with green crab traps, which will be emptied once a week by a local harvester. Observing what happens in Brunswick will contribute data on the green crab-eelgrass relationship, Neckles said, and inform best practices for eelgrass restoration in the future.

Devereaux said there is much local anecdotal evidence linking green crab disturbance to eelgrass loss.

Green crabs prey on soft-shell clams, and “the predominant shellfish towns – Brunswick, Harpswell and Freeport – got hit hardest” in terms of clam and eelgrass loss, he said.

Devereaux said he started noticing eelgrass decline in 2012. “Within 13 months the eelgrass was completely gone,” he said.

But there is hope.

If a stable “founder” population of eelgrass can be established, Neckles said, seed will travel and more eelgrass will proliferate naturally.

And according to her, more eelgrass means cleaner water, safer shores, more fish and more birds.

Neckles will monitor the plots and observe which planting methods are most effective for re-establishing eelgrass beds. She hopes this study will serve as a pilot for restoration projects not just in Casco Bay, but throughout the state.

As the tide moved in and Neckles’s team planted the final shoots of eelgrass on Tuesday, Bell said there is something special about Maine.

Bell, who has done coastal restoration work in Massachusetts and Washington, said “here, everybody sort of gets it … (the environment) is much more part of the culture.”

This group of scientists hopes that the right combination of people and research will bring the vital eelgrass habitat back to Casco Bay.