Doughty Cove from the bridge on Long Reach Lane. The cove is off-limits for shellfish harvesting from June through October because of pollution. (J.W. OLIVER PHOTO)

A study set to begin this spring will investigate the source of bacterial contamination that has shut down “prolific” shellfish beds in several Harpswell coves.

The study will look at the area of Morgan Cove and Spruce Cove, on the northeast side of Harpswell Neck; and the area from Doughty Cove to Laurel Cove, across the north side of Sebascodegan Island.

The town will pay for the study with a $12,175 grant from the Maine Shellfish Restoration and Resilience Fund and a $5,000 match from the Harpswell Marine Resources Committee.

As the study begins to identify sources of pollution, the town hopes to address the problems and work with the state to reopen the flats or reduce the duration of closures.

The flats in Morgan Cove and Spruce Cove encompass about 93 acres and are off-limits year-round unless a harvester obtains a special state permit. The flats between Doughty Cove and Laurel Cove encompass about 379 acres and are subject to seasonal closures: Doughty Cove from June through October, the rest of the area from June through September.

The state has closed both areas within the last few years and both areas “provided prolific shellfish harvesting” for Harpswell’s clammers, according to a letter from Harpswell Marine Resources Administrator Paul Plummer to the Maine Shellfish Restoration and Resilience Fund.

The Portland consulting firm FB Environmental will conduct the study. The firm has experience working with “numerous” Maine communities to reopen shellfish flats, according to the grant application.

Harpswell has 55 commercial shellfish harvesters. The value of its hard-shell and soft-shell clam harvests in 2020 was $825,817.83. Open shellfish beds are “important to the economic health” of Harpswell, the application states.

The Maine Department of Marine Resources uses data about the presence of fecal coliform bacteria to determine the status of a shellfish bed, “but little is known about the potential sources of pollution” in Harpswell, according to the grant application.

Between May and September, FB Environmental will collect samples in the study areas, twice in dry weather and once after at least a half-inch of rain.

Contamination during dry weather can point to pollution from a faulty septic system, while contamination after rainfall can point to pollution from animal waste on shore, because “wet weather often mobilizes fecal sources on the landscape and transports them to nearby rivers and streams,” according to the application.

In addition to bacteria, FB Environmental will test the samples for nitrate and nitrite, as well as optical brighteners. Each test provides clues.

Nitrate and nitrite “can indicate human septic waste if in extremely high conditions,” according to the application. Similarly, optical brighteners “are whitening agents commonly found in human wastewater systems” and “can indicate a human contamination source.”

Finally, the firm will send samples to a lab at the University of New Hampshire for “microbial source tracking,” a technique that uses mitochondrial DNA “to determine the source animal of fecal bacteria,” according to the application. This process can determine whether the bacteria comes from humans, dogs, livestock or wild animals, like beavers or geese.

FB Environmental will provide the results of the study and recommendations for next steps by the end of November. The firm might recommend follow-up with landowners or “bracket sampling” to further narrow the source of pollution.

The application calls the study “an important first step in identifying and tracking potential pollutant sources,” but says more work will be necessary before the flats can reopen.

“The goal of the water quality monitoring is to gain a baseline understanding of the pollution contributing to the shellfish area closures and to identify action items for future restoration of the shellfish flats,” the application states. “The ultimate goal is to reopen closed areas by restoring water quality.”

A grant from the Broad Reach Fund supports the Harpswell Anchor’s reporting on the working waterfront.