Poor harvest looms for Peconic Bay scallop season for the 6th year in a row

The 2025 Peconic Bay scallop season is on track to be another disaster, according to early bay surveys, but reinforcements are on the way in the form of more than 700,000 disease-tolerant scallops.

In a survey of one of 21 sectors of the Peconic Bay off Greenport on Tuesday, Cornell Cooperative Extension aquaculture and shellfish restoration specialist Harrison Tobi donned scuba gear and traversed three separate 50-meter underwater lines in search of scallops. He surfaced with only seven juveniles in his mesh bag, and no adults of the size that baymen harvest for sale at market.

"It doesn’t look good," Tobi said, for the scallop season that starts Nov. 3 in bays across Long Island, and in the Peconic in particular.

It's the sixth year in a row that the Peconic Bay has seen historically low levels of scallops, after experiencing some of the bay’s most productive years just prior to 2019. Population numbers are "not great and, unfortunately, it's routine," Tobi said.

Scientists have discounted prior theories that warming bay waters and low oxygen levels during the summer spawning season led to the die-offs in summer, just after they breed.

Pathogen tied to die-offs

Instead, they have identified a pathogen that impacts all scallop tissue, and is particularly detrimental to their kidneys. The pathogen kills the scallops before they reach full adult size after their summer spawn. It’s the reason surveys can show larger numbers of juvenile scallops in spring, but few to none in October, just prior to the season open.

To help reverse the trend, biologists at the Cornell Cooperative Extension are breeding bay scallops from other waters with a slight variation in genetics that allows them to be more tolerant of the pathogen. The scallops, from Martha’s Vineyard and Moriches Bay, are the same genetic species as the Peconic scallops, but of a lineage with a tolerance to the pathogen.

This year’s more than 700,000 recruits that will make up future generations of scallops come chiefly from Martha’s Vineyard, where the pathogen also has been identified but the scallops appear considerably more tolerant — some showing up to a 95% survival rate, said Tobi. There’s also a large mix of Moriches Bay scallops, which are also genetically identical except for the tolerance variation, called a single nucleotide polymorphism, or SNP.

Of the more than 700,000 scallops now hung in special lantern nets in a breeder sanctuary in Orient Harbor, more than 400,000 come from Martha’s Vineyard, while up to 200,000 are from Moriches Bay, and the balance from the intolerant Peconic Bay scallops, which show only a 5% to 25% tolerance to the pathogen.

(Moriches Bay scallops show a tolerance somewhere in between. Tobi said it's also important to include Peconic Bay scallops in the sanctuary because "we don’t want to lose genetics of the Peconics: Maybe they are better suited to some other environmental condition.")

Building new lineage

The effort to diversify the spawner sanctuary in Orient started last year, when more than half the 350,000 scallops in lantern nets were Moriches Bay scallops.

One of the reasons Peconic Bay scallops are intolerant of the pathogen is because of the all-out effort to rebuild the population after it was devastated by brown tide in the 1980s and 1990s. Marine biologists starting in 2005 used the existing population to breed large numbers of scallops in labs, but the relatively small number of scallops used to produce hundreds of thousands of new ones may have lessened genetic diversity, the key to survival, scientists said.

"We have genetic data showing that the Peconic population has lost genetic diversity over time, making them potentially more susceptible to the parasite," Tobi said. "It was just the straw that broke the camel’s back. It was bound to happen."

By introducing new lineages with a wider variety of genetically divergent scallops of the same species into Peconic Bay, scientists hope to both provide tolerance against the pathogen, and a diverse genetic pool in the face of other potential threats.

Scallops live for around two years, and do most of their spawning from May to July. The harvest season extends from November to March, well after breeding occurs. Figures show there hasn't been much to harvest in recent years.

Peconic Bay scallop landings for the 2024-25 season were little better than the prior five years, Tobi said, amounting to around 6,700 pounds. That compares with 5,537 pounds for the 2022-23 season and 6,057 pounds for the 2023-24 season.

In the 2018-19 season, just before the die-off, baymen harvested 110,802 pounds.

In the meantime, the cost for the scallops has soared from around $15 a pound six years ago to $35 or more in recent years, Tobi said.

Expanding spawner sanctuaries

Just about all of the scallops hanging in the lantern nets in Orient Harbor, spawned from about 300 scallops in Cornell’s Southold hatchery, have been seeding and fertilizing nearby waterways with new eggs to boost the local population. Tobi said some of those scallops will be planted in waters around the Peconic Bay as soon as this fall, though the bulk will be released next year, and new breeders brought in thereafter.

To broaden the impact across the bay and to involve local baymen and aquaculturists, Tobi said, Cornell also is drawing up a plan to work with local oyster farms to increase the use of spawner sanctuaries well beyond Orient Harbor, most notably to the west. At present, the Orient sanctuary is the only one of its kind in Peconic Bay, and no local growers farm scallops.

In some cases oyster farmers could deploy the same lantern nets, each fitted with up to 175 scallops, to spawn scallops at their government-leased oyster farms across the East End. Some oyster farmers are interested in growing bay scallops, Tobi said.

"We’ll deploy bay scallops at their farms to monitor for the potential for aquaculture, but we’ll also be collecting data for restoration," he said. "We’re really expanding to involve as many people as possible from as many walks of life as possible, to bridge the gap between research and industry."

The expansion program is "really just starting," he emphasized, and awaits funding.

The Cornell program, which is funded about 90% by Suffolk County, has also been using state and federal grants and preservation funds to work on programs to rebuild the Peconic Bay and surrounding scallop populations. Disaster recovery funds from New York State, after the Peconic Bay’s mass die-off, are also helping.

While expressing hope for a turnaround of scallop populations over the next several years, Tobi emphasized, "This isn’t a science experiment."

He added, "This is applied science to a problem, which is the economy, which is these baymen, which is their families." Many baymen depend on the seasonal revenue to get them through the fall and winter.