Groton ― Mystic Oysters’ refrigerated van, which normally delivers oysters the company cultivates to seafood distributors and restaurants five days a week this time of year, is parked.

And its boats are tied up.

For the first time in 30 years, Jim Markow, who owns the operation, has had to start contemplating laying off some of his employees.

“It’s a helpless feeling,” he said Thursday. “Terrifying.”

It was Markow and his team that first detected signs of contamination in oysters off Morgan Point, the peninsula that forms the southern end of Noank. That discovery eventually prompted the state Department of Agriculture to impose a “precautionary closure” of approved shellfish-growing waters in Groton and Stonington.

The U.S. Food and Drug Administration issued an alert Tuesday warning against the consumption of oysters harvested in the area from Aug. 28 to 30.

Markow said he noticed the problem about three weeks ago during Mystic Oysters’ routine sampling of oysters. Bacteria counts, he said, “came up alarmingly high.”

“We started sampling storm drains, which is where E. coli lives,” he said. “We’re working with the town to identify where the contamination is coming from. We’re desperately trying to find the source and get back to work again.”

Once the problem is corrected, it’ll be another 21 days before Mystic Oysters and its like will be able to resume harvesting oysters in the area.

An email thread provided by Town Manager John Burt shows Markow alerted his office to the problem in an Aug. 18 phone call, which he forwarded to Greg Hanover, the town’s director of public works. In the call, Markow said he thought broken pipes from Morgan Point houses connected to grinder pumps could be the culprit.

“Apparently there is a periodic sewage smell there lately,” Burt wrote to Hanover, who asked Harold Clarke, the assistant director of public works, about it.

In response, Clarke reported that his staff had checked all the grinder pumps along Pearl Street and Morgan Point in Noank and “didn’t see anything or smell anything down there. … We also checked other areas around Noank, the pump station and Esker Point. We haven’t found anything, but we’ll keep looking.”

At this point, the state Department of Agriculture and Ledge Light Health District had been apprised of the problem.

Emails that are part of the thread indicate the discovery of the contamination led to the closing of shellfish-harvesting areas used by four local companies: Mystic Oysters, CT Cultured Oysters, Stonington Farms Shellfish and Sixpenny Oysters. All of the companies support government agencies’ efforts to solve the contamination problem, according to one of the emails.

“The problem is not only a shellfish issue but is a public health issue as well,” the author wrote.

Burt said a review of town utility records showed eight houses on Morgan Point are connected by a grinder pump that grinds the waste into a fine slurry and moves it into the town’s low-pressure sewer system.

All of the houses on the west side of Pearl Street and the Noank Shipyard are similarly connected.

In addition, four catch basins near the end of Pearl Street discharge to the west of 182 Pearl St. into West Cove. A private catch basin on Morgan Point Road (a private road at the end of Pearl Street) discharges to the east into the Mystic River.

Burt said he met with Markow and state and local officials in Noank on Aug. 30, and walked the Morgan Point site, where the ground showed no sign of a sewage leak. On Sept. 1, he said results of water tests conducted by the state showed high readings for Enterococcus bacteria in samples taken from Pearl Street catch basins. The bacteria are commonly found in the intestines of humans.

Alissa Dragan, a supervising environmental analyst with the agriculture department’s Bureau of Aquaculture, informed Burt that further testing at Morgan Point would take place Friday. A Pleasant Street storm drain and the sewer line from Morgan Point were to be examined by a camera that could detect any cracks or cross connections that could pose a hazard.

Burt said the town will seek permission from individual homeowners, if necessary, to conduct dye tests that could reveal leaks in the lines connecting homes to grinder pumps.

b.hallenbeck@theday.com