Southold Seeks Genetic Shellfishery Testing

Southold Town, which has some of the most extensive and productive creek networks on the East End, has been taking a proactive approach for years to making sure as many town waters as possible are open for shellfishing, and this spring they’re hoping to add genetic testing to their arsenal of tools to understand bacterial pollution here.

Cutbacks at the New York State Department of Environmental Conservation have long plagued the department’s oversight of shellfishing here — many waters are closed by default when samples come back positive for bacteria that can cause shellfish poisoning.

There’s just one understaffed lab state-wide authorized to certify waters safe for shellfishing according to FDA standards, and when that lab can’t test waters frequently enough, the DEC’s default position is to limit the shellfishing allowed in those waters, even if they may be safe.

After years of training citizen water testers to sample water to meet DEC protocols, the Southold Town Trustees and the Southold Town Shellfish Advisory Committee are now looking to Suffolk County for $12,000 in funding to use genetic testing to find the source of bacteriological contamination in four creeks here.

These new and expensive testing methods, which can be conducted by Cornell Cooperative Extension of Suffolk County’s marine laboratory, enable scientists to discover whether waterfowl, mammals or humans are the source of the fecal bacteria that closes shellfish beds.

The Trustees are applying for the grant through the county’s Water Quality Protection and Restoration Program, which requires a 50 percent match from the town. Applications are due in late February.

The sampling and testing would be done by trained members of the town’s Shellfish Advisory Committee and CCEs marine lab at Cedar Point in Southold, which is equipped to conduct Bacterial DNA Source Tracking.

The Town’s Shellfish Advisory Committee has identified four water bodies where they are looking to find the source of heightened fecal coliform bacteria levels:

The first is a tributary of Hallock’s Bay in Orient, where a large-scale animal agriculture operation has been proposed. The Trustees are hoping to conduct the testing before the operation begins, along with “dye flow studies in the area of the ag operation leading to the DEC sampling point to ascertain the potential for impairment and develop recommendations for changes to structures.”

The second area is East Creek in Cutchogue, where the Southold Town Bayman’s Association has requested a Conditional Shellfish Program.

“There are concerns that waterside sanitary systems on this creek are in need of upgrade and may be discharging human sourced coliforms that contribute to the current closed status,” according to the committee’s fund request presentation.

The third area is a manmade freshwater pond off of Silveremere Road in Greenport, where harmful algal blooms have been documented. The town has proposed to genetically test the source waters of the pond to see if human coliform is responsible “to determine if an engineered solution is possible where non-conforming sanitary systems may be enriching the HAB in an area of poor drainage.”

The fourth area is the site of a six-million oyster aquaculture operation in Orient Harbor, which is scheduled by the DEC for an expansion of its seasonal closure area. The town proposes using genetic sampling and using tracing dyes to determine the source of the contamination.

Beth Young

Beth Young built her first boat out of driftwood tied together with phragmites behind her family’s apartment above the old Mill Creek Inn in Southold. Nowadays, she spends most of her time kayaking, learning about shellfish, writing newspaper stories, trying to sail a Sunfish, and watching the way the bay changes from day to day. You can send her a message at

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