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Using microbial source tracking to identify contamination sources in Port Jefferson Harbor, Setauket Harbor, and Conscience Bay on Long Island, New York

March 10, 2022

The U.S. Geological Survey worked in cooperation with the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering Port Jefferson Harbor, Setauket Harbor, and Conscience Bay, an embayment complex on the northern shore of Suffolk County, Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the harbor and analyzed for fecal coliform bacteria, an indicator of fecal contamination, to determine the need for closure of shellfish beds for harvest and consumption. Fecal coliform and other bacteria are an indicator of the potential presence of pathogenic (disease-causing) bacteria. However, indicator bacteria alone cannot determine the biological or geographical sources of contamination; therefore, microbial source tracking was implemented to determine various biological sources of contamination. In addition, information such as the location, weather and season, and surrounding land use where a sample was collected help determine the geographical source and conveyance of land-based water to the embayment.

Our analysis revealed that the most substantial source of fecal contamination to the Port Jefferson Harbor complex was discharge from sites draining ponds and wetlands, particularly during the summer months. Fecal coliform bacteria at sites where ponds and wetlands drain are increased by stormwater runoff, which is another substantial source of fecal contamination. Human markers, likely originating from the outfall of the Port Jefferson sewage treatment plant, were found at least once in every sample collected within Port Jefferson Harbor; however, fecal coliform concentrations were low, indicating that the sewage treatment plant is not a likely source of fecal contamination to the embayment. Canine markers detected in Conscience Bay were associated with high fecal coliform, particularly in wet summer samples. Waterfowl markers were most often detected in source water for Port Jefferson Harbor, but in Conscience Bay, waterfowl was frequently detected within the bay itself. Resuspension of bed sediment may contribute to fecal contamination in the harbor, but more targeted analyses are needed to support this finding. There was little evidence of groundwater-contributing fecal bacteria by direct discharge from the subsurface. A classification scheme was developed to convey the degree of fecal contamination to stakeholders and resource managers. Based on this classification scheme, the Culvert North of State Route 25A, Culvert North of Shore Road, Old Mill Creek Culvert, and Mill Pond Culvert to Conscience Bay sites were identified as locations that contribute substantial fecal contamination to the Port Jefferson Harbor complex.

Citation Information

Publication Year 2022
Title Using microbial source tracking to identify contamination sources in Port Jefferson Harbor, Setauket Harbor, and Conscience Bay on Long Island, New York
DOI 10.3133/sir20215141
Authors Tristen N. Tagliaferri, Shawn C. Fisher, Christopher M. Kephart, Natalie Cheung, Ariel P. Reed, Robert J. Welk
Publication Type Report
Publication Subtype USGS Numbered Series
Series Title Scientific Investigations Report
Series Number 2021-5141
Index ID sir20215141
Record Source USGS Publications Warehouse
USGS Organization New York Water Science Center