Using Microbial Source Tracking To Identify Contamination Sources in Port Jefferson Harbor, Setauket Harbor, and Conscience Bay on Long Island, New York

Abstract

The U.S. Geological Survey worked collaboratively with the New York State Department of Environmental Conservation to assess the potential sources of fecal con¬tamination entering seven estuarine embayments across Long Island, New York, from June 2018 to July 2019. Water sam¬ples are routinely collected by the New York State Department of Environmental Conservation in Long Island embayments and analyzed for fecal coliform bacteria, an indicator of fecal contamination, to determine the closure of shellfish beds for harvest and consumption. Concentrations of fecal coliform signify the potential for pathogenic (disease-causing) bacteria to be present. Indicator bacteria alone cannot determine the biological or geographical sources of contamination. Microbial source tracking is a method used to determine these sources of contamination. Microbial source tracking laboratory tech¬niques can ascertain whether genetic material obtained from Bacteroides or Helicobacter bacteria in water or sediment is consistent with humans, canines (dogs), ruminants (deer, sheep), or waterfowl. Bacteroides and Helicobacter are genera of bacteria found in the gut of most warm-blooded animals. These techniques can also quantify the concentration of genetic markers found. Information such as sample location, weather, and sea¬son, surrounding land use, and additional water-quality data help determine the geographical source and conveyance of land-based water to the embayment. The presence of genetic material and fecal coliform bacteria in samples collected at the same time is important to show that the fecal coliform bacteria are likely from the host source detected. It is pos¬sible for waters with waste infiltration to have genetic material present but no fecal indicators, such as disinfected water from a sewage treatment plant or from groundwater that has passed through a sandy aquifer. Water samples were collected in the summer and winter seasons. In each of the two seasons, one sample was collected in dry weather, and one, after substantial rainfall. Groundwater and sediment samples were also collected throughout the study. Surface-water source sites sampled for Port Jefferson Harbor and Setauket Harbor include the culvert north of State Route 25A, the culvert north of Shore Road, the Old Mill Creek culvert, the outfall near Danfords Marina, and the Port Jefferson sewage treatment plant. The Mill Pond culvert was sampled as a surface water source site for Conscience Bay. Human, canine, and waterfowl fecal contributions to the Port Jefferson Harbor complex were frequently detected across the landscape. Among the potential sources of fecal contaminated water contributing to the Port Jefferson Harbor complex—groundwater, pond and wetland drainage, storm¬water, marinas (boats), and the Port Jefferson sewage treat¬ment plant—pond and wetland drainage and stormwater from municipal separate storm sewer system conveyances were found to be the most likely transport mechanism of fecal contamination. The most substantial source of fecal contamination to the Port Jefferson Harbor complex was found to be from sites draining ponds and wetlands, particularly during the summer season with higher concentrations of fecal coliform bacte¬ria in wet weather. These sites include the culvert north of Shore Road, the culvert north of State Route 25A, Old Mill Creek, and Mill Pond to Conscience Bay. Discharge from the single stormwater outfall sample (outfall at Danfords Marina) was also a substantial contributor of fecal coliform bacteria. Contributions of fecal contamination did not appear to be attributable to the Port Jefferson sewage treatment plant or to boats and marinas in Port Jefferson Harbor. While the micro¬bial source tracking results indicated influence from septic systems, it has not been shown that groundwater contributes to fecal coliform bacteria loads. One of the two groundwater samples along the shoreline of Port Jefferson Harbor where microbial source tracking analyses were conducted showed evidence of human and waterfowl waste that did not have corresponding fecal coliform bacteria detections, indicating limited transport of bacteria in the subsurface groundwater through the sandy aquifer material, which is consistent with results throughout Long Island. Sediment sampled along with the groundwater sample at the Public Beach and Dog Park is unlikely to act as a source during resuspension events, such as an ebbing (outgoing) tide, storm-driven waves (particularly at low tide), and boat wakes. A classification scheme was developed that considered conditions such as high fecal coliform bacteria concentrations (particularly during dry weather samples) and contributions from human and canine waste based on detection of micro¬bial source tracking markers. The class of sites were assessed to assist stakeholders and resource managers in prioritizing which source sites are consistently contributing fecal coliform bacteria to the Port Jefferson Harbor complex throughout the year. The culvert north of State Route 25A, the culvert north of Shore Road, the Old Mill Creek culvert, the outfall near Danfords Marina (only one sample collected), and the Mill Pond culvert to Conscience Bay were classified as locations that contribute substantial fecal contamination to the Port Jefferson Harbor complex.