Sampling Methods

Samples were collected and analyzed in accordance with methods detailed in Tagliaferri and others (2021). Surface-water samples in Sag Harbor were collected from June 2018 to June 2019, and groundwater and sediment samples were collected in June 2019. All water-quality and sediment data collected in the field and those analyzed in laboratories as part of this study are available from the U.S. Geological Survey (USGS) National Water Information System (NWIS) database (U.S. Geological Survey, 2020a).

Wet conditions were defined as more than 0.25 inch (in.) of precipitation in 24 hours or 0.50 in. in 48 hours. Dry conditions were defined as less than 0.25 in. of precipitation in 72 hours. Rainfall totaled 0.68 in. on August 12, 2018, designating samples collected in Sag Harbor on August 13, 2018, as summer wet samples (more than 0.25 in. within 24 hours). Winter wet samples were collected in Sag Harbor on March 4, 2019, with 1.30 in. of precipitation falling March 4, 2019. Rainfall values were obtained from the Montauk Airport weather station (KMTP; Weather Underground, 2022). From June 2018 to June 2019, 10 sites were sampled within Sag Harbor, yielding 31 surface-water samples, 2 groundwater samples, and 1 sediment sample collected concurrently with the groundwater sample at the Windmill Beach site. Of the surface-water sites, four were considered source sites (waters flowing directly into the harbor from the land through culverts and groundwater discharge), and four were considered receptor sites (the harbor itself). Sixteen surface-water samples were collected under wet conditions, and 15, under dry conditions; 15 surface-water samples were collected in the summer, and 16, in the winter.

Laboratory Methods

Laboratory methods used for this study are detailed in Fisher and others (2020). Samples for fecal coliforms were analyzed at Suffolk County Department of Health Services Public Environmental Health Laboratory (PEHL). Additional information was either observed or compiled to facilitate interpretation of data. Precipitation measurements from the Montauk Airport weather station (Weather Underground, 2022) were used to determine whether weather conditions were considered dry or wet. Relative tide stage as noted by USGS field personnel and verified based on tidal predictions available (National Oceanic and Atmospheric Administration, undated) was documented along with the sample information in NWIS (U.S. Geological Survey, 2020a). Land-cover and sewer district geographic information system coverages (Nassau County, 2015; Suffolk County, 2020; U.S. Geological Survey, 2020b) were used for data interpretation. These data support the MST results to increase confidence in the geographical source of the water and likely transport mechanisms of fecal contamination to Sag Harbor.

Microbial Source Tracking

In Sag Harbor, at least one human-, canine-, or waterfowl-associated marker was detected in 14 of 31 surface-water samples. The only sample that contained multiple markers (human- and canine-associated) was the dry winter sample at the Sag Harbor Sewage Treatment Plant Outfall site. Human-associated Bacteroides (HF183) markers were the most frequently detected (eight positive detections), followed by waterfowl-associated Helicobacter (GFD) markers (five positive detections) and canine-associated Bacteroides (BacCan) markers (two positive detections). All samples collected at the Sag Harbor Sewage Treatment Plant Outfall (source) site were positive for HF183, as were three of four samples at the Ferry Road Bridge (receptor) site and one of four at the Paynes Creek Mouth (receptor) site. The BacCan marker was detected in two source samples and no receptor samples, suggesting minimal canine contamination in Sag Harbor during this study. There were five detections for the GFD marker, three in wet summer conditions and two in dry winter conditions. Two detections were in receptor sites, and three were in source sites, suggesting the presence of avian fecal contamination throughout the Sag Harbor landscape.

Host Specific Markers

Reporting limits for the three predominant MST markers (HF183, BacCan, and GFD) detected in Sag Harbor varied slightly because of analytical processes, such as required dilutions because of matrix interferences. Understanding occurrence of the predominant MST markers in Sag Harbor can be used to help prioritize locations for additional investigation and infrastructure improvement and provide a baseline for host contributions when prioritizing sites of concern for assessing FC and after total maximum daily load implementation.

HF183

At Sag Harbor, the human marker was detected at concentrations above the reporting limit in 8 of the 31 samples from 4 surface-water sites (table 1). The human marker was also detected at two receptor sites (Ferry Road Bridge and Paynes Creek Mouth) and one source site (Sag Harbor Sewage Treatment Plant Outfall). This is indicative of minimal inputs from potential inland sources (including illicit connections to the stormwater drain system). Concentrations of HF183 were of the same order of magnitude (hundreds of copies per 100 milliliters [mL]) at receptor sites and were variable at the single source site with positive detections (hundreds to tens of thousands of copies per 100 mL; fig. 3). Concentrations of positive HF183 detections within the harbor were close to the reporting limit and not associated with high FC concentrations (table 1.2; U.S. Geological Survey, 2020a), making it unlikely that the source was from boats and marina discharges. The Sag Harbor Sewage Treatment Plant Outfall site was the only source site where the human marker was detected in all four samples; however, these samples were associated with low to nondetectable FC concentrations. The concentrations of HF183 in samples collected during the winter (18,000 and 76,000 copies/100 mL) were considerably higher than in the summer (680 and 6,300 copies/100 mL). Of the eight samples positive for HF183, five had concentrations below detection for FC, one had just above the detection limit (20 most probable number per 100 mL [MPN/100 mL]), and two were not tested for FC (table 1.2; U.S. Geological Survey, 2020a). The sediment and groundwater samples at the Windmill Beach site and the groundwater sample collected at the Harbor Avenue Beach site were negative for HF183.

Table 1.    

Summary of microbial source tracking results in surface-water samples for sites sampled in Sag Harbor on Long Island, New York.

[Ratios are number of samples with detections greater than reporting limit per total number of samples. Reporting limits vary due to analytical processes and matrix interferences. BacCan, canine-associated Bacteroides marker; GFD, waterfowl-associated Helicobacter marker; HF183, human-associated Bacteroides marker; Rum2Bac, ruminant-associated Bacteroides marker]

Table 1.    Summary of microbial source tracking results in surface-water samples for sites sampled in Sag Harbor on Long Island, New York.

Variable	Ratio of positive detections (detection greater than reporting limit)
	HF183	Rum2Bac	GFD	BacCan
Summer	4:15	0:15	3:15	1:15
Winter	4:16	0:16	2:16	1:16
Dry	5:15	0:15	2:15	2:15
Wet	3:16	0:16	3:16	0:16
Source	4:15	0:15	3:15	2:15
Receptor	4:16	0:16	2:16	0:16

BacCan

Twenty-nine of 31 surface-water samples had concentrations below the detection limit for the canine marker. Two positive BacCan detections were in dry conditions, one, in summer (2,400 copies/100 mL) at the Ligonee Brook Culvert site, and one, in winter (1,300 copies/100 mL) at the Sag Harbor Sewage Treatment Plant Outfall site (fig. 4). The positive BacCan detection at the Ligonee Brook Culvert site (2,400 copies/100 mL) corresponded to the second highest FC concentration detected within Sag Harbor (300 MPN/100 mL; table 1.2; U.S. Geological Survey, 2020a). The concentration of fecal coliform at the Sag Harbor Sewage Treatment Plant Outfall site was below detection (less than [<] 18 MPN/100 mL) despite a positive detection for the canine marker in the same sample. The sediment and groundwater samples collected at the Windmill Beach site and the groundwater sample collected at the Harbor Avenue Beach site were negative for BacCan. The absence of the canine marker in the majority of Sag Harbor samples during this study indicates little to no canine contribution to FC.

GFD

The waterfowl marker was detected in 3 of 15 surface-water samples taken at source sites and 2 of 16 samples collected at receptor sites at Sag Harbor (table 1). Three of the five positive GFD detections were during wet summer conditions, with concentrations ranging from 960 to 4,600 copies/100 mL (fig. 5). The one positive waterfowl marker detection collected during dry conditions also had the lowest concentration (680 copies/100 mL) of GFD in all Sag Harbor. The highest concentration of GFD was at the FI R 5s “6” site (4,600 copies/100 mL), with a corresponding FC concentration of 40 MPN/100 mL (table 1.2; U.S. Geological Survey, 2020a). The second highest concentration of GFD (2,100 copies/100 mL) was at the Paynes Creek near Marjorie Lane site and corresponded to the highest FC concentration observed within Sag Harbor during this study (2,400 MPN/100 mL; table 1.2; U.S. Geological Survey, 2020a). Two of the five samples positive for the waterfowl marker exhibited FC concentrations above 49 MPN/100 mL, the 90th percentile concentration determined by the NYSDEC as part of the National Shellfish Sanitation Program (NSSP) closure criteria (U.S. Food and Drug Administration, 2019). The sediment and groundwater samples collected at the Windmill Beach site and the groundwater sample collected at the Harbor Avenue Beach site were negative for waterfowl markers.

Fecal Coliform Bacteria

Concentrations in samples from source sites ranged from at or below the reporting limit in 64 percent of samples to 2,400 MPN/100 mL in one summer sample from the Paynes Creek near Marjorie Lane site. Concentrations for samples collected at receptor sites ranged from at or below the reporting limit in 69 percent of samples to 80 MPN/100 mL in one summer sample from the Paynes Creek Mouth site (table 1.2; U.S. Geological Survey, 2020a). Of the 31 surface-water samples collected in Sag Harbor, the concentrations of 19 samples were below the FC reporting limit, 8 samples were above, and 4 samples were not tested for FC. Six of the eight FC samples with concentrations above the reporting limit for FC were sampled under wet conditions, suggesting that FC concentrations are influenced by weather-related events in this embayment. Six samples had concentrations that were greater than 49 MPN/100 mL.

The two culverts sampled during this study (the Ligonee Brook Culvert and Otter Pond Culvert sites) had similar FC concentrations but differing marker detections. The Ligonee Brook Culvert site exhibited FC concentrations similar to the Otter Pond Culvert site in the dry summer sample (300 copies/100 mL each) and the wet summer sample (110 and 130 MPN/100 mL respectively), but the Otter Pond Culvert site had no marker detections, whereas the Ligonee Brook Culvert site had positive detections for the canine and waterfowl markers. The only other site that exhibited no positive marker detections (and exhibited FC concentrations at or below the reporting limit for FC) was the Ligonee Brook Mouth site, which is just downgradient from the Ligonee Brook Culvert site.

The relation between FC and marker detection is not straightforward. Fecal coliform and specific host-associated markers may decay at different rates and be present in different abundances. Host-associated markers were shown to decay more rapidly than FC (Drozd and others, 2013; Rogers and others, 2011). In general, the highest FC concentrations were during wet weather conditions.

Nonpoint Sources of Fecal Coliform Bacteria

Potential nonpoint contributors of freshwater to Sag Harbor include groundwater seepage and direct stormwater runoff not conveyed by the municipal separate storm sewer systems. Groundwater collected from the Windmill Beach and Harbor Avenue Beach sites had concentrations below detection for all MST markers, making groundwater an unlikely contributor to fecal contamination to the harbor during this study. Another nonpoint source that can contribute to fecal contamination in water samples is sediment during resuspension (O’Mullan and others, 2019). To better understand the contribution of shoreline beach sediment, a sample was collected at the Windmill Beach site, in which no MST markers were detected (table 1.2; U.S. Geological Survey, 2020a).

Ligonee Brook Culvert—Priority Rank 2

The samples collected at the Ligonee Brook Culvert site had the highest instance of canine markers in Sag Harbor along with elevated concentrations of FC in wet and dry summer samples (110 MPN/100 mL and 300 MPN/100 mL respectively). Human and ruminant markers were not detected; however, waterfowl markers were detected in the summer, wet weather sample, whereas canine markers were detected in the summer, dry weather sample. This is likely due to congregation of waterfowl and the use of public spaces for dog walking in summer months. Winter samples had no marker detections and low FC in both wet and dry weather. Seasonal influences on FC concentrations are predicted at this site due to the observed increase in FC concentration during the summer season relative to winter samples. The culvert flows continuously and is suspected to contribute high FC concentrations related to stormwater catch basins and inland ponds, particularly during the summer season.

Otter Pond Culvert—Priority Rank 4

The Otter Pond culvert collects stormwater and directs discharge from inland ponds and wetlands into Upper Sag Harbor Cove. This location is primarily affected by upland surface-water and stormwater drainage that contributes substantial FC to Upper Sag Harbor Cove during the summer season. Fecal coliform was detected only in the summer samples, both of which had concentration above 49 MPN/100 mL, the 90th percentile concentration determined by the NYSDEC as part of the NSSP closure criteria (U.S. Food and Drug Administration, 2019). Human, canine, waterfowl, and ruminant markers were not detected at this site during this study, indicating transport and degradation of the MST markers in the summer months or fecal contamination from an untested source organism.

Paynes Creek Near Marjorie Lane—Priority Rank 5

Samples collected at the Paynes Creek near Marjorie Lane site exhibited the highest instance of fecal coliform in Sag Harbor (2,400 MPN/100 mL). Waterfowl markers were detected in the wet, summer sample and the dry, winter sample. The highest waterfowl marker concentration at this site (2,100 copies/100 mL) also corresponded to the highest FC concentration at this site and the Harbor as a whole (2,400 MPN/100 mL). The low priority rank for Paynes Creek may be an artifact of missing the dry summer sample. Despite Paynes Creek having the highest FC and waterfowl marker concentrations, the median FC concentration is below detection and no human or canine markers were found in the three samples collected, designating this site as priority rank 5 (Tagliaferri, 2020). Populations of birds are greatest in the summer season and may contribute to the seasonal observation of FC. The lower FC and marker concentration (or lack thereof) in the winter samples contrasts with the higher FC and marker concentration in the wet summer sample. This suggests seasonal influence of FC in Sag Harbor; however, the dry, summer sample was unavailable for this analysis, thereby limiting our understanding of this FC source. Human, ruminant, and canine markers were not detected at this site during this study, indicating minimal to no FC contributions from onsite wastewater disposal systems or boat septic at this site.

Sag Harbor Sewage Treatment Plant Outfall—Priority Rank 5

The Sag Harbor Sewage Treatment Plant Outfall site exhibited low FC concentrations that ranged from nondetect (<18 MPN/100 mL) to 20 MPN/100 mL in samples analyzed by the PEHL (table 1.2; U.S. Geological Survey, 2020a). Human markers were detected in all four samples at concentrations of 680 to 76,000 copies/100 mL, which was consistently higher than other source sites. These results show that the sewage treatment plant outfall is not a significant source of FC to Sag Harbor but may contribute to the presence of human markers detected in receptor samples.

Sediment—Priority Rank 5

Recent research (Hassard and others, 2016; O’Mullan and others, 2019) has shown that resuspension of sediment along natural shorelines can cause a spike in FC concentrations. Therefore, it is likely that, during conditions that result in high wave energy, sediment can act as a source of FC when sediment is resuspended in the water column because of tidal movement, storms, or boat activity. Fecal coliform concentrations are not available for the sandy sediment sample collected at the Windmill Beach on the southeast side of Sag Harbor. Human, waterfowl, and canine markers were not detected, indicating minimal to no contribution of fecal contamination from these sources. Sediment in this area is likely not a significant source of FC to Sag Harbor.

Groundwater—Priority Rank 5

The lack of positive detections for FC and MST markers in groundwater during this study strongly suggests that direct groundwater seepage is an unlikely contributor of FC to Sag Harbor.