Assessment of fecal contamination sources to Alley Creek, Queens County, New York

Science Center Objects

PROBLEM Alley Creek, a tributary to Little Neck Bay (Queens County, New York; figure 1) has been designated as impaired by the New York State Department of Environmental Conservation (NYS DEC) for primary and secondary contact and included on the 303(d) Impaired Waterways for pathogens related to combined sewer overflow contributions. The New York City Department of Environmental Protection (...

Alley Creek, a tributary to Little Neck Bay (Queens County, New York; figure 1) has been designated as impaired by the New York State Department of Environmental Conservation (NYS DEC) for primary and secondary contact and included on the 303(d) Impaired Waterways for pathogens related to combined sewer overflow contributions. The New York City Department of Environmental Protection (NYC DEP) and New York City Parks & Recreation have developed a long-term control plan (2014) and a watershed management plan (2015), respectively, to improve water quality and ecosystem health. Point and non-point sources of pathogens are implicated, including stormwater and combined-sewer outfalls, groundwater seepage, and diverted surface waters. Historical fecal indicator bacteria (FIB) data for routine and source-specific monitoring of shellfish areas, bathing beaches, and outfalls exist; however, host-specific analyses are required to help better understand relative contributions of fecal contamination in stormwater, groundwater, and surface waters with respect to human (septic/sewage) contributions. In recent years, NYC DEP has worked to mitigate some of the obvious sources contributing to elevated FIB concentrations (for example, reducing combined sewer overflow (CSO) inputs to the creek and Little Neck Bay) and has conducted bacterial source tracking assessments (AECOM USA, 2014). However, it was inconclusive whether the extent to which sources of pathogens impacting the Alley Creek and Little Neck Bay are the result of human or wildlife.
Currently, no microbial source tracking (MST) method (library-based or independent) exists that will allow for direct determination of proportions of FIB concentrations with respect to host (that is, human, canine, waterfowl, or ruminant). However, with a study design that samples repeatedly under various hydrologic and precipitation conditions, quantification of genetic markers via library-independent polymerase chain reaction (qPCR) methods have been shown to be reliable and comparable amongst each other (Boehm and others, 2013), and thus allow for trends in the MST marker concentrations to prioritize sites, and sources at those sites, to help inform decisions. The U.S. Geological Survey (USGS) proposes to assess the sources and receptors (receiving waters) of FIB using host-specific Bacteroides MST, which is currently being used by USGS in cooperation with NYS DEC and other partners in waterbodies across Long Island and NYC.

 Figure 1. Sample locations within Alley Creek watershed. TI-008, TI-024, and TI-025 correspond to New York City Department of Environmental Protection site identifiers.

Figure 1. Sample locations within Alley Creek watershed. TI-008, TI-024, and 
TI-025 correspond to New York City Department of Environmental Protection 
site identifiers.



1. Identify the source(s) and relative host contribution of bacterial contamination using MST (Bacteroides) and chemical analyses in contributing waters to Alley Creek using qPCR methodology.
2. Evaluate fecal contamination sources to Alley Creek seasonally and spatially, during both wet and dry conditions, and based on tidal influence.
3.Complete an assessment of fecal contamination sources from known sources to Alley Creek identified by NYC DEP and provide interpretation via a USGS Scientific Investigations Report.
Microbial source tracking is a tool used to better classify and allocate the contributions of fecal contamination, particularly from nonpoint sources once a problem is identified. MST protocols followed by the USGS typically include several microbiological targets or source identifiers, detection methods via qPCR, and analytical approaches to link data from water samples to the fecal sources, depending on the objectives of the study (Stoeckel, 2005). Host-specific genetic markers have been identified in groups of bacteria found in the gut of most warm-blooded animals, primarily from the genus Bacteroides. The human associated Bacteroides marker (HF183) (Seurinck and others, 2005; Green and others, 2014); a canine-associated marker (BacCan) (Kildare and others, 2007); a waterfowl-associated Helicobacter marker (GFD) (Green and others, 2012); and a ruminant-associated Bacteroides marker (Rum2Bac) (Mieszkin and others, 2009) are used to differentiate the biological hosts contributing fecal material to the waterbody. Results from the MST marker analyses will be quantitative, with concentrations in copies of genes per 100 milliliters (copies/100 mL) and can be used to compare relative concentrations within each marker to gage the relative contributions of a specific host across the area and through time. However, as with other MST methods, concentrations of the different MST markers cannot be directly compared to each other nor correlated directly with FIB concentrations. For example, 5,000 copies/100 mL of HF183 is not equivalent (and thus cannot be compared) to 5,000 copies of BacCan; but, 5,000 copies/100 mL of HF183 is greater than 1,000 copies/100 mL of HF183 and it can be said that the results of indicate a greater presence of human influence per volume collected. That said, results will allow for reliable and repeatable identification of sources that can be correlated with weather, season, and tidal conditions.
Additionally, analysis for the pepper mild mottle virus (PMMoV) will be included as a novel measure of human-specific fecal contamination. PMMoV has been found to be the most abundant virus type in human fecal samples (Zhang and others, 2006) and has also shown promise as a general indicator of fecal contamination as well as a conservative tracer of viral pathogens such as enteric viruses. Use of PMMoV as an MST marker has been increasing recently due to its high abundance and stability in aquatic environments including several studies investigating human fecal/sewage pollution in coastal waters (Kitajima and others, 2018).
A chemical analysis of 113 pharmaceuticals—constituents that are specific to septic influence—will be used to provide another layer of evidence for human contamination by correlating with MST results in surface water and groundwaters—filtered surface water and runoff samples will be archived at -20 degrees Celsius until MST results are received, at which time roughly half will be submitted for analyses; all groundwater samples will be analyzed immediately for pharmaceuticals. Criteria for submitting a pharmaceutical sample for analysis will include detection of the HF183 marker and (or) the BacCan marker; depending on the number of samples meeting these criteria, at least two samples without HF183 or BacCan markers will be submitted for comparison. Taken together, the MST, pharmaceutical, and FIB data along with ancillary data such as land use, locations of point sources, wildlife populations, and tidal exchange/circulation can provide confidence in the sources and transport mechanisms of pathogens.
The USGS would coordinate with the NYC DEP to collect and analyze water and sediment samples in Alley Creek and at outfalls and surface waters. Further, a site visit will be conducted to familiarize USGS staff with sample locations and determine sites for potential groundwater and sediment sampling. Sample collection and processing will be according to the USGS National Field Manual for the Collection of Water-Quality Data (USGS, variously dated). The following approach is proposed:
1. Surface-water and outfall samples will be collected during dry-weather conditions twice per season beginning in April 2020 (spring) through to March 2021, one sample collected each for high and low tide, from a total of four sites within Alley Creek watershed with chronically high pathogen concentrations. Further, a single wet weather sample will be collected from the outfall or surface water site within Alley Creek once per season—wet weather will be defined as greater than 0.1 inch within a 48-hour period per the NYC DEP municipal separate storm sewer system (MS4) monitoring protocol. Total number of proposed surface water and outfall samples for the one-year assessment is 36 (figure 1; table 1). The following analyses will be performed:
  a. Fecal indicator bacteria: Enterococci and fecal coliform at the NYC DEP laboratory (Brooklyn, NY)
  b. Host-specific genetic marker analysis: Genetic markers will include those for human, dog, ruminant, and waterfowl at the USGS Ohio Microbiological Laboratory (Columbus, Ohio)
  c. Host-specific viral marker analysis: Genetic markers for PMMoV (humans) at the USGS Ohio Microbiological Laboratory (Columbus, Ohio)
  d. Pharmaceuticals: 113 compounds typically associated with septic/sewage influence for correlating with MST results to add evidence to the human waste component at the USGS National Water Quality Laboratory (Denver, Colorado)
  e. Physical parameters: temperature, specific conductance/salinity, pH, dissolved oxygen, and turbidity.
2. Groundwater samples (up to three; figure 1; table 1) will be collected by drive-point piezometers near the shore at shallow depths (just below to 5 feet below the water table) and from a natural spring adjacent to Alley Creek (Alley Pond Spring, USGS station ID 404523073444001) to provide insight into the sources of indicator bacteria and pharmaceutical via seepage.
3. Bed-sediment and storm-sewer sludge samples (up to four; table 1) will be collected to assess the potential for resuspension and infrastructure contributions to fecal contamination to Alley Creek.
4. Quality control samples (four sets) will include blank and replicate samples for FIB, MST markers, and pharmaceuticals. Quality assurance procedures according to USGS policy and methods will be followed throughout the project. Results from samples of wildlife and canine fecal material and sewage treatment plant effluent collected during the 2018-19 NYS DEC MST study throughout Suffolk and Nassau Counties will be used as reference host-specific marker for the environmental MST samples.
5. Ancillary data will be collected to better inform interpretation:
  a. Historical FIB data collected by NYS DEC and NYC DEP
  b. Weather conditions from available National Weather Service (NWS) and other verifiable NYC weather stations
  c. Tidal data available from National Oceanographic and Atmospheric Administration (NOAA)
   Physical parameters  FIB MST markers  Pharmaceuticals
Surface water and outfall  36  36  36  18
 Groundwater  3  3  3  3
 Bed sediment and storm-sewer sludge  --  4  4  --


Table 1. Proposed number of samples by analysis and site type.
AECOM USA, 2014, Combined Sewer Overflow Long Term Control Plan for Alley Creek and Little Neck Bay: New York City Department of Environmental Protection, Capital Project No. WP-169, 304 p.
Boehm, A.B., Van De Werfhorst, L.C., Griffith, J.F., Holden, P.A., Jay, J.A., Shanks, O.C., Wang, D., and Weisberg, S.B., 2013, Performance of forty-one microbial source tracking methods: A twenty-seven lab evaluation study: Water Research, v. 47, p. 6812–6828.
Evenson, E.J., Orndorff, R.C., Blome, C.D., Böhlke, J.K., Hershberger, P.K., Langenheim, V.E., McCabe, G.J., Morlock, S.E., Reeves, H.W., Verdin, J.P., Weyers, H.S., and Wood, T.M., 2013, U.S. Geological Survey water science strategy—Observing, understanding, predicting, and delivering water science to the Nation: U.S. Geological Survey Circular 1383–G, 49 p. [Also available at]
Green, H.C., Dick, L.K., Gilpin, B., Samadpour, M., and Field, K.G., 2012, Genetic markers for rapid PCR-based identification of gull, Canada goose, duck, and chicken fecal contamination in water: Applied and Environmental Microbiology, v. 78, no. 2, p. 503-510.
Green, H.C., Haugland, R.A., Varma, M., Millen, H.T., Borchardt, M.A., Field, K.G., Walters, W.A., Knight, R., Sivaganesan, M., Kelty, C.A., and Shanks, O.C., 2014, Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples: Applied and Environmental Microbiology, v. 80, no. 10, p. 3086–3094.
Kildare, B.J., Leutenegger, C.M., McSwain, B.S., Bambic, D.G., Rajal, V.B., and Wuertz, S., 2007, 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: a Bayesian approach: Water research, v. 41, no. 16, p. 3701-3715.
Kitajima, M., Sassi, H.P., and Torrey, J.R., 2018, Pepper mild mottle virus as a water quality indicator: npj Clean Water, v. 1, p. 1–9.
Mieszkin, S., Yala, J.F., Joubrel, R., and Gourmelon, M., 2009, Phylogenetic analysis of Bacteroidales 16S rRNA gene sequences from human and animal effluents and assessment of ruminant faecal pollution by real-time PCR: Journal of Applied Microbiology, v. 108, p. 974-984.
New York City Parks Natural Resources Group, 2015, Alley Creek watershed management and habitat restoration plan: New York City Parks and Recreation, 337 p.
Seurinck, S., Defoirdt, T., Verstraete, W., and Siciliano, S.D., 2005, Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater: Environmental microbiology, v. 7, no. 2, p. 249-259.
Stoeckel, D.M., 2005, Selection and application of microbial source tracking tools for water-quality investigations: U.S. Geological Survey Techniques and Methods Book 2, Chapter A3, 43 p.
U.S. Geological Survey [USGS], variously dated, The national field manual for the collection of water-quality data: U.S. Geological Survey Techniques and Method, book 9, chaps. A1–A9, also available at
Zhang, T., Breitbart, M., Lee, W.H., Run, J.Q., Wei, C.L., Hibberd, M.L., Liu, E.T., Rohwer, F., and Ruan, Y., 2006, RNA viral community in human feces: prevalence of plant pathogenic viruses: PLOS Biology, v. 4, no. 1, p. 108–118.

Project Location by County

Queens County, NY