Geology topics

Christopher M. Kephart

Publications and source records attributed to Christopher M. Kephart.

At least 19 recordsLinked to original sources

USGS2026

Variability of discharge, nutrients, and Escherichia coli from tile drains in a small agricultural stream, a synoptic study in the School Branch watershed, Hendricks County, Indiana

The U.S. Geological Survey, in cooperation with the Indiana Department of Environmental Management, sampled a 1-mile stream reach of School Branch in Hendricks County, Indiana. Sampling consisted of 24 tile drain sites and surface-water sites both upstream and downstream from the tile drains. This study intended to (1) assess the variability of discharge, nutrients, and Escherichia coli ( E. coli ) among tiles within a stream reach in variable conditions; (2) define how the tiles affect the stream hydrology and water quality; and (3) determine potential management implications. Samples were collected on three dates—round 1 on June 12, 2018, after fertilizer was applied; round 2 on September 11, 2018, in fall harvest conditions; and round 3 on April 16, 2019, before fertilizer was applied—to encompass differing precipitation events, multiple seasons, and field conditions. Sites were sampled for water-quality parameters, dissolved and total nutrients (ammonia, nitrate plus nitrite, total nitrogen, orthophosphate, and total phosphorus), E. coli , and instantaneous discharge. Instantaneous nutrient loads were calculated from tiles and at the upstream and downstream surface-water sites. Nutrient concentrations and instantaneous loads varied depending on the tile and the sampling date. Tiles contributed between 26.5 and 66.0 percent of increased discharge between the surface-water sites. Tiles contributed between 34.7 and 87.4 percent and between 19.7 and 65.9 percent of the increased total nitrogen and phosphorus loads, respectively, for the downstream site relative to the upstream site. Most of the total nitrogen and total phosphorus from the tiles was in the dissolved forms (nitrate plus nitrite and orthophosphate). Surface-water samples had a nitrate plus nitrite to total nitrogen ratio of 71 to 93 percent, with an average of 82 percent; tile samples ranged from 44 to nearly 100 percent, with an average of 91 percent dissolved nitrogen. Surface-water samples had an orthophosphate to total phosphorus ratio of 30 to 65 percent, with an average of 53 percent; tile samples ranged from 32 to nearly 100 percent, with an average of 85 percent dissolved phosphorus. E. coli was detected in all but 5.79 percent of tile and surface-water samples. The E. coli results indicated the possibility of human or animal fecal contamination by way of septic systems leaking or directly linked to the tiles draining into the study area. Consequently, five microbial source tracking samples were collected from the upstream and downstream surface-water sites between August 3, 2021, and May 18, 2022. Human, canine, ruminant, and avian sources of fecal contamination were evaluated. The microbial source tracking samples indicated that human-specific sources are likely consistently contributing to elevated fecal contamination. Differences in discharge, nutrient concentrations, nutrient loads, and E. coli concentrations show that many factors affect how tiles alter the hydrology and water quality of receiving waters. The timing and severity of precipitation events, season, and the antecedent conditions of the field or watershed before sampling can affect the results. Tiles with the largest discharge rate had the most potential effect on the water quality and quantity of the stream. Targeting high-flowing tiles may affect efforts to improve overall water quality.

Indiana↗

USGS2025

Microbial source tracking in Cedar and Crane Creeks near Curtice, Ohio, 2021

Elevated concentrations of Escherichia coli ( E. coli ) bacteria and signs of sewage lead to impairment of Cedar and Crane Creeks near the town of Curtice, Ohio. In 2021, the U.S. Geological Survey, in cooperation with Ohio Environmental Protection Agency, collected samples and analyzed them for concentrations of E. coli and microbial source tracking (MST) markers to help characterize the locations and sources of fecal contamination and better inform potential remediation strategies. The study included a total of 118 samples collected at 12 sites (6 on Cedar Creek and 6 on Crane Creek) from May to September 2021 during wet and dry weather conditions. All samples were analyzed for E. coli concentrations, and human and canine-associated MST markers. A subset of samples was analyzed for MST markers associated with swine, ruminant, cattle, horse, waterfowl, and poultry. Human-origin fecal contamination was found at all sites sampled in this study and concentrations of the human-associated MST marker HF183/BacR287 were significantly correlated with E. coli concentrations. The HF183/BacR287 marker was detected in 114 of 118 samples and the detection frequency in samples at each site ranged from 90 to 100 percent. E. coli concentrations exceeded the Ohio Environmental Protection Agency’s regulatory statistical threshold (410 most probable number of E. coli per 100 milliliters) in 91 percent of samples. These findings verified that Cedar and Crane Creeks are impaired by bacteria, and the HF183/BacR287 marker results support that human-origin fecal contamination is the dominant contributor to that impairment. The canine-associated MST marker BacCan was also prevalent in collected samples (detected in 112 of 118 samples); however, BacCan can also be detected in human waste, so it is not feasible to ascertain whether canine feces is a source of contamination in these watersheds. Human fecal contamination was nearly uniform among sites, but the Martin Williston Road ditch effluent site along Crane Creek had a significantly higher median HF183/BacR287 concentration than the other Crane Creek sites. Results indicate that the Martin Williston Road ditch is a potential source of human-origin fecal contamination to Crane Creek. There is likely additional human fecal contamination upstream from the study area.

Ohio↗

USGS2024

The U.S. Geological Survey Ohio Water Microbiology Laboratory

The U.S. Geological Survey Ohio Water Microbiology Laboratory is a part of the Ohio-Kentucky-Indiana Water Science Center. The mission of the laboratory is to provide microbiological data of public health significance from surface waters, groundwaters, and sediments for a variety of study objectives. The laboratory conducts internal projects, works with external cooperators, and assists U.S. Geological Survey offices and National programs. The laboratory offers guidance, study design, and data interpretation expertise to collaborators, all following rigorous quality control and quality assurance procedures.

Fact Sheet↗

USGS2023

Assessing Escherichia coli and microbial source tracking markers in the Rio Grande in the South Valley, Albuquerque, New Mexico, 2020–21

The Rio Grande, in southern Albuquerque, New Mexico, is a Clean Water Act Section 303(d) Category 5 impaired reach for Escherichia coli ( E. coli ). The reach is 5 miles in length, extending from Tijeras Arroyo south to the Isleta Pueblo boundary. An evaluation of E. coli and microbial source tracking markers (human-, canine-, and waterfowl-specific sources) was conducted by the U.S. Geological Survey to determine the extent and source of fecal bacteria within the impaired reach of the Rio Grande, primarily during the dry season (November through June) in 2020 and 2021. Samples were collected in the river cross section at three locations within each site and collected during both the dry season and the wet season, thereby providing data over a range of flow conditions to better understand the extent and source of fecal bacteria. Because fecal microorganisms may readily attach to sediments, riverbed material samples were also collected. During the dry season, E. coli concentrations in water were primarily detected below the New Mexico Surface Water Quality Standard of 410 colony forming units per 100 milliliters and mostly human and canine sources were detected. However, approximately 40 percent of the water samples exceeded the Isleta Pueblo water quality standard of 88 colony forming units per 100 milliliters. E. coli concentrations in bed material were detected at low concentrations, and the bed material was a sandy substrate, with little fine-grained material, a suitable habitat that would allow for bacterial growth during the dry season. Significant spatial and temporal differences, where p-values were less than 0.05, were found in water-quality samples for E. coli (seasonal) and the human tracker concentrations (between sites and within a cross section of a site). Given the lack of correlation between discharge and E. coli concentration and the human marker being most prevalent in the study area, the sources of E. coli in the dry season are likely nonpoint sources. The results from this study will help decision makers determine the efficacy of their best management practices and guide new practices to improve water quality in the reach.

New Mexico↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in South Oyster Bay on Long Island, New York

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 South Oyster Bay, a shallow embayment on the southern shore of Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the bay 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. Analysis revealed that the most substantial source of fecal contamination to South Oyster Bay was stormwater, particularly during the summer months. The highest frequency of fecal coliform detections in source sites were under wet summer conditions, and the highest fecal coliform concentrations were under wet summer conditions at the Cedar Creek near Bay Place and Unqua Lake Culvert sites (more than 16,000 most probable number per 100 milliliters each). The human-associated Bacteroides marker was the most frequently detected microbial source tracking marker in South Oyster Bay (50 percent positive detections). The human marker was detected at least twice in all surface water source and receptor sites, except for the Massapequa Lake East Culvert source site that did not have any positive human marker detections. Canine contamination was prolific at source sites but was associated with low fecal coliform concentrations in the winter months. All detections of the canine-associated Bacteroides marker were in samples collected during the winter season and were associated with fecal coliform concentrations below the reporting limit, indicating that birds are not a persistent source of fecal coliform to South Oyster Bay. The absence of fecal coliform and human markers in groundwater samples collected throughout the larger study area indicates that water from cesspools or septic tanks do not contribute fecal coliform to the bay. Further, microbial source tracking markers were not detected in the sandy sediment collected at Zachs Bay. Based a classification scheme developed to convey the degree of fecal contamination to stakeholders and resource managers, the Cedar Creek near Bay Place and Unqua Lake Culvert sites were identified as locations that contribute substantial fecal contamination to South Oyster Bay.

New York↗

USGS2022

Assessment of fecal contamination sources to Alley Creek, Queens County, New York, August 2020–June 2021

Alley Creek, a tributary to Little Neck Bay in Queens County, New York, has been designated by the New York State Department of Environmental Conservation as impaired (Class I) for fecal coliform because of pollution from combined sewer overflow, including stormwater runoff. The U.S. Geological Survey, in cooperation with the New York City Department of Environmental Protection, conducted a 1-year study from August 2020 to June 2021 using microbial source tracking (MST) methods to assess potential host sources of fecal contamination (for example, human, canine, and waterfowl) from the following: three outfall sites, TI–025, TI–008, and TI–024; an artesian well (Q277) adjacent to Alley Creek; and natural waters within the Alley Creek watershed and Little Neck Bay. In addition to analyzing for MST markers, field measurements such as water temperature and specific conductance, samples for total suspended solids, and fecal indicator bacteria (FIB; enterococci and fecal coliform) were collected. Pharmaceutical compounds were also collected for analysis, and the results of sampling were compared spatially and temporally to help support management decisions related to mitigation of fecal sources to Alley Creek. Factors that could affect concentrations, including tidal conditions, seasonality, and weather conditions, also were assessed. A sediment resuspension laboratory experiment was designed to replicate tidal activity in Alley Creek using sediment collected in the sewers and on the shoreline, as well as water collected from Oakland Lake. These sediment samples were assessed to understand the relation between sediment resuspension and FIB in the water column. The human MST markers used for this study, Bacteroides HF183/BacR287, and crAssphage CPQ_056 and CPQ_064, were detected in most samples (27 of 28) collected at the three outfall sites along Alley Creek, whereas the canine marker BacCan was less prevalent (20 of 28 samples) but exhibited a pattern of relative concentrations similar to the human markers. The waterfowl MST GFD marker was detected in 7 of 28 samples collected at the three outfall sites. Human MST markers were not detected at Oakland Lake (which drains through a combined sewer line to Alley Creek at TI–008), indicating minimal or nonexistent influence of sewage contamination in the lake. Groundwater samples collected from Q277 did not contain any MST markers, and concentrations of fecal coliform were less than 10 colony forming units per 100 milliliters. Although FIB did not correlate well with total suspended solids for individual sample sets, samples collected following precipitation and high-turbidity events were typically found to have higher concentrations of FIB than dry-weather samples. Results from the pharmaceutical compounds analysis provided additional evidence for determining known and suspected human sources when coupled with MST markers. Together, the MST, pharmaceutical, and FIB data generated by this study, along with supplementary data such as locations of point sources, locations of wildlife populations, and tidal exchange data, may provide reliable information on source identification and transport mechanisms of fecal contamination to Alley Creek.

New York↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in Great South Bay on Long Island, New York

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 a part of Great South Bay (referred to as Great South Bay for the purposes of this report) near the hamlets of West Sayville, Sayville, and Bayport on the southern shore of Suffolk County on Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the bay 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. Analysis revealed that the most substantial source of fecal contamination to Great South Bay was discharge from sites draining ponds and wetlands into the tributaries sampled, Brown and Green Creeks, 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. Sites with high concentrations of fecal coliform bacteria in the summer exacerbated by stormwater include the Brown Creek Culvert at Middle Road, Mill Pond Culvert near South Street, and Green Creek Culvert near Montauk Highway sites. The canine Bacteroides (BacCan) marker was the most frequently detected microbial source tracking marker with 15 positive detections in surface water across the landscape, followed by the waterfowl Helicobacter (GFD) marker with 9 detections and the human Bacteroides (HF183) marker with 4 detections in surface water (excluding 2 detections in sediment). The ruminant Bacteroides (Rum2Bac) marker was not detected in any samples collected during this study. The detection frequency of BacCan was similar for all sampling conditions and seasons, suggesting canine influence is unrelated to weather events and is a year-round occurrence. BacCan was detected in 14 of 16 source samples and only 1 of 16 receptor samples, which suggests that canine fecal contamination is likely diluted in the bay. There was a similar amount of marker detections when comparing weather condition (wet or dry) and season (winter or summer), suggesting that fecal contamination was unrelated to weather events or time of year. Eight waterfowl marker detections were in samples collected during the winter, and only one during the summer, implicating seasonal avian fecal contamination throughout the embayment. The human marker was detected in only one surface-water receptor sample, during the wet winter sampling event at the Green Creek Mid-Bay site. Three of four human marker detections were in the samples collected during the wet winter sampling event, indicating that weather and season may influence the presence of human markers in Great South Bay, but human markers are not overly prevalent.

New York↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in Lake Montauk on Long Island, New York

The U.S. Geological Survey worked in cooperation with the Concerned Citizens of Montauk and the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering Lake Montauk, an artificial embayment on the tip of the southern fork 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. Overall, human and waterfowl markers were infrequently and sporadically present in source and receptor samples at low concentrations. By evaluating the microbial source tracking markers alongside fecal coliform data and land-use information, geographical sources of fecal contamination discharging from various source sites, such as culverts and ponds, were better differentiated. Analysis revealed that stormwater runoff and pond drainage were the most likely transport mechanisms for fecal contamination to Lake Montauk. When considering Lake Montauk as a whole, the highest frequency of fecal coliform detections in source site samples was found to be under wet summer conditions, as evidenced by the high fecal coliform concentrations at the South Beach, Stepping Stones Pond, and Stepping Stones Pond Culvert sites (300, 220, and more than 16,000 most probable number per 100 milliliters, respectively). No point sources of fecal coliform contamination to Lake Montauk were identified; however, receptor site samples adjacent to marinas (Lake Montauk Inlet and Star Island North sites) had a high frequency of human marker detections but were associated with fecal coliform concentrations at or below the reporting limit. The absence of fecal coliform and human microbial source tracking markers in groundwater samples indicated that water from septic systems did not influence the lake during this study. Further, the sandy sediment sample collected at the South Beach site was negative for all microbial source tracking markers and is unlikely to contribute fecal coliform from the tested host organisms when resuspended in the water column through tidal shifts or boat activity.

New York↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in Sag Harbor on Long Island, New York

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 Sag Harbor, an embayment complex on the northern shore of the south fork 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. Analysis revealed that the most substantial source of fecal contamination to Sag Harbor 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 were detected in all four samples at the Sag Harbor Sewage Treatment Plant Outfall site but were associated with low fecal coliform concentrations, indicating that the sewage treatment plant is not a likely source of fecal contamination to the embayment. The Ligonee Brook Culvert, Paynes Creek near Marjorie Lane, and Otter Pond Culvert sites were identified as locations that contribute fecal contamination to Sag Harbor. These three locations had high fecal coliform bacteria concentrations in the summer, one of which was positive for canine microbial source tracking markers (Ligonee Brook Culvert), and another positive for waterfowl markers (Paynes Creek near Marjorie Lane). The absence of fecal coliform bacteria and human microbial source tracking markers in groundwater samples indicates that water from septic systems does not influence the harbor; however, elevated fecal coliform bacteria concentrations were not often detected. Further, the sandy sediment alongside Sag Harbor is unlikely to contribute fecal coliform bacteria when resuspended in the water column through tidal shifts or boat activity.

New York↗

USGS2022

Using microbial source tracking to identify fecal contamination sources in Patchogue and Bellport Bays on Long Island, New York

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 Patchogue and Bellport Bays, two embayments on the south shore of Suffolk County, Long Island, New York. Water samples are routinely collected by the New York State Department of Environmental Conservation in the bays 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. Analysis revealed that the most substantial source of fecal contamination to Patchogue and Bellport Bays was discharge from sites draining ponds and wetlands into the rivers and tributaries sampled, 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. Overall, canine- and waterfowl-associated bacterial contributions were prevalent in source samples in both bays. Human-associated markers were present in surface-water source samples and completely absent in receptor samples in Patchogue Bay. The Fireplace Neck receptor site in Bellport Bay had a human-associated marker present in the summer wet sample only. Human markers were detected at the sample site downstream from the Patchogue wastewater treatment plant but were associated with low fecal coliform concentrations, indicating that the wastewater treatment plant is not a likely source of fecal contamination to Patchogue Bay. The lack of human-associated marker detections within Patchogue and Bellport Bays in summer source samples coupled with low to no detections of fecal coliform, especially where small marinas are present in creeks and tributaries, suggest that boats do not substantially contribute fecal coliform bacteria to the bays. There was little evidence of groundwater-contributing fecal bacteria by direct discharge from the subsurface. Further, the sandy sediment alongside Patchogue and Bellport Bays is unlikely to contribute fecal coliform bacteria from the test host organisms when resuspended in the water column. A classification scheme was developed to convey the degree of fecal contamination to stakeholders and resource managers. Based on this classification scheme, the Corey Creek Near Middle Road, Patchogue River Near Division Street, and Swan River Mouth sampling sites were identified as locations that contribute substantial fecal contamination to Patchogue Bay. In Bellport Bay, the Culvert at Beaverdam Creek site was identified as the location contributing the most substantial fecal contamination.

New York↗

USGS2022

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

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.

New York↗

USGS2022

Understanding sources and distribution of Escherichia coli at Lake St. Clair Metropark Beach, Macomb County, Michigan

Lake St. Clair Metropark Beach (LSCMB) in Michigan is a public beach near the mouth of the Clinton River that has a history of beach closures for public health concerns. The Clinton River is designated as a Great Lakes Area of Concern, and the park has a Beneficial Use Impairment for beach closings because of elevated Escherichia coli ( E. coli ) concentrations. The U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency and in collaboration with the Michigan Department of the Environment, Great Lakes, and Energy, Macomb County Health Department, and Huron-Clinton Metroparks, completed a 2-year study to determine sources of E. coli in LSCMB. Samples were collected during dry and wet weather periods to observe the sampling sites under different conditions. Nearshore surface water samples were collected biweekly July through October in 2018 and May through September in 2019. There were 20 sampling sites along the shoreline of the park and in the channel north of the park. In addition to collecting nearshore surface-water samples, samples were collected from shallow groundwater, lake-bottom material, standing water on the beach and surrounding the recreational beach area, solids (beach sands and detritus), and offshore surface-water sites. In 2019, additional samples for microbial source tracking (MST) were collected on three dates in midsummer and were analyzed for human (HF183) and bird/waterfowl (GFD) MST markers. The concentrations of E. coli at LSCMB (in order of highest to lowest E. coli concentrations) were as follows: shallow groundwater nearest to the water’s edge, surface sands and organic matter (detritus), standing water on the beach, nearshore surface water in and surrounding the recreational beach area, lake-bottom material, and offshore surface water. The combination of low E. coli concentrations offshore and higher concentrations nearshore indicate nearshore sources, possibly from beach sands or groundwater, rather than sources coming from offshore Lake St. Clair waters. The subset of samples for MST analysis did not have enough positive results to illustrate MST trends, but this study demonstrated that both human and waterfowl sources can affect the water quality at LCSMB.

Michigan↗

USGS2021

Using microbial source tracking to identify fecal contamination sources in an embayment in Hempstead Harbor on Long Island, New York

The U.S. Geological Survey worked collaboratively with the New York State Department of Environmental Conservation to assess the potential sources of fecal contamination entering Hempstead Harbor, an embayment on the northern shore of Nassau 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, surrounding land use, and additional water-quality data (including nutrient and stable isotopes of nitrate analyses) for the location where a sample was collected help determine the geographical source and conveyance of land-based water to the embayment. Our analysis revealed an abundance of human and canine fecal contamination throughout the Hempstead Harbor landscape and that water from municipal separate storm sewer system conveyances was the most likely transport mechanism of this fecal contamination. 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 at Glenwood Road and the outfall and the spillway at Skillman Street were identified as locations that contribute substantial fecal contamination to Hempstead Harbor.

New York↗

USGS2021

Overview and methodology for a study to identify fecal contamination sources using microbial source tracking in seven embayments on Long Island, New York

Between June 2018 and July 2019, the U.S. Geological Survey collaborated with the New York State Department of Environmental Conservation to analyze water quality in seven embayments on Long Island, New York, for a study to examine fecal contamination using microbial source tracking. This report documents the approach, methodology, and quality-assurance data used in the study. All samples and field data were collected in accordance with U.S. Geological Survey National Field Manual procedures. Samples were analyzed for host-specific deoxyribonucleic acid (DNA) markers, fecal coliform bacteria, inorganic and total organic nitrogen, and stable isotopes of nitrate and ammonium. Samples for quality control were collected for microbiological analyses at a rate of 1 per 20 environmental samples. A total of 14 blank and 15 replicate samples were collected for DNA markers, 52 sequential field replicates were analyzed by the Public Environmental Health Laboratory of the Suffolk County Department of Health Services and the New York State Department of Conservation Marine Laboratory for fecal coliform, and 7 blank and 7 replicate samples were collected to be analyzed for nutrients. Results from quality-control samples collected throughout the course of the study confirmed that sampling procedures were adequate and did not disqualify any data from analysis.

New York↗

USGS2021

Evaluation of a modified rapid viability-polymerase chain reaction method for Bacillus atrophaeus spores in water matrices

A rapid method that provides information on the viability of organisms is needed to protect public health and ensure that remediation efforts following a release of a biological agent are effective. The rapid viability-polymerase chain reaction (RV-PCR) method combines broth culture and molecular methods to provide results on whether viable organisms are present in less than 15 h. In this study, a modified RV-PCR (mRV-PCR) method was compared to a membrane-filtration culture method for the detection of viable Bacillus spores in water matrices. Samples included small and large volumes of chlorine and non‑chlorine treated tap water. Large volume water samples (up to 100 L), were processed by ultrafiltration using a semi-automated waterborne pathogen concentrator, followed by centrifugation as a secondary concentration technique. The concentrated samples were analyzed by mRV-PCR and culture methods. The overall agreement between the mRV-PCR and culture methods when seed concentrations were greater than 10 spores per sample volume analyzed was 96%. The total time from the start of sample processing to the final sample result for the mRV-PCR method was decreased by approximately 2 h, in comparison to the previously published RV-PCR method because of the incorporation of shorter, more efficient primary and secondary concentration steps and a shorter DNA extraction technique. Overall, this study confirmed that RV-PCR is a promising approach for identifying viable Bacillus spores in small- and large-volume water samples and for producing results in less time than traditional culture methods.

Journal of Microbiological Methods↗

USGS2020

Assessment of water quality and fecal contamination sources at Hook Pond, East Hampton, New York

Summary The U.S. Geological Survey, in cooperation with the Village of East Hampton, New York, conducted a 1-year study from August 2017 to August 2018 to provide data necessary to improve understanding of the sources of nutrients and pathogens to Hook Pond watershed to allow for possible mitigation or reduction of loads. Chronic eutrophication and recent concern over harmful cyanobacteria in Hook Pond are the result of past and present land uses and a changing climate that have prompted the Village of East Hampton and local businesses to study and remediate factors contributing to the persistent loading of nutrients, organic contaminants, and pathogens. This assessment of Hook Pond, Hook Pond Dreen, and shallow groundwater provides the most comprehensive set of water-quality data to date. Interpretations presented in this study and the data on which they are based can be used to support management decisions, inform and contribute to modeling, and serve as a baseline for future assessments. Results from continuous monitoring of water temperature, specific conductance, and elevation at Hook Pond site 10 (Maidstone Club golf cart bridge), as well as ancillary weather and tidal data from nearby stations, were used to help explain seasonal and storm-related concentration variation of nitrogen, phosphorus, wastewater-indicator compounds, and pathogens. Data collected were also compared to existing historical data. Physicochemical constituents measured on a routine basis throughout the pond and along the tributary showed the spatial variability in water temperature, specific conductance, dissolved oxygen, pH, turbidity, and chlorophyll a and phycocyanin fluorescence. A lakebed survey was compiled based on the year-round sampling throughout the pond for future comparisons. Water-quality data from shallow groundwater at points around Hook Pond and adjacent to Hook Pond Dreen were interpreted and quantified to estimate relative contributions and species of nutrients, wastewater-indicator compounds, and microbial source tracking (MST) markers to base flow. To supplement the continuous water-surface elevation data, a single set of discharge measurements was collected under normal (nonstorm) conditions to better understand the relative contributions and dilution of surface waters by contaminated groundwater. The nutrient and physicochemical data from this study can be used in conjunction with current and future models and decision support tools to guide planned and ongoing restoration efforts, such as dredging to reduce sediment accumulation, opening a pathway to the ocean (which would change the salinity and flow dynamics of the pond and adjacent groundwater), and addressing growing concerns over cyanobacterial blooms, while serving as a baseline for measuring changes resulting from sea-level rise, climate change, and changes in nutrient loading. The microbial source tracking and indicator bacteria results can help direct efforts to reduce runoff and direct contributions of fecal contamination from dogs and waterfowl along Hook Pond Dreen. The results can also be used to assess the current state of wastewater infrastructure surrounding and contributing to Hook Pond Dreen, based on detection of human markers throughout the year and with both Bacteroides and coliphage methods.

New York↗

USGS2019

Spatial and temporal distribution of bacterial indicators and microbial-source tracking within Tumacácori National Historical Park and the upper Santa Cruz River, southern Arizona and northern Mexico, 2015–2016

Tumacácori National Historical Park (TUMA) in southern Arizona protects the culturally important Mission San José de Tumacácori, while also managing a part of the ecologically diverse riparian corridor of the Santa Cruz River. The quality of the water flowing through depends solely on upstream watershed activities, and among the water-quality issues concerning TUMA is the microbiological pathogens in the river introduced by human and animal sources that pose a significant human health risk to employees and visitors. The U.S. Geological Survey (USGS) conducted a 3-year study to understand the sources, timing, and distribution of the fecal-indicator bacteria Escherichia coli ( E. coli ) within TUMA and the upstream watershed. The information provided in this investigation is a result of a comprehensive approach to quantify the spatial and temporal variability of E. coli and suspended sediment in the Upper Santa Cruz River Watershed. Several types of flow were sampled from base flow to flood flow and at high frequency intervals (rise, peak, and recession) to determine daily variability, as well as seasonal variability. Hydrologic data collection and estimation techniques were used to establish a hydrologic relation with E. coli and suspended sediment. Furthermore, source tracking was used to describe the potential sources of E. coli . Models were developed that are expected to be useful for predicting E. coli concentrations to help TUMA managers understand instantaneous conditions to keep the public and staff informed about potentially harmful water-quality conditions. In addition, the concentration, flux, and source information will provide more accurate data for other surface-water modeling and can be useful in the development of total maximum daily load standards. This will help TUMA describe the water-quality conditions at the park and waters flowing through the park, as well as prioritize and help carry out future best-management actions to address these issues.

Tumacácori National Historical Park, Upper Santa C↗

USGS2019

Escherichia coli and microbial source tracking marker concentrations in and near a constructed wetland in Maumee Bay State Park, Oregon, Ohio, 2015–16

Elevated Escherichia coli ( E. coli ) concentrations at the Maumee Bay State Park (MBSP) Lake Erie beach have resulted in frequent recreational water-quality advisories. After the construction of a wetland along Berger Ditch in Maumee Bay State Park, Oregon, Ohio, samples were collected and analyzed for concentrations of E. coli and microbial source tracking (MST) markers. This study was done by the U.S. Geological Survey, in cooperation with the University of Toledo, to provide data that can be used to help evaluate the effects of the wetland on water quality in MBSP. From July 2015 to February 2016, 116 samples were collected from six sites. Median GenBac (general marker) and E. coli concentrations were higher in samples from Berger Ditch sites than in samples from the wetland sites. No statistically significant difference was found between median E. coli concentrations in samples collected at Berger Ditch sites upstream and downstream from the wetland. The frequency of detection of the human-associated Bacteroides MST marker (HF183) decreased from 39 percent upstream from the wetland to 22 percent downstream from the wetland; however, the HF183 median concentrations from these two groups of samples were nearly the same (2,700 to 2,800 copies per 100 milliliters from upstream to downstream). The waterfowl-associated Helicobacter MST marker (GFD) was detected in 13 percent of samples from the Berger Ditch site upstream from the wetland, although it was not detected in samples from the Berger Ditch site downstream from the wetland. The ruminant-associated MST marker, Rum2Bac, was not detected at any site during this study.

Ohio↗