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USGS2008

GAP Analysis Bulletin Number 15

The Mission of the Gap Analysis Project (GAP) <http://gapanalysis.nbii.gov> is to promote conservation by providing broad geographic information on biological diversity to resource managers, planners, and policy makers who can use the information to make informed decisions. As part of the National Biological Information Infrastructure (NBII) <http://www.nbii.gov>?a collaborative program to provide increased access to data and information on the nation?s biological resources--GAP data and analytical tools have been used in hundreds of applications: from basic research to comprehensive state wildlife plans; from educational projects in schools to ecoregional assessments of biodiversity. The challenge: keeping common species common means protecting them BEFORE they become threatened. To do this on a state or regional basis requires key information such as land cover descriptions, predicted distribution maps for native animals, and an assessment of the level of protection currently given to those plants and animals. GAP works cooperatively with Federal, state, and local natural resource professionals and academics to provide this kind of information. GAP activities focus on the creation of state and regional databases and maps that depict patterns of land management, land cover, and biodiversity. These data can be used to identify ?gaps? in conservation--instances where an animal or plant community is not adequately represented on the existing network of conservation lands. GAP is administered through the U.S. Geological Survey. Through building partnerships among disparate groups, GAP hopes to foster the kind of collaboration that is needed to address conservation issues on a broad scale. For more information, contact: John Mosesso National GAP Director 703-648-4079 Kevin Gergely National GAP Operations Manager 208-885-3565

GAP Bulletin↗

USGS2024

Asynchronous movement patterns between breeding and stopover locations in a long-distance migratory songbird

The species-specific migratory patterns and strategies of many songbirds remain unknown or understudied, as research in animal ecology is biased toward the breeding period, with the fewest studies on the migratory period across taxa. Identifying large-scale spatiotemporal migratory patterns is challenging, as individuals within a species may vary in their migratory behavior and strategies. The Yellow Warbler ( Setophaga petechia ) is a Nearctic-Neotropical migrant that is relatively well studied during the breeding season, but its species-wide migratory patterns remain understudied. Our aim in studying Yellow Warbler movement ecology was to characterize temporal migration patterns during fall migration. We sought to determine the temporal migration pattern among breeding locations, as determined by the hydrogen stable isotope values in feather samples collected at disjunct (~2000 km) stopover sites in the Gulf of Maine (n = 50) and the Gulf of Mexico (n = 150). We used a similarity matrix to group individuals into a geographic cluster by breeding location, which was then used as the response variable in a modeling analysis. Our results provide evidence that Yellow Warblers exhibit an asynchronous, type 1 temporal migration pattern with southern breeding populations initiating migration prior to northern populations. Using hydrogen isotopes, we identified the temporal migration patterns between geographic clusters, representing an individual’s breeding location, and stopover sites along the Gulf of Maine and Gulf of Mexico, which fills a gap in understanding Yellow Warbler migration ecology.

Avian Conservation and Ecology↗

USGS2024

Temperature impacts on dengue incidence are nonlinear and mediated by climatic and socioeconomic factors: A meta-analysis

Temperature can influence mosquito-borne diseases like dengue. These effects are expected to vary geographically and over time in both magnitude and direction and may interact with other environmental variables, making it difficult to anticipate changes in response to climate change. Here, we investigate global variation in temperature–dengue relationship by analyzing published correlations between temperature and dengue and matching them with remotely sensed climatic and socioeconomic data. We found that the correlation between temperature and dengue was most positive at intermediate (near 24°C) temperatures, as predicted from an independent mechanistic model. Positive temperature–dengue associations were strongest when temperature variation and population density were high and decreased with infection burden and rainfall mean and variation, suggesting alternative limiting factors on transmission. Our results show that while climate effects on diseases are context-dependent they are also predictable from the thermal biology of transmission and its environmental and social mediators.

PLOS Climate↗

USGS2006

River size and fish assemblages in southwestern South Dakota

We studied relations between river size, fish species diversity, and fish species composition along four major rivers in the Great Plains of southwestern South Dakota to assess patterns of species diversity and composition. We expected diversity to increase with river size and fish composition to change via species addition downstream. Previous surveys of 52 sampling stations provided fish assemblage data, and we used the Geographic Information System (GIS) to determine watershed area by station. Watershed area did not predict species richness or species diversity (Fisher's ??), so species richness of 12 ?? 3.5 SD species and Fisher's ?? of 2.3 ?? 0.87 SD characterized species diversity in the study area. Cluster analysis of faunal similarity (S??rensen's Index) among the 52 sampling stations identified two geographically distinct faunal divisions, so species composition was variable within the study area, but changed via species replacements among faunas rather than species additions downstream. Nonnative species were a minor component of all faunas. Uniform species diversity may be a recent phenomenon caused by impacts of Missouri River dams on native large-river fishes and the unsuitability of rivers in the Great Plains for nonnative species. Variation in faunal composition may also be recent because it was affected by dams. ?? Copyright by the Center for Great Plains Studies, University of Nebraska-Lincoln.

Great Plains Research↗

USGS2005

Geographic variation in survival and migratory tendency among North American Common Mergansers

Movement ecology and demographic parameters for the Common Merganser ( Mergus merganser americanus ) in North America are poorly known. We used band-recovery data from five locations across North America spanning the years 1938–1998 to examine migratory patterns and estimate survival rates. We examined competing time-invariant, age-graduated models with program MARK to study sources of variation in survival and reporting probability. We considered age, sex, geographic location, and the use of nasal saddles on hatching year birds at one location as possible sources of variation. Year-of-banding was included as a covariate in a post-hoc analysis. We found that migratory tendency, defined as the average distance between banding and recovery locations, varied geographically. Similarly, all models accounting for the majority of variation in recovery and survival probabilities included location of banding. Models that included age and sex received less support, but we lacked sufficient data to adequately assess these parameters. Model-averaged estimates of annual survival ranged from 0.21 in Michigan to 0.82 in Oklahoma. Heterogeneity in migration tendency and survival suggests that demographic patterns may vary across geographic scales, with implications for the population dynamics of this species.

Journal of Field Ornithology↗

USGS2021

Using fecal DNA and closed-capture models to estimate feral horse population size

Accurate population estimates provide the foundation for managing feral horses ( Equus caballus ferus ) across the western United States. Certain feral horse populations are protected by the Wild and Free-Roaming Horses and Burros Act of 1971 and managed by the Bureau of Land Management (BLM) or the United States Forest Service on designated herd management areas (HMAs) or wild horse territories, respectively. Horses are managed to achieve an appropriate management level (AML), which represents the number of horses determined by BLM to contribute to a thriving natural ecological balance and avoid deterioration of the range. To achieve AML for each HMA, BLM resource managers need accurate and precise population estimates. We tested the use of non-invasive fecal samples in a genetic capture-recapture framework to estimate population size in a closed horse population at the Little Book Cliffs HMA, Colorado, USA, with a known size of 153 individuals. We collected 1,957 samples over 3 independent sampling periods in 2014 and amplified them at 8 microsatellite loci. We applied mark-recapture models to determine population size using 954 samples that amplified at all 8 loci. We subsampled and reanalyzed our dataset to simulate different data collection protocols and evaluated effects on accuracy and precision of estimates using N-mixture modeling, full likelihood closed-capture modeling, and capwire single-occasion modeling that used data from all 3 sampling periods. Our model results were accurate and precise for analyses that used data from all 3 occasions; however, capwire single-occasion modeling was not accurate when we analyzed each sampling period separately. For all subsampling analysis scenarios, reducing sample size decreased precision, whether by reducing number of field staff, field days, or geographic areas surveyed on each period. Reducing spatial coverage of the survey area did not result in accurate population estimates and only marginally lowered the number of samples that would need to be collected to maintain accuracy. Because laboratory analysis contributes the greatest expense for this method ($80 U.S./sample), reducing fecal sample size is advantageous. Our results demonstrate that non-invasive sampling combined with good survey design and careful genetic and capture-recapture analyses can provide an alternative method to estimate the number of feral horses in a closed population. This method may be especially appropriate in situations where aerial inventories are not practical or accurate because of low sighting conditions. But the higher costs associated with laboratory sample analyses may reduce the method's feasibility compared to helicopter surveys.

Colorado↗

USGS2013

Methods for estimating annual exceedance-probability discharges for streams in Iowa, based on data through water year 2010

A statewide study was performed to develop regional regression equations for estimating selected annual exceedance-probability statistics for ungaged stream sites in Iowa. The study area comprises streamgages located within Iowa and 50 miles beyond the State’s borders. Annual exceedance-probability estimates were computed for 518 streamgages by using the expected moments algorithm to fit a Pearson Type III distribution to the logarithms of annual peak discharges for each streamgage using annual peak-discharge data through 2010. The estimation of the selected statistics included a Bayesian weighted least-squares/generalized least-squares regression analysis to update regional skew coefficients for the 518 streamgages. Low-outlier and historic information were incorporated into the annual exceedance-probability analyses, and a generalized Grubbs-Beck test was used to detect multiple potentially influential low flows. Also, geographic information system software was used to measure 59 selected basin characteristics for each streamgage. Regional regression analysis, using generalized least-squares regression, was used to develop a set of equations for each flood region in Iowa for estimating discharges for ungaged stream sites with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities, which are equivalent to annual flood-frequency recurrence intervals of 2, 5, 10, 25, 50, 100, 200, and 500 years, respectively. A total of 394 streamgages were included in the development of regional regression equations for three flood regions (regions 1, 2, and 3) that were defined for Iowa based on landform regions and soil regions. Average standard errors of prediction range from 31.8 to 45.2 percent for flood region 1, 19.4 to 46.8 percent for flood region 2, and 26.5 to 43.1 percent for flood region 3. The pseudo coefficients of determination for the generalized least-squares equations range from 90.8 to 96.2 percent for flood region 1, 91.5 to 97.9 percent for flood region 2, and 92.4 to 96.0 percent for flood region 3. The regression equations are applicable only to stream sites in Iowa with flows not significantly affected by regulation, diversion, channelization, backwater, or urbanization and with basin characteristics within the range of those used to develop the equations. These regression equations will be implemented within the U.S. Geological Survey StreamStats Web-based geographic information system tool. StreamStats allows users to click on any ungaged site on a river and compute estimates of the eight selected statistics; in addition, 90-percent prediction intervals and the measured basin characteristics for the ungaged sites also are provided by the Web-based tool. StreamStats also allows users to click on any streamgage in Iowa and estimates computed for these eight selected statistics are provided for the streamgage.

Iowa↗

USGS2021

GIS object data properties

Data properties are characteristics of GIS attribute systems and values whose design and format impacts analytical and computational processing. Geospatial data are expressed at conceptual, logical, and physical levels of database abstraction intended to represent geographical information. The appropriate design of attribute systems and selection of properties should be logically consistent and support appropriate scales of measurement for representation and analysis. Geospatial concepts such as object-field views and dimensional space for relating objects and qualities form data models based on a geographic matrix and feature geometry. Three GIS approaches and their attribute system design are described: tessellations, vectors, and graphs.

Book chapter↗

USGS2015

Mapping geoelectric fields during magnetic storms: Synthetic analysis of empirical United States impedances

Empirical impedance tensors obtained from EarthScope magnetotelluric data at sites distributed across the midwestern United States are used to examine the feasibility of mapping magnetic storm induction of geoelectric fields. With these tensors, in order to isolate the effects of Earth conductivity structure, we perform a synthetic analysis—calculating geoelectric field variations induced by a geomagnetic field that is geographically uniform but varying sinusoidally with a chosen set of oscillation frequencies that are characteristic of magnetic storm variations. For north-south oriented geomagnetic oscillations at a period of T 0 =100 s, induced geoelectric field vectors show substantial geographically distributed differences in amplitude (approximately a factor of 100), direction (up to 130 ∘ ), and phase (over a quarter wavelength). These differences are the result of three-dimensional Earth conductivity structure, and they highlight a shortcoming of one-dimensional conductivity models (and other synthetic models not derived from direct geophysical measurement) that are used in the evaluation of storm time geoelectric hazards for the electric power grid industry. A hypothetical extremely intense magnetic storm having 500 nT amplitude at T 0 =100 s would induce geoelectric fields with an average amplitude across the midwestern United States of about 2.71 V/km, but with a representative site-to-site range of 0.15 V/km to 16.77 V/km. Significant improvement in the evaluation of such hazards will require detailed knowledge of the Earth's interior three-dimensional conductivity structure.

Geophysical Research Letters↗

USGS2007

Soil nematode communities are ecologically more mature beneath late- than early-successional stage biological soil crusts

Biological soil crusts are key mediators of carbon and nitrogen inputs for arid land soils and often represent a dominant portion of the soil surface cover in arid lands. Free-living soil nematode communities reflect their environment and have been used as biological indicators of soil condition. In this study, we test the hypothesis that nematode communities are successionally more mature beneath well-developed, late-successional stage crusts than immature, early-successional stage crusts. We identified and enumerated nematodes by genus from beneath early- and late-stage crusts from both the Colorado Plateau, Utah (cool, winter rain desert) and Chihuahuan Desert, New Mexico (hot, summer rain desert) at 0-10 and 10-30 cm depths. As hypothesized, nematode abundance, richness, diversity, and successional maturity were greater beneath well-developed crusts than immature crusts. The mechanism of this aboveground-belowground link between biological soil crusts and nematode community composition is likely the increased food, habitat, nutrient inputs, moisture retention, and/or environmental stability provided by late-successional crusts. Canonical correspondence analysis of nematode genera demonstrated that nematode community composition differed greatly between geographic locations that contrast in temperature, precipitation, and soil texture. We found unique assemblages of genera among combinations of location and crust type that reveal a gap in scientific knowledge regarding empirically derived characterization of dominant nematode genera in deserts soils and their functional role in a crust-associated food web. ?? 2006 Elsevier B.V. All rights reserved.

Applied Soil Ecology↗

USGS2013

Sediment transport in the San Francisco Bay Coastal System: An overview

The papers in this special issue feature state-of-the-art approaches to understanding the physical processes related to sediment transport and geomorphology of complex coastal-estuarine systems. Here we focus on the San Francisco Bay Coastal System, extending from the lower San Joaquin-Sacramento Delta, through the Bay, and along the adjacent outer Pacific Coast. San Francisco Bay is an urbanized estuary that is impacted by numerous anthropogenic activities common to many large estuaries, including a mining legacy, channel dredging, aggregate mining, reservoirs, freshwater diversion, watershed modifications, urban run-off, ship traffic, exotic species introductions, land reclamation, and wetland restoration. The Golden Gate strait is the sole inlet connecting the Bay to the Pacific Ocean, and serves as the conduit for a tidal flow of ~ 8 x 109 m 3 /day, in addition to the transport of mud, sand, biogenic material, nutrients, and pollutants. Despite this physical, biological and chemical connection, resource management and prior research have often treated the Delta, Bay and adjacent ocean as separate entities, compartmentalized by artificial geographic or political boundaries. The body of work herein presents a comprehensive analysis of system-wide behavior, extending a rich heritage of sediment transport research that dates back to the groundbreaking hydraulic mining-impact research of G.K. Gilbert in the early 20th century.

California↗

USGS2019

Phylogeography and evolution of infectious hematopoietic necrosis virus in China

Infectious hematopoietic necrosis virus (IHNV) is a well-known rhabdoviral pathogen of salmonid fish. In this study, a comprehensive analysis of 40 IHNV viruses isolated from thirteen fish farms in nine geographically dispersed Chinese provinces during 2012 to 2017 is presented. Identity of nucleotide and amino acid sequences among all the complete glycoprotein (G) genes from Chinese isolates was 98.0–100% and 96.7–100%, respectively. Coalescent phylogenetic analyses revealed that all the Chinese IHN virus characterized in this study were in a monophyletic clade that had a most recent common ancestor with the J Nagano (JN) subgroup within the J genogroup of IHNV. Within the Chinese IHNV clade isolates obtained over successive years from the same salmon fish farm clustered in strongly supported subclades, suggesting maintenance and diversification of virus over time within individual farms. There was also evidence for regional virus transmission within provinces, and some cases of longer distance transmission between distant provinces, such as Gansu and Yunnan. The data demonstrated that IHNV has evolved into a new subgroup in salmon farm environments in China, and IHNV isolates are undergoing molecular evolution within fish farms. We suggest that Chinese IHNV comprises a separate JC subgroup within the J genogroup of IHNV.

Molecular Phylogenetics and Evolution↗

USGS2001

Habitat evaluation using GIS a case study applied to the San Joaquin Kit Fox

Concern over the fate of plant and animal species throughout the world has accelerated over recent decades. Habitat loss is considered the main culprit in reducing many species' abundance and range, leading to numerous efforts to plan and manage habitat preservation. Our work uses Geographic Information Systems (GIS) data and modeling to define a spatially explicit analysis of habitat value, using the San Joaquin Kit Fox (Vulpes macrotis mutica) of California (USA) as an example. Over the last 30 years, many field studies and surveys have enhanced our knowledge of the life history, behavior, and needs of the kit fox, which has been proposed as an umbrella or indicator species for grassland habitat in the San Joaquin Valley of California. There has yet been no attempt to convert much of this field knowledge into a model of spatial habitat value useful for planning purposes. This is a significant omission given the importance and visibility of the imperiled kit fox and increasing trends toward spatially explicit modeling and planning. In this paper we apply data from northern California to derive a small-cell GIS raster of habitat value for the kit fox that incorporates both intrinsic habitat quality and neighborhood context, as well the effects of barriers such as roads. Such a product is a useful basis for assessing the presence and amounts of good (and poor) quality habitat and for eventually constructing GIS representations of viable animal territories that could be included in future reserves. ?? 2001 Elsevier Science B.V.

Landscape and Urban Planning↗

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 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 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 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↗

USGS2001

Critical habitat for ovigerous Dungeness crabs

The Dungeness crab, Cancer magister , supports an important fishery in the northeastern Pacific Ocean, yet there is limited knowledge of ovigerous female brooding locations and brooding behavior. Our earlier research suggests that ovigerous crabs aggregate at the same brooding locations for many years. Within these locations, ovigerous females occur in high densities, with the majority of the aggregation buried within the sediment. These locations often have similar water depths and sediment types and appear to be critical for this life history stage. Our study was designed to examine the bathymetric distribution of Dungeness crabs in bays with and without sea otters at eight locations within the Glacier Bay area by conducting transects with a video-equipped manned submersible. Two of the bays investigated contained large aggregations of ovigerous females. At both sites the substrate was composed primarily of sand. However, only a small percentage of the 33 km of transects were classified as sand. These data suggest that sand substrate may be a limiting resource. Since crab brooding aggregations represent a large portion of the crab population within a small area, and because they are a critical component of Dungeness life history, areas with these characteristics need to be investigated, mapped, and protected from development or exploitation. The areas requiring protection from the impact of anthropogenic wastes, fishing, and logging activities could be quite small, thus limiting conflict with alternative users.

Conference Paper↗