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USGS2021

Animal reservoirs and hosts for emerging alphacoronaviruses and betacoronaviruses

The ongoing global pandemic caused by coronavirus disease has once again demonstrated the role of the family Coronaviridae in causing human disease outbreaks. Because severe acute respiratory syndrome coronavirus 2 was first detected in December 2019, information on its tropism, host range, and clinical manifestations in animals is limited. Given the limited information, data from other coronaviruses might be useful for informing scientific inquiry, risk assessment, and decision-making. We reviewed endemic and emerging infections of alphacoronaviruses and betacoronaviruses in wildlife, livestock, and companion animals and provide information on the receptor use, known hosts, and clinical signs associated with each host for 15 coronaviruses detected in humans and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.

Emerging Infectious Diseases↗

USGS2023

DNA virome composition of two sympatric wild felids, bobcat (Lynx rufus) and puma (Puma concolor) in Sonora, Mexico

With viruses often having devastating effects on wildlife population fitness and wild mammals serving as pathogen reservoirs for potentially zoonotic diseases, determining the viral diversity present in wild mammals is both a conservation and One Health priority. Additionally, transmission from more abundant hosts could increase the extinction risk of threatened sympatric species. We leveraged an existing circular DNA enriched metagenomic dataset generated from bobcat ( Lynx rufus , n = 9) and puma ( Puma concolor , n = 13) scat samples non-invasively collected from Sonora, Mexico, to characterize fecal DNA viromes of each species and determine the extent that viruses are shared between them. Using the metaWRAP pipeline to co-assemble viral genomes for comparative metagenomic analysis, we observed diverse circular DNA viruses in both species, including circoviruses, genomoviruses, and anelloviruses. We found that differences in DNA virome composition were partly attributed to host species, although there was overlap between viruses in bobcats and pumas. Pumas exhibited greater levels of alpha diversity, possibly due to bioaccumulation of pathogens in apex predators. Shared viral taxa may reflect dietary overlap, shared environmental resources, or transmission through host interactions, although we cannot rule out species-specific host-virus coevolution for the taxa detected through co-assembly. However, our detection of integrated feline foamy virus (FFV) suggests Sonoran pumas may interact with domestic cats. Our results contribute to the growing baseline knowledge of wild felid viral diversity. Future research including samples from additional sources (e.g., prey items, tissues) may help to clarify host associations and determine the pathogenicity of detected viruses.

Sonora↗

USGS2023

Biting midges (Diptera: Ceratopogonidae) as putative vectors of zoonotic Onchocerca lupi (Nematoda: Onchocercidae) in northern Arizona and New Mexico, southwestern United States

Onchocerca lupi (Rodonaja, 1967) is an understudied, vector-borne, filarioid nematode that causes ocular onchocercosis in dogs, cats, coyotes, wolves, and is also capable of infecting humans. Onchocercosis in dogs has been reported with increasing incidence worldwide. However, despite the growing number of reports describing canine O. lupi cases as well as zoonotic infections globally, the disease prevalence in endemic areas and vector species of this parasite remains largely unknown. Here, our study aimed to identify the occurrence of O. lupi infected dogs in northern Arizona, New Mexico, and Utah, United States and identify the vector of this nematode. A total of 532 skin samples from randomly selected companion animals with known geographic locations within the Navajo Reservation were collected and molecularly surveyed by PCR for the presence of O. lupi DNA (September 2019–June 2022) using previously published nematode primers (COI) and DNA sequencing. O. lupi DNA was detected in 50 (9.4%) sampled animals throughout the reservation. Using positive animal samples to target geographic locations, pointed hematophagous insect trapping was performed to identify potential O. lupi vectors. Out of 1,922 insects screened, 38 individual insects and 19 insect pools tested positive for the presence of O. lupi, all of which belong to the Diptera family. This increased surveillance of definitive host and biological vector/intermediate host is the first large scale prevalence study of O. lupi in companion animals in an endemic area of the United States, and identified an overall prevalence of 9.4% in companion animals as well as multiple likely biological vector and putative vector species in the southwestern United States. Furthermore, the identification of these putative vectors in close proximity to human populations coupled with multiple, local zoonotic cases highlight the One Health importance of O. lupi .

Arizona, New Mexico↗

USGS2023

A coupled human and natural systems framework to characterize emerging infectious diseases: The case of fibropapillomatosis in marine turtles

Emerging infectious diseases of wildlife have markedly increased in the last few decades. Unsustainable, continuous, and rapid alterations within and between coupled human and natural systems have significantly disrupted wildlife disease dynamics. Direct and indirect anthropogenic effects, such as climate change, pollution, encroachment, urbanization, travel, and trade, can promote outbreaks of infectious diseases in wildlife. We constructed a coupled human and natural systems framework identifying three main wildlife disease risk factors behind these anthropogenic effects: (i) immune suppression, (ii) viral spillover, and (iii) disease propagation. Through complex and convoluted dynamics, each of the anthropogenic effect listed in our framework can lead, to some extent, to one or more of the identified risk factors accelerating disease outbreaks in wildlife. In this review, we present a novel framework to study anthropogenic impacts within coupled human and natural systems that facilitate emergence of infectious disease involving wildlife. We demonstrate the utility of the framework by applying it to Fibropapillomatosis disease of marine turtles. We aim to articulate the intricate and complex nature of anthropogenically-exacerbated wildlife infectious diseases as multifactorial. This paper supports the adoption of a One Health approach and invites the collaboration of multiple disciplines for the achievement of effective and long-lasting conservation and wildlife emerging diseases mitigation outcomes.

Animals↗

USGS2022

Plague and trace metals in natural systems

All pathogenic organisms are exposed to abiotic influences such as the microclimates and chemical constituents of their environments. Even those pathogens that exist primarily within their hosts or vectors can be influenced directly or indirectly. Yersinia pestis , the flea-borne bacterium causing plague, is influenced by climate and its survival in soil suggests a potentially strong influence of soil chemistry. We summarize a series of controlled studies conducted over four decades in Russia by Dr. Evgeny Rotshild and his colleagues that investigated correlations between trace metals in soils, plants, and insects, and the detection of plague in free-ranging small mammals. Trace metal concentrations in plots where plague was detected were up to 20-fold higher or lower compared to associated control plots, and these differences were >2-fold in 22 of 38 comparisons. The results were statistically supported in eight studies involving seven host species in three families and two orders of small mammals. Plague tended to be positively associated with manganese and cobalt, and the plague association was negative for copper, zinc, and molybdenum. In additional studies, these investigators detected similar connections between pasturellosis and concentrations of some chemical elements. A One Health narrative should recognize that the chemistry of soil and water may facilitate or impede epidemics in humans and epizootics in non-human animals.

International Journal of Environmental Research an↗

USGS2001

Shallow ground-water quality beneath rice areas in the Sacramento Valley, California, 1997

In 1997, the U.S. Geological Survey installed and sampled 28 wells in rice areas in the Sacramento Valley as part of the National Water-Quality Assessment Program. The purpose of the study was to assess the shallow ground-water quality and to determine whether any effects on water quality could be related to human activities and particularly rice agriculture. The wells installed and sampled were between 8.8 and 15.2 meters deep, and water levels were between 0.4 and 8.0 meters below land surface. Ground-water samples were analyzed for 6 field measurements, 29 inorganic constituents, 6 nutrient constituents, dissolved organic carbon, 86 pesticides, tritium (hydrogen- 3), deuterium (hydrogen-2), and oxygen-18. At least one health-related state or federal drinking-water standard (maximum contaminant or long-term health advisory level) was exceeded in 25 percent of the wells for barium, boron, cadmium, molybdenum, or sulfate. At least one state or federal secondary maximum contaminant level was exceeded in 79 percent of the wells for chloride, iron, manganese, specific conductance, or dissolved solids. Nitrate and nitrite were detected at concentrations below state and federal 2000 drinking-water standards; three wells had nitrate concentrations greater than 3 milligrams per liter, a level that may indicate impact from human activities. Ground-water redox conditions were anoxic in 26 out of 28 wells sampled (93 percent). Eleven pesticides and one pesticide degradation product were detected in ground-water samples. Four of the detected pesticides are or have been used on rice crops in the Sacramento Valley (bentazon, carbofuran, molinate, and thiobencarb). Pesticides were detected in 89 percent of the wells sampled, and rice pesticides were detected in 82 percent of the wells sampled. The most frequently detected pesticide was the rice herbicide bentazon, detected in 20 out of 28 wells (71 percent); the other pesticides detected have been used for rice, agricultural, and non-agricultural purposes. All pesticide concentrations were below state and federal 2000 drinking-water standards. The relation of the ground-water quality to natural processes and human activities was tested using statistical methods (Spearman rank correlation, Kruskal?Wallis, or rank-sum tests) to determine whether an influence from rice land-use or other human activities on ground-water chemistry could be identified. The detection of pesticides in 89 percent of the wells sampled indicates that human activities have affected shallow ground-water quality. Concentrations of dissolved solids and inorganic constituents that exceeded state or federal 2000 drinking-water standards showed a statistical relation to geomorphic unit. This is interpreted as a relation to natural processes and variations in geology in the Sacramento River Basin; the high concentrations of dissolved solids and most inorganic constituents did not appear to be related to rice land use. No correlation was found between nitrate concentration and pesticide occurrence, indicating that an absence of high nitrate concentrations is not a predictor of an absence of pesticide contamination in areas with reducing ground-water conditions in the Sacramento Valley. Tritium concentrations, pesticide detections, stable isotope data, and dissolved-solids concentrations suggest that shallow ground water in the ricegrowing areas of the Sacramento Valley is a mix of recently recharged ground water containing pesticides, nitrate, and tritium, and unknown sources of water that contains high concentrations of dissolved solids and some inorganic constituents and is enriched in oxygen-18. Evaporation of applied irrigation water, which leaves behind salt, accounts for some of the elevated concentrations of dissolved solids. More work needs to be done to understand the connections between the land surface, shallow ground water, deep ground water, and the drinking-water supplies in the Sacramento Valley.

Water-Resources Investigations Report↗

USGS2017

Conservation, biodiversity and infectious disease: scientific evidence and policy implications

Habitat destruction and infectious disease are dual threats to nature and people. The potential to simultaneously advance conservation and human health has attracted considerable scientific and popular interest; in particular, many authors have justified conservation action by pointing out potential public health benefits . One major focus of this debate—that biodiversity conservation often decreases infectious disease transmission via the dilution effect—remains contentious. Studies that test for a dilution effect often find a negative association between a diversity metric and a disease risk metric, but how such associations should inform conservation policy remains unclear for several reasons. For one, diversity and infection risk have many definitions, making it possible to identify measures that conform to expectations. Furthermore, the premise that habitat destruction consistently reduces biodiversity is in question, and disturbance or conservation can affect disease in many ways other than through biodiversity change. To date, few studies have examined the broader set of mechanisms by which anthropogenic disturbance or conservation might increase or decrease infectious disease risk to human populations. Due to interconnections between biodiversity change, economics and human behaviour, moving from ecological theory to policy action requires understanding how social and economic factors affect conservation. This Theme Issue arose from a meeting aimed at synthesizing current theory and data on ‘biodiversity, conservation and infectious disease’ (4–6 May 2015). Ecologists, evolutionary biologists, economists, epidemiologists, veterinary scientists, public health professionals, and conservation biologists from around the world discussed the latest research on the ecological and socio-economic links between conservation, biodiversity and infectious disease, and the open questions and controversies in these areas. By combining ecological understanding with insights from the social and economic sciences, the papers in this Theme Issue address the complex relationships, patterns and ecological mechanisms that influence conservation, infectious disease, and the policy options available to protect nature and human health.

Philosophical Transactions of the Royal Society B:↗

USGS2025

Avian influenza spillover into poultry: Environmental influences and biosecurity protections

With the continued spread of highly pathogenic avian influenza (HPAI), understanding the complex dynamics of virus transfer at the wild – agriculture interface is paramount. Spillover events (i.e., virus transfer from wild birds into poultry) are related to proximity to infected wild bird populations and environmental conditions. By accounting for such dynamics, we can take a combined approach to assess the impacts of biosecurity measures implemented at poultry farms while simultaneously accounting for their local risk levels. We implemented a Bayesian joint-likelihood logistic regression for the Continental U.S. comparing models of spatiotemporal risk according to land use, weather, and predicted waterfowl distributions followed by integrating a farm-level case-control questionnaire dataset focused on identifying trends in HPAI spillover risk associated with a farm's biosecurity practices. We found that estimates of waterfowl abundance, along with mean precipitation and temperature during winter, were most correlated with spatiotemporal HPAI risk. Additionally, we identified multiple biosecurity practices associated with reduced risk to HPAI, where the strongest relationships were related to litter decontamination treatments, vehicle wash stations, and avoiding shared dead-bird disposal sites with other farms. This model broadly guides surveillance of HPAI in wild and domestic populations, identifying when and where we are most likely to see increased instances of the virus while also providing insights into how poultry farms can better protect themselves from risk.

contiguous United States↗

USGS2010

Intrusions and infectious disease emergence

No abstract available.

New York↗

USGS2017

Groundwater-quality data in 12 GAMA study units: Results from the 2006–10 initial sampling period and the 2008–13 trend sampling period, California GAMA Priority Basin Project

The Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) program was developed in response to the Groundwater Quality Monitoring Act of 2001 and is being conducted by the U.S. Geological Survey in cooperation with the California State Water Resources Control Board. From 2004 through 2012, the GAMA-PBP collected samples and assessed the quality of groundwater resources that supply public drinking water in 35 study units across the State. Selected sites in each study unit were sampled again approximately 3 years after initial sampling as part of an assessment of temporal trends in water quality by the GAMA-PBP. Twelve of the study units, initially sampled during 2006–11 (initial sampling period) and sampled a second time during 2008–13 (trend sampling period) to assess temporal trends, are the subject of this report. The initial sampling was designed to provide a spatially unbiased assessment of the quality of untreated groundwater used for public water supplies in the 12 study units. In these study units, 550 sampling sites were selected by using a spatially distributed, randomized, grid-based method to provide spatially unbiased representation of the areas assessed (grid sites, also called “status sites”). After the initial sampling period, 76 of the previously sampled status sites (approximately 10 percent in each study unit) were randomly selected for trend sampling (“trend sites”). The 12 study units sampled both during the initial sampling and during the trend sampling period were distributed among 6 hydrogeologic provinces: Coastal (Northern and Southern), Transverse Ranges and Selected Peninsular Ranges, Klamath, Modoc Plateau and Cascades, and Sierra Nevada Hydrogeologic Provinces. For the purposes of this trend report, the six hydrogeologic provinces were grouped into two hydrogeologic regions based on location: Coastal and Mountain. The groundwater samples were analyzed for a number of synthetic organic constituents (volatile organic compounds, pesticides, and pesticide degradates), constituents of special interest (perchlorate and 1,2,3-trichloropropane), and natural inorganic constituents (nutrients, major and minor ions, and trace elements). Isotopic tracers (tritium, carbon-14, and stable isotopes of hydrogen and oxygen in water) also were measured to help identify processes affecting groundwater quality and the sources and ages of the sampled groundwater. More than 200 constituents and water-quality indicators were measured during the trend sampling period. Quality-control samples (blanks, replicates, matrix-spikes, and surrogate compounds) were collected at about one-third of the trend sites, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. On the basis of detections in laboratory and field blank samples collected by GAMA-PBP study units, including the 12 study units presented here, reporting levels for some groundwater results were adjusted in this report. Differences between replicate samples were mostly within acceptable ranges, indicating low variability in analytical results. Matrix-spike recoveries were largely within the acceptable range (70 to 130 percent). This study did not attempt to evaluate the quality of water delivered to consumers. After withdrawal, groundwater used for drinking water typically is treated, disinfected, and blended with other waters to achieve acceptable water quality. The comparison benchmarks used in this report apply to treated water that is served to the consumer, not to untreated groundwater. To provide some context for the results, however, concentrations of constituents measured in these groundwater samples were compared with benchmarks established by the U.S. Environmental Protection Agency and the State of California. Comparisons between data collected for this study and benchmarks for drinking water are for illustrative purposes only and are not indicative of compliance or non-compliance with those benchmarks. Most organic constituents that were detected in groundwater samples from the trend sites were found at concentrations less than health-based benchmarks. One volatile organic compound—perchloroethene—was detected at a concentration greater than the health-based benchmark in samples from one trend site during the initial and trend sampling periods. Chloroform was detected in at least 10 percent of the samples at trend sites in both sampling periods. Methyl tert -butyl ether was detected in samples from more than 10 percent of the trend sites during the initial sampling period. No pesticide or pesticide degradate was detected in greater than 10 percent of the samples from trend sites or at concentrations greater than their health-based benchmarks during either sampling period. Nutrients were not detected at concentrations greater than their health-based benchmarks during either sampling period. Most detections of major ions and trace elements in samples from trend sites were less than health-based benchmarks during both sampling periods. Arsenic and boron each were detected at concentrations greater than the health-based benchmark in samples from four trend sites during the initial and trend sampling periods. Molybdenum was detected in samples from four trend sites at concentrations greater than the health-based benchmark during both sampling periods. Samples from two of these trend sites had similar molybdenum concentrations, and two had substantially different concentrations during the initial and trend sampling periods. Uranium was detected at a concentration greater than the health-based benchmark only at two trend sites.

California↗

USGS2022

Mortality associated with extreme heat in Washington State: The historical and projected public health burden

Extreme heat is one of the most important pathways illustrating the connection between climate and human health, and climate change is expected to exacerbate this public health issue. This study first used a case-crossover analysis to characterize the historical (1980–2018) association between summertime heat and non-traumatic mortality in Washington State. A separate analysis was conducted for each of the state’s ten climate divisions to produce distinct exposure–response curves expressing odds of mortality as a function of humidex. Stratified analyses were used to assess the impact of age, sex, race/ethnicity, and select causes of death, and the reported results are pooled across all divisions using meta-analysis. The historical heat–mortality relationship was combined with climate projections to estimate the impact of climate change on heat-related deaths in 2030, 2050, and 2080 under two warming scenarios. The odds ratio (OR) and 95% confidence intervals of mortality at the 99th percentile of humidex compared to the 50th percentile did not include the null value in four climate divisions (E Olympic Cascade Foothills, NE Olympic San Juan, Northeastern, and Puget Sound Lowlands). The statewide odds of mortality are 8% higher (6%, 10%) on 99th percentile days compared to 50th percentile days, driven primarily by an OR of 1.09 (1.06, 1.11) in the Puget Sound Lowlands. Risk is higher for women than men and for Blacks than Whites. Risk increases with age and for diabetic, circulatory, cardiovascular, ischemic, cerebrovascular, and respiratory deaths. The 95% confidence intervals of projected heat-attributable mortality did not overlap with zero in three climate divisions (E Olympic Cascade Foothills, NE Olympic San Juan, and Puget Sound Lowlands). In these three divisions, the average percent increase in heat-attributable mortality across both warming scenarios is 35%, 35%, and 603% in 2030, 2050, and 2080, respectively. This research is the most extensive study of heat-related mortality in Washington to date and can help inform public health initiatives aiming to improve present and future health outcomes in the state.

Washington↗

USGS2014

Groundwater-quality data in the North San Francisco Bay Shallow Aquifer study unit, 2012: results from the California GAMA Program

Groundwater quality in the 1,850-square-mile North San Francisco Bay Shallow Aquifer (NSF-SA) study unit was investigated by the U.S. Geological Survey (USGS) from April to August 2012, as part of the California State Water Resources Control Board (SWRCB) Groundwater Ambient Monitoring and Assessment (GAMA) Program’s Priority Basin Project (PBP). The GAMA-PBP was developed in response to the California Groundwater Quality Monitoring Act of 2001 and is being conducted in collaboration with the SWRCB and Lawrence Livermore National Laboratory (LLNL). The NSF-SA study unit was the first study unit to be sampled as part of the second phase of the GAMA-PBP, which focuses on the shallow aquifer system. The GAMA NSF-SA study was designed to provide a spatially unbiased assessment of untreated-groundwater quality in the shallow aquifer systems and to facilitate statistically consistent comparisons of untreated-groundwater quality throughout California. The shallow aquifer system in the NSF-SA study unit was defined as the part of the aquifer system that is used by many private domestic wells and is shallower than the primary aquifer system used by many public-supply wells. In the NSF-SA study unit located in Marin, Mendocino, Napa, Solano, and Sonoma Counties, groundwater samples were collected from 71 wells. Seventy of the wells were selected by using a spatially distributed, randomized grid-based method to provide statistical representation of the study unit (grid wells), and one well was selected to aid in evaluation of water-quality issues (understanding well). The groundwater samples were analyzed for organic constituents (volatile organic compounds [VOCs], pesticides, and pesticide degradates); constituents of special interest (perchlorate and 1,2,3-trichloropropane [1,2,3-TCP]); naturally occurring inorganic constituents (trace elements, nutrients, major and minor ions, silica, and total dissolved solids [TDS]); and radioactive constituents (radon-222 and gross alpha and gross beta radioactivity). Naturally occurring isotopes (stable isotopes of hydrogen, oxygen, boron, strontium, and inorganic carbon in water, tritium activities, and carbon-14 abundances) were measured to help identify the sources and ages of the sampled groundwater. In total, 207 constituents and water-quality indicators were measured. Three types of quality-control samples (blanks, replicates, and matrix spikes) were collected at up to 13 percent of the wells in the NSF-SA study unit, and the results for these samples were used to evaluate the quality of the data for the groundwater samples. Blanks rarely contained detectable concentrations of any constituent, suggesting that contamination from sample-collection procedures was not a significant source of bias in the data for the groundwater samples. Replicate samples generally were within the limits of acceptable analytical reproducibility. Matrix-spike recoveries were within the acceptable range (70 to 130 percent) for approximately 91 percent of the compounds. Most of the wells sampled for this study were private domestic wells. Private domestic wells are not regulated in California, and groundwater from these wells is rarely analyzed for water-quality constituents. Although regulatory benchmarks for drinking-water quality do not apply to private domestic wells, to provide some context for the results, concentrations of constituents measured in the untreated groundwater were compared with regulatory and non-regulatory health-based benchmarks established by the U.S. Environmental Protection Agency (USEPA) and California Department of Public Health (CDPH), to non-regulatory health-based benchmarks established by the USGS in cooperation with the USEPA, and to non-regulatory benchmarks established for aesthetic concerns by the CDPH. Comparisons between data collected for this study and benchmarks for drinking water are for illustrative purposes only and are not indicative of compliance or non-compliance with those benchmarks. Most of the organic and inorganic constituents that were detected in groundwater samples from the 70 grid wells in the NSF-SA study unit were detected at concentrations less than drinking-water benchmarks. Of the 149 organic and special-interest constituents analyzed for in groundwater samples, 31 were detected; concentrations of most detected constituents were less than regulatory and non-regulatory health-based benchmarks. One VOC, benzene, and one insecticide, dieldrin, were detected at concentrations above their respective health-based benchmarks. In total, VOCs were detected in 40 percent of the grid wells sampled, pesticides and pesticide degradates were detected in 13 percent, and perchlorate was detected in 27 percent of the 70 grid wells sampled. Groundwater samples from 70 grid wells were analyzed for trace elements, major and minor ions, nutrients, and radioactive constituents; most detected concentrations were less than health-based benchmarks. Exceptions are 12 detections of manganese greater than the USGS Health-Based Screening Level (HBSL), 7 detections of arsenic greater than the USEPA maximum contaminant level (MCL-US) of 10 micrograms per liter (μg/L), 2 detections of boron greater than the HBSL of 6,000 μg/L, 2 detections of fluoride greater than the CDPH maximum contaminant level (MCL-CA) of 2 milligrams per liter (mg/L), 2 detections of nitrate greater than the MCL-US of 10 mg/L, and two detections of radon-222 greater than the proposed MCL-US of 4,000 picocuries per liter. Results for constituents with non-regulatory benchmarks set for aesthetic concerns from the grid wells showed that iron concentrations greater than the CDPH secondary maximum contaminant level (SMCL-CA) of 300 μg/L were detected in 13 grid wells. Chloride was detected at a concentration greater than the SMCL-CA recommended benchmark of 250 mg/L in two grid wells. Sulfate concentrations greater than the SMCL-CA recommended benchmark of 250 mg/L were measured in two grid wells, and the concentration in one of these wells was also greater than the SMCL-CA upper benchmark of 500 mg/L. TDS concentrations greater than the SMCL-CA recommended benchmark of 500 mg/L were measured in 15 grid wells, and concentrations in 4 of these wells were also greater than the SMCL-CA upper benchmark of 1,000 mg/L.

California↗

USGS2021

Spatial and temporal variability of nutrients and algae in the Republican River and Milford Lake, Kansas, June through November 2017 and May through November 2018

Milford Lake has been listed as impaired and designated hypereutrophic because of excessive nutrient loading, specifically biologically available orthophosphate. It is the largest lake by surface area in Kansas and is a reservoir built for purposes including water supply and recreation. In 2015, the Kansas Department of Health and Environment (KDHE) divided the lake into three zones (Zones A, B, and C) for recreational monitoring of harmful algal blooms (HABs). Upstream Zone C has historically been more affected by HABs than Zones B and A, and Zone C has historically had the highest phosphorus concentrations. The U.S. Geological Survey, in cooperation with the KDHE, completed a study in 2017–18 to assess the spatial and temporal variability of nutrients and algae in the Republican River (the primary inflow to Milford Lake) and Milford Lake using spatially and temporally dense data. During the study period, discrete water-quality samples were collected at 36 lake sites, 21 river sites, and 1 pond. All samples were analyzed for nutrients; some samples were also analyzed for chlorophyll, phycocyanin, microcystin, and (or) phytoplankton community composition and abundance. Results from this study provide perspective for understanding the potential role nutrient and algal conditions have in facilitating the formation of HABs and may inform future actions to prevent and mitigate HABs and their potential effects on human and environmental health. In 2017, one low-flow floating synoptic on the Republican River into Zone C of Milford Lake and one 24-hour synoptic in Zone C of Milford Lake were completed. Results from the low-flow floating synoptic on July 17, 2017, at 21 river sites, 8 lake sites, and 1 pond site indicated that the Republican River was not contributing dissolved orthophosphate or total phosphorus concentrations higher than those in the main body of Milford Lake. No patterns in nutrient or total microcystin concentrations were evident from the 24-hour synoptic at two sites on August 24–25, 2017. Total nitrogen was dominated by total Kjeldahl nitrogen (TKN) at both sites. Different oscillation activity in algal biomass and chlorophyll at the two sites demonstrated the variable nature of algal accumulations and their effects on nutrient and dissolved oxygen concentrations. Different patterns in chlorophyll and microcystin concentrations indicate that the relation between algal biomass and cyanotoxin concentrations were different at the two sites, possibly because of differences among algal communities present at each site. Three whole-lake synoptics through Zones A, B, and C in Milford Lake were completed on July 10, August 9, and October 16–17, 2018, at 30 lake sites. Orthophosphate was consistently at least 77 percent of total phosphorus at all sites except the two most uplake sites. At the two most uplake sites, orthophosphate was between 52 and 72 percent of the total phosphorus present at the site. Concentrations of TKN were not consistently increasing or decreasing during 2018. Total nitrogen was dominated by TKN in July and August. Very low concentrations of dissolved nitrate plus nitrite indicate that the nutrient was likely tied up in algal biomass. By October, total nitrogen was approximately one-half TKN and one-half dissolved nitrate plus nitrite. Higher concentrations of dissolved orthophosphate and dissolved nitrate plus nitrite in October than in July and August were likely caused by reduced biological activity (less uptake of nutrients) and lower air and water temperatures. Multiple inflow events (streamflow greater than median daily value) between August and October also may have moved nutrients through the lake. Chlorophyll, phycocyanin, microcystin, and phytoplankton samples were collected at eight sites in 2018. Most sites had their highest chlorophyll concentrations in August. The three most uplake sites had their highest phycocyanin concentrations in July, whereas the other five sites had their highest phycocyanin concentrations in August. Two of 23 samples had detections of total microcystin (0.11 and 0.12 microgram per liter). Phytoplankton community composition mainly consisted of Bacillariophyta, Chlorophyta, Cryptophyta, and Cyanobacteria. Phytoplankton community composition and abundance data described broad seasonal patterns and did not capture the full range of possible conditions at each site.

Kansas↗

USGS2023

Simulation of groundwater flow at the former Badger Army Ammunition Plant, Sauk County, Wisconsin

To help support remedial efforts at the former Badger Army Ammunition Plant the U.S. Geological Survey built and calibrated a transient groundwater flow model using the Newton Raphson formulation (MODFLOW–NWT) of the U.S. Geological Survey’s modular three-dimensional finite-difference code. The model simulates the groundwater flow system at the site from 1984 to 2020. The former Badger Army Ammunition Plant is a 7,275-acre site in Sauk County, Wisconsin. The plant produced smokeless gunpower and solid rocket propellent as munitions components. Peak production periods were during World War II, the Korean War, and the Vietnam War. Subsequent groundwater contamination investigations have found four plumes at the site. A health risk assessment identified at least one contaminant of concern for human health risk present in three of the plumes: the propellant burning ground plume, the deterrent burning ground plume, and the central plume. A cooperative study began between the U.S. Army Environmental Command and U.S. Geological Survey to better understand the groundwater flow system at the former Badger Army Ammunition Plant. Field data, including aquifer tests, streamflow measurements, continuous groundwater elevations, and groundwater gradients with the Wisconsin River were collected and used to inform and calibrate the groundwater flow model. The model was used to assess the variability of the groundwater system over the study period, the components of the groundwater budget, and groundwater flow directions from identified source areas towards the Wisconsin River. Model performance assessment focused on using particle tracking to compare groundwater flowpaths that originate in the contaminant source areas to the observed plume footprints. This focus on plume behavior geometry should help constrain the advective component of a future groundwater transport model of the site.

Wisconsin↗

USGS2008

Ground-water quality data in the Kern County Subbasin study unit, 2006— Results from the California GAMA Program

Ground-water quality in the approximately 3,000 square-mile Kern County Subbasin study unit (KERN) was investigated from January to March, 2006, as part of the Priority Basin Assessment Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Assessment project was developed in response to the Groundwater Quality Monitoring Act of 2001, and is being conducted by the California State Water Resources Control Board (SWRCB) in collaboration with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory (LLNL). The Kern County Subbasin study was designed to provide a spatially unbiased assessment of raw (untreated) ground-water quality within KERN, as well as a statistically consistent basis for comparing water quality throughout California. Samples were collected from 50 wells within the San Joaquin Valley portion of Kern County. Forty-seven of the wells were selected using a randomized grid-based method to provide a statistical representation of the ground-water resources within the study unit. Three additional wells were sampled to aid in the evaluation of changes in water chemistry along regional ground-water flow paths. The ground-water samples were analyzed for a large number of man-made organic constituents (volatile organic compounds [VOCs], pesticides, and pesticide degradates), constituents of special interest (perchlorate, N-nitrosodimethylamine [NDMA], and 1,2,3-trichloropropane [1,2,3-TCP]), naturally occurring inorganic constituents (nutrients, major and minor ions, and trace elements), radioactive constituents, and microbial indicators. Naturally occurring isotopes (tritium, carbon-14, and stable isotopes of hydrogen, oxygen, nitrogen, and carbon) and dissolved noble gases also were measured to help identify the source and age of the sampled ground water. Quality-control samples (blanks, replicates, and laboratory matrix spikes) were collected and analyzed at approximately 10 percent of the wells, and the results for these samples were used to evaluate the quality of the data from the ground-water samples. Assessment of the quality-control information resulted in censoring of less than 0.4 percent of the data collected for ground-water samples. This study did not attempt to evaluate the quality of water delivered to consumers; after withdrawal from the ground, raw ground water typically is treated, disinfected, or blended with other waters to maintain acceptable water quality. Regulatory thresholds apply, not to the raw ground water, but to treated water that is served to the consumer. However, to provide some context for the results, concentrations of constituents measured in the raw ground water were compared with health-based thresholds established by the U.S. Environmental Protection Agency (USEPA) and the California Department of Public Health (CDPH), and as well as with thresholds established for aesthetic concerns (secondary maximum contaminant levels, SMCL-CA) by CDPH. VOCs and pesticides each were detected in approximately 60 percent of the grid wells, and detections of all compounds but one were below health-based thresholds. The fumigant, 1,2-dibromo-3-chloropropane (DBCP), was detected above the USEPA maximum contaminant level (MCL-US) in one sample. Detections of most inorganic constituents were also below health-based thresholds. Constituents detected above health-based thresholds include: nitrate, (MCL-US, 2 samples), arsenic (MCL-US, 2 samples), and vanadium (California notification level, NL-CA, 1 sample). All detections of radioactive constituents were below health-based thresholds, although nine samples had activities of radon-222 above the lower proposed MCL-US. Most of the samples from KERN wells had concentrations of major elements, total dissolved solids, and trace elements below the non-enforceable thresholds set for aesthetic concerns.

California↗

USGS2011

Organic contaminants, trace and major elements, and nutrients in water and sediment sampled in response to the Deepwater Horizon oil spill

Beach water and sediment samples were collected along the Gulf of Mexico coast to assess differences in contaminant concentrations before and after landfall of Macondo-1 well oil released into the Gulf of Mexico from the sinking of the British Petroleum Corporation's Deepwater Horizon drilling platform. Samples were collected at 70 coastal sites on the Gulf of Mexico between May 7 and July 7, 2010, to document baseline, "pre-landfall" conditions. A subset of these sites was resampled during October 4 to 14, 2010, after oil had made landfall on the Gulf of Mexico coast ("post-landfall") to determine if actionable concentrations of oil were present along shorelines. Few organic contaminants were detected in water; their detection frequencies were generally low and similar in pre-landfall and post-landfall samples. Only one organic contaminant, toluene, had significantly higher concentrations in post-landfall than pre-landfall water samples. No samples exceeded any human-health benchmarks, and only one sample exceeded an aquatic-life benchmark-the toxic-unit benchmark for polycyclic aromatic hydrocarbons (PAH) mixtures was exceeded in one post-landfall water sample from Louisiana. No exceedance was observed in the corresponding pre-landfall water sample at this site. In sediment, several PAHs were detected at over 20 percent of sites. Concentrations of 3 parent PAHs and 17 alkylated PAH groups were significantly higher in post-landfall samples than pre-landfall samples. One pre-landfall sample from Texas exceeded the sediment toxic-unit benchmark for PAH mixtures; this site was not sampled during the post-landfall period, so no comparison between sampling periods could be made. Twenty-seven percent of sediment samples exceeded empirical sediment-quality benchmarks (upper screening values) for PAHs, indicating these samples are in the probable-effect range. A higher percentage of post-landfall samples exceeded upper screening-value benchmarks (37 percent) than did pre-landfall samples (22 percent), but there was no significant difference in the proportion of samples exceeding one or more benchmarks between paired pre-landfall and post-landfall samples. Seven sites had the largest concentration differences between post-landfall and pre-landfall samples for fifteen alkylated PAHs. Five of these seven sites (1 site in Louisiana, 1 in Mississippi, and 3 in Alabama) were identified on the basis of diagnostic geochemical biomarkers as containing Macondo-1 oil in post-landfall sediments and tarballs, as described in a companion report by Rosenbauer and others (2010). For trace and major elements in water, analytical reporting levels for several elements were highly variable; after censoring to a common reporting threshold, concentrations were significantly different between pre-landfall and post-landfall samples for a few elements, all of which are elements in seawater. No human-health benchmarks were exceeded, although these were available for only two elements. Aquatic-life benchmarks for trace elements were exceeded in almost 50 percent of water samples. Post-landfall samples exceeded one or more acute benchmarks in 21 percent, and chronic benchmarks in 93 percent of samples, compared to 1 percent (acute) and 39 percent (chronic) for pre-landfall samples. The elements responsible for the most exceedances in post-landfall samples were boron (48 samples), copper (22), and manganese (12). Nickel and vanadium, which U.S. Environmental Protection Agency specifically identified as relevant to the oil spill, were responsible for exceedances in only one of the fifty-two post-landfall samples with exceedances. These results represent the minimum number of exceedances for several trace elements because a substantial number of samples could not be compared with benchmarks because the element was determined during only one sampling period (boron and vanadium) or the reporting level for the sample was higher than the applicable benchmark value (for example, cobalt, copper, lead, and nickel). The high and variable reporting levels for trace elements in water also precluded the statistical comparison between sampling periods of the proportion of samples exceeding benchmarks. For trace elements in whole (unsieved) sediment, 47 percent of samples exceeded empirical upper screening-value benchmarks, indicating these samples are in the probable-effect range. However, there was no significant difference in the proportion of samples exceeding one or more benchmarks between paired pre-landfall post-landfall samples. Benchmark exceedance frequencies could be conservatively high, because they are based on measurements of total trace-element concentrations, including the sediment matrix. In fine sediment (the less than 63-micrometer sediment fraction), one or more trace or major elements were anthropogenically enriched relative to national baseline values for U.S. streams for almost all sediment samples (123 of 124). Sixteen percent of sediment samples exceeded upper screening-value benchmarks for, and were enriched in, one or more of the element(s) barium (in 14 samples), vanadium (5), aluminum (3), manganese (3), arsenic (2), chromium (2), and cobalt (1). These samples, collected from Louisiana and Texas, were evenly divided between the pre-landfall (9 samples) and post-landfall (10 samples) periods. Considering all the information evaluated in this report, there were significant differences between pre-landfall and post-landfall samples for PAH concentrations in sediment. Pre-landfall and post-landfall samples did not differ significantly in concentrations or benchmark exceedances for most organics in water or trace elements in sediment. For trace elements in water, aquatic-life benchmarks were exceeded in almost 50 percent of samples, but the high and variable analytical reporting levels precluded statistical comparison of benchmark exceedances between sampling periods. Concentrations of several PAH compounds in sediment were significantly higher in post-landfall samples than pre-landfall samples, and five of seven sites with the largest differences in PAH concentrations also had diagnostic geochemical evidence of Deepwater Horizon Macondo-1 oil from Rosenbauer and others (2010).

Open-File Report↗

USGS2012

Organic contaminants, trace and major elements, and nutrients in water and sediment sampled in response to the Deepwater Horizon oil spill

Alabama, Arkansas, Florida, Georgia, Louisiana, Te↗

USGS2015

Status and understanding of groundwater quality in the Northern Coast Ranges study unit, 2009: California GAMA Priority Basin Project

Groundwater quality in the 633-square-mile (1,639-square-kilometer) Northern Coast Ranges (NOCO) study unit was investigated as part of the Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) Program and the U.S. Geological Survey (USGS) National Water-Quality Assessment Program. The study unit is composed of two study areas (Interior Basins and Coastal Basins) and is located in northern California in Napa, Sonoma, Lake, Colusa, Mendocino, Glenn, Humboldt, and Del Norte Counties. The GAMA-PBP is being conducted by the California State Water Resources Control Board in collaboration with the USGS and the Lawrence Livermore National Laboratory. The GAMA NOCO study was designed to provide a spatially unbiased assessment of the quality of untreated (ambient) groundwater in the primary aquifer system within the study unit. The assessment is based on water-quality and ancillary data collected in 2009 by the USGS from 58 sites and on water-quality data from the California Department of Public Health (CDPH) database. The primary aquifer system is defined by the perforation intervals of sites listed in the CDPH water-quality database for the NOCO study unit. Groundwater quality in the primary aquifer system may differ from the quality in the shallow or deep water-bearing zones. The first component of this study, the status assessment of the current quality of the groundwater resource, was performed by using data from samples analyzed for inorganic constituents (such as trace elements and major and minor ions), organic constituents (volatile organic compounds and pesticides and pesticide degradates), the special-interest constituent perchlorate, and microbial indicators. This status assessment is intended to characterize the quality of groundwater resources in the primary aquifer system of the NOCO study unit, not the quality of treated drinking water delivered to consumers by water purveyors. Relative-concentrations (sample concentration divided by the health- or aesthetic-based benchmark concentration) were used for evaluating groundwater quality for those constituents that have Federal or California regulatory or nonregulatory benchmarks for drinking-water quality. A relative-concentration greater than (>) 1.0 indicates a concentration greater than a benchmark, and a relative-concentration less than or equal to (≤) 1.0 indicates a concentration less than or equal to a benchmark. Relative-concentrations of organic constituents and perchlorate were classified as “high” (relative-concentration >1.0), “moderate” (0.1 < relative-concentration ≤1.0), or “low” (relative-concentration ≤0.1). Relative-concentrations of inorganic constituents were classified as “high” (relative-concentration >1.0), “moderate” (0.5 < relative-concentration ≤1.0), or “low” (relative-concentration ≤0.5). Aquifer-scale proportion was used as the primary metric in the status assessment for evaluating regional-scale groundwater quality. High aquifer-scale proportion was defined as the percentage of the area of the primary aquifer system with a relative-concentration >1.0 for a particular constituent or class of constituents; the percentage is based on an aerial rather than a volumetric basis. Moderate and low aquifer-scale proportions were defined as the percentage of the primary aquifer system with moderate and low relative-concentrations, respectively. Two statistical approaches—grid-based and spatially weighted—were used to evaluate aquifer-scale proportions for individual constituents and classes of constituents. Grid-based and spatially weighted estimates were comparable in the NOCO study unit (within 90 percent confidence intervals). Inorganic constituents (one or more) with health-based benchmarks were detected at high relative-concentrations in 10.3 percent and at moderate relative-concentrations in 13.8 percent of the primary aquifer system. The high aquifer-scale proportion of inorganic constituents primarily reflected high aquifer-scale proportions of boron (in 8.6 percent of the primary aquifer system), arsenic (in 3.4 percent), and barium (in 1.7 percent). Inorganic constituents with aesthetic-based benchmarks were detected at high relative-concentrations in 39.7 percent and at moderate relative-concentrations in 10.3 percent of the primary aquifer system. The constituents present at high relative-concentrations were iron (25.9 percent) and manganese (39.7 percent). Relative-concentrations of organic constituents with health-based benchmarks (one or more) were high in 0.2 percent, moderate in 1.7 percent, and low in 39.7 percent of the primary aquifer system. Organic constituents were not detected in 58.4 percent of the primary aquifer system. Of the 168 organic constituents analyzed, 11 constituents were detected. Two organic constituents had detection frequencies >10 percent: the trihalomethane chloroform and the herbicide simazine. For the 10 detected organic constituents that had health-based benchmarks, nearly all detections had low relative-concentrations. The special-interest constituent perchlorate was detected at moderate relative-concentrations in 1.7 percent and at low relative-concentrations in 22.4 percent of the primary aquifer system. Perchlorate was not detected in 75.9 percent of the primary aquifer system. The second component of this study, the understanding assessment , evaluated relations between constituent concentrations and values of selected potential explanatory factors to identify the factors potentially affecting the concentrations and occurrences of constituents found at high relative-concentrations or, for organic constituents, with detection frequencies >10 percent. The potential explanatory factors evaluated were land use (including density of septic tanks and leaking or formerly leaking underground fuel tanks), well construction (well depth and depth to the top of the perforated interval in the well), hydrologic conditions (aridity index, field water temperature, and distance to nearest hot spring and geothermal well), pH, dissolved oxygen concentration, study area, groundwater age distribution, and geochemical conditions. High and moderate relative-concentrations of boron primarily occurred in the Interior Basins study area and may be attributed to groundwater interacting with hydrothermal systems. High and moderate relative-concentrations of boron were associated with elevated groundwater temperatures, groundwater chemistry characteristics similar to those of geothermal waters, and distance to known geothermal areas. Boron concentrations generally were higher where low dissolved oxygen concentrations or anoxic conditions exist. High and moderate relative-concentrations of arsenic predominantly occur in the Interior Basins study area under reducing conditions. Arsenic concentrations also may be influenced by hydrothermal systems (when present). Chloroform, simazine, and perchlorate were observed in the Interior Basins and Coastal Basins study areas, predominantly at shallow sites with top-of-perforation depths ≤70 feet below land surface, with modern water (post-1950s), and with oxic groundwater conditions.

California↗