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USGS2019

Light exposure along particle flowpaths in large rivers

Sunlight is a critical resource in aquatic systems driving photosynthesis, photodegradation of organic matter and contaminants, animal behavior, and the activity of human pathogens. In rivers, solutes, materials, and organisms are turbulently mixed across the water column during downstream transport and exposed to highly variable sunlight. However, there are no measurements of suspended particles' sunlight exposure during downstream transport to characterize this variability, and it is unclear if current measurement approaches and optical theory capture the light exposure of suspended particles. We deployed neutrally buoyant drifters and stationary buoys in the Upper Mississippi (WI, U.S.A.) and Neuse Rivers (NC, U.S.A.) to measure underwater sunlight from the perspective of suspended particles. In our study sites, underwater sunlight varied more along flowpaths measured by drifters than over time measured by fixed‐site buoys; sunlight exposure along flowpaths was dominated by bursts of light (sunflecks) that accounted for 62–99% of the cumulative sunlight exposure; and modeled sunlight exposure using optical theory was consistently 56–1700% higher than measured sunlight exposure along flowpaths. Our results suggested that suspended particles in the study reaches experienced darker conditions than predicted and have important implications for how to quantify underwater sunlight in rivers.

North Carolina, Wisconsin↗

USGS2020

Compilation of mercury data and associated risk to human and ecosystem health, Bad River Band of Lake Superior Chippewa, Wisconsin

Mercury is an environmentally ubiquitous neurotoxin, and its methylated form presents health risks to humans and other biota, primarily through dietary intake. Because methylmercury bioaccumulates and biomagnifies in living tissue, concentrations progressively increase at higher trophic positions in ecosystem food webs. Therefore, the greatest health risks are for organisms at the highest trophic positions and for humans who consume organisms such as fish from these high trophic positions. Data on environmental mercury concentrations in various media and biota provide a basis for comparison among sites and regions and for evaluating ecosystem health risks. The U.S. Geological Survey, in cooperation with the Natural Resources Department, Bad River Band of Lake Superior Chippewa, have compiled a dataset from analyses of mercury concentrations in surface water, bed sediment, fish tissue, Rana clamitans (green frog) tissue, Haliaeetus leucocephalus (bald eagle) feathers, Lontra canadensis (North American river otter) hair, Zizania palustris (northern wild rice), and litterfall from samples collected in the Bad River watershed, Wisconsin during 2004–18. These data originated from either the Natural Resources Department or another agency based on samples collected within or near to Bad River Tribal lands before transfer to the U.S. Geological Survey for compilation and analysis at the onset of the project. This report describes the compiled mercury dataset, provides comparisons to similar measurements in the region and elsewhere, and evaluates health risks to humans and to the sampled biota. Except for litterfall, data were not collected on a consistent, regular basis over a sufficient period to evaluate temporal patterns. The reported mercury concentrations are generally similar to those reported elsewhere in the upper Great Lakes region. Reported values are consistent with atmospheric deposition as the principal source and reflect a favorable environment for mercury methylation. Fish mercury concentrations increased at higher food web positions and generally increased with length in most species measured. Sander vitreus (walleye) present the greatest risk to humans among fishes considered here because of their high trophic position and associated elevated mercury concentrations in combination with relatively high walleye consumption rates by the Native American community. Methylmercury concentrations in wild rice are generally low and likely pose little health risk. Despite reports of declining atmospheric mercury deposition across eastern North America during the past decade, a downward trend in litterfall mercury deposition was not evident in samples collected during 2012–18. Limitations in this data compilation and analysis were noted due to missing information such as collection dates and site locations for some samples. Regular monitoring of mercury in litterfall and surface waters along with periodic collection of fish would enable evaluation of temporal change in the mercury cycle that might affect future risk to humans and aquatic ecosystem inhabitants.

Wisconsin↗

USGS2012

Prioritizing pesticide compounds for analytical methods development

The U.S. Geological Survey (USGS) has a periodic need to re-evaluate pesticide compounds in terms of priorities for inclusion in monitoring and studies and, thus, must also assess the current analytical capabilities for pesticide detection. To meet this need, a strategy has been developed to prioritize pesticides and degradates for analytical methods development. Screening procedures were developed to separately prioritize pesticide compounds in water and sediment. The procedures evaluate pesticide compounds in existing USGS analytical methods for water and sediment and compounds for which recent agricultural-use information was available. Measured occurrence (detection frequency and concentrations) in water and sediment, predicted concentrations in water and predicted likelihood of occurrence in sediment, potential toxicity to aquatic life or humans, and priorities of other agencies or organizations, regulatory or otherwise, were considered. Several existing strategies for prioritizing chemicals for various purposes were reviewed, including those that identify and prioritize persistent, bioaccumulative, and toxic compounds, and those that determine candidates for future regulation of drinking-water contaminants. The systematic procedures developed and used in this study rely on concepts common to many previously established strategies. The evaluation of pesticide compounds resulted in the classification of compounds into three groups: Tier 1 for high priority compounds, Tier 2 for moderate priority compounds, and Tier 3 for low priority compounds. For water, a total of 247 pesticide compounds were classified as Tier 1 and, thus, are high priority for inclusion in analytical methods for monitoring and studies. Of these, about three-quarters are included in some USGS analytical method; however, many of these compounds are included on research methods that are expensive and for which there are few data on environmental samples. The remaining quarter of Tier 1 compounds are high priority as new analytes. The objective for analytical methods development is to design an integrated analytical strategy that includes as many of the Tier 1 pesticide compounds as possible in a relatively few, cost-effective methods. More than 60 percent of the Tier 1 compounds are high priority because they are anticipated to be present at concentrations approaching levels that could be of concern to human health or aquatic life in surface water or groundwater. An additional 17 percent of Tier 1 compounds were frequently detected in monitoring studies, but either were not measured at levels potentially relevant to humans or aquatic organisms, or do not have benchmarks available with which to compare concentrations. The remaining 21 percent are pesticide degradates that were included because their parent pesticides were in Tier 1. Tier 1 pesticide compounds for water span all major pesticide use groups and a diverse range of chemical classes, with herbicides and their degradates composing half of compounds. Many of the high priority pesticide compounds also are in several national regulatory programs for water, including those that are regulated in drinking water by the U.S. Environmental Protection Agency under the Safe Drinking Water Act and those that are on the latest Contaminant Candidate List. For sediment, a total of 175 pesticide compounds were classified as Tier 1 and, thus, are high priority for inclusion in analytical methods available for monitoring and studies. More than 60 percent of these compounds are included in some USGS analytical method; however, some are spread across several research methods that are expensive to perform, and monitoring data are not extensive for many compounds. The remaining Tier 1 compounds for sediment are high priority as new analytes. The objective for analytical methods development for sediment is to enhance an existing analytical method that currently includes nearly half of the pesticide compounds in Tier 1 by adding as many additional Tier 1 compounds as are analytically compatible. About 35 percent of the Tier 1 compounds for sediment are high priority on the basis of measured occurrence. A total of 74 compounds, or 42 percent, are high priority on the basis of predicted likelihood of occurrence according to physical-chemical properties, and either have potential toxicity to aquatic life, high pesticide useage, or both. The remaining 22 percent of Tier 1 pesticide compounds were either degradates of Tier 1 parent compounds or included for other reasons. As with water, the Tier 1 pesticide compounds for sediment are distributed across the major pesticide-use groups; insecticides and their degradates are the largest fraction, making up 45 percent of Tier 1. In contrast to water, organochlorines, at 17 percent, are the largest chemical class for Tier 1 in sediment, which is to be expected because there is continued widespread detection in sediments of persistent organochlorine pesticides and their degradates at concentrations high enough for potential effects on aquatic life. Compared to water, there are fewer available benchmarks with which to compare contaminant concentrations in sediment, but a total of 19 Tier 1 compounds have at least one sediment benchmark or screening value for aquatic organisms. Of the 175 compounds in Tier 1, 77 percent have high aquatic-life toxicity, as defined for this process. This evaluation of pesticides and degradates resulted in two lists of compounds that are priorities for USGS analytical methods development, one for water and one for sediment. These lists will be used as the basis for redesigning and enhancing USGS analytical capabilities for pesticides in order to capture as many high-priority pesticide compounds as possible using an economically feasible approach.

Scientific Investigations Report↗

USGS2018

Reconnaissance of mixed organic and inorganic chemicals in private and public supply tapwaters at selected residential and workplace sites in the United States

Safe drinking water at the point-of-use (tapwater, TW) is a United States public health priority. Multiple lines of evidence were used to evaluate potential human health concerns of 482 organics and 19 inorganics in TW from 13 (7 public supply, 6 private well self-supply) home and 12 (public supply) workplace locations in 11 states. Only uranium (61.9 μg L –1 , private well) exceeded a National Primary Drinking Water Regulation maximum contaminant level (MCL: 30 μg L –1 ). Lead was detected in 23 samples (MCL goal: zero). Seventy-five organics were detected at least once, with median detections of 5 and 17 compounds in self-supply and public supply samples, respectively (corresponding maxima: 12 and 29). Disinfection byproducts predominated in public supply samples, comprising 21% of all detected and 6 of the 10 most frequently detected. Chemicals designed to be bioactive (26 pesticides, 10 pharmaceuticals) comprised 48% of detected organics. Site-specific cumulative exposure–activity ratios (∑ EAR ) were calculated for the 36 detected organics with ToxCast data. Because these detections are fractional indicators of a largely uncharacterized contaminant space, ∑ EAR in excess of 0.001 and 0.01 in 74 and 26% of public supply samples, respectively, provide an argument for prioritized assessment of cumulative effects to vulnerable populations from trace-level TW exposures.

Environmental Science & Technology↗

USGS1988

National water summary 1986: Hydrologic events and ground-water quality

Ground water is one of the most important natural resources of the United States and degradation of its quality could have a major effect on the welfare of the Nation. Currently (1985), ground water is the source of drinking water for 53 percent of the Nation's population and for more than 97 percent of its rural population. It is the source of about 40 percent of the Nation's public water supply, 33 percent of water for irrigation, and 17 percent of freshwater for selfsupplied industries. Ground water also is the source of about 40 percent of the average annual streamflow in the United States, although during long periods of little or no precipitation, ground-water discharges provide nearly all of the base streamflow. This hydraulic connection between aquifers and streams implies that if a persistent pollutant gets into an aquifer, it eventually could discharge into a stream. Information presented in the 1986 National Water Summary clearly shows that the United States has very large amounts of potable ground water available for use. Although naturally occurring constituents, such as nitrate, and human-induced substances, such as synthetic organic chemicals, frequently are detected in ground water, their concentrations usually do not exceed existing Federal or State standards or guidelines for maximum concentrations in drinking water. Troublesome contamination of ground water falls into two basic categories related to the source or sources of the contamination. Locally, high concentrations of a variety of toxic metals, organic chemicals, and petroleum products have been detected in ground water associated with point sources such as wastedisposal sites, storage-tank leaks, and hazardous chemical spills. These types of local problems commonly occur in densely populated urban areas and industrialized areas. Larger, multicounty areas also have been identified where contamination frequently is found in shallow wells. These areas generally are associated with broad-scale, or nonpoint, sources of contamination such as agricultural activities or highdensity domestic waste disposal (septic systems) in urban centers. At present, only a very small percentage of the total volume of potable ground water in the United States is contaminated from both point and nonpoint sources; however, available data, especially data about the occurrence of synthetic organic and toxic substances, generally are inadequate to determine the full extent of ground-water contamination in the Nation's aquifers or to define trends in groundwater quality. Most information about the occurrence of these substances has come from the study of individual sites or areas where contamination had already been detected or suspected. Management and protection of ground water present a major challenge to the Nation. Current and projected costs of detection and cleanup of existing ground-water contamination are staggering and, even so, complete removal of pollutants from ground water in the vicinity of some waste sites might not be technically feasible. At all levels of government, the task of protecting the resource for its most beneficial uses is difficult and controversial. Despite increasing awareness that some of the Nation's ground water is contaminated with a variety of toxic metals, synthetic organic chemicals, radionuclides, pesticides, and other contaminants that might present a long-term risk to human health, public policy towards ground-water protection is still in the formative stages. Despite increasing efforts devoted to ground-water protection by State and Federal regulatory and resource-management agencies, the extent of ground-water contamination is likely to appear to increase over the next few years because more agencies will be searching for evidence of contamination, and they will be using increasingly sensitive analytical procedures. Increased technology and expanded monitoring activities probably will detect the effects of past contamination and land uses on water quality. The significant time lag between a waterquality change in one part of an aquifer system and the effects of that change at a downgradient site, such as a well, results from the generally slow movement of ground water. This lag between cause and observed effect needs to be considered in evaluating the effectiveness of current and future ground-water policies and remedial measures. Conclusive answers to questions about the location, extent, and severity of ground-water contamination, and about trends in ground-water quality, must await further collection and analysis of data from the Nation's aquifers. Generalizations, however, can be made, and the 1986 National Water Summary, which describes the natural quality of ground-water resources in each State and the major contamination problems that have been identified as of 1986, provides a national perspective of the ground-water-quality situation. The 1986 National Water Summary follows the format of previous volumes. It contains three parts, and the contents of each of these parts are highlighted below.

Water Supply Paper↗

USGS1998

Toxic equivalency factors (TEFs) for PCBs, PCDDs, PCDFs for humans and wildlife

An expert meeting was organized by the World Health Organization (WHO) and held in Stockholm on 15-18 June 1997. The objective of this meeting was to derive consensus toxic equivalency factors (TEFs) for polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and dioxinlike polychlorinated biphenyls (PCBs) for both human, fish, and wildlife risk assessment. Based on existing literature data, TEFs were (re)evaluated and either revised (mammals) or established (fish and birds). A few mammalian WHO-TEFs were revised, including 1,2,3,7,8-pentachlorinated DD, octachlorinated DD, octachlorinated DF, and PCB 77. These mammalian TEFs are also considered applicable for humans and wild mammalian species. Furthermore, it was concluded that there was insufficient in vivo evidence to continue the use of TEFs for some di-ortho PCBs, as suggested earlier by Ahlborg et al. [Chemosphere 28:1049-1067 (1994)]. In addition, TEFs for fish and birds were determined. The WHO working group attempted to harmonize TEFs across different taxa to the extent possible. However, total synchronization of TEFs was not feasible, as there were orders of a magnitude difference in TEFs between taxa for some compounds. In this respect, the absent or very low response of fish to mono-ortho PCBs is most noticeable compared to mammals and birds. Uncertainties that could compromise the TEF concept were also reviewed, including nonadditive interactions, differences in shape of the dose-response curve, and species responsiveness. In spite of these uncertainties, it was concluded that the TEF concept is still the most plausible and feasible approach for risk assessment of halogenated aromatic hydrocarbons with dioxinlike properties.

Environmental Health Perspectives↗

USGS2020

Threats posed by the Fungal Kingdom to humans, wildlife, and agriculture

The Fungal Kingdom includes at least six million eukaryotic species and is remarkable with respect to its profound impact on global health, biodiversity, ecology, agriculture, manufacturing, and biomedical research. Approximately 625 fungal species have been reported to infect vertebrates, 200 of which can be human-associated, either as commensals and members of our microbiome or as pathogens that cause infectious diseases. These organisms pose a growing threat to human health with the global increase in the incidence of invasive fungal infections, prevalence of fungal allergy, and the evolution of fungal pathogens resistant to some or all current classes of antifungals. More broadly, there has been an unprecedented and worldwide emergence of fungal pathogens impacting animal and plant biodiversity. Approximately 8,000 species of fungi and Oomycetes are associated with plant disease. Indeed, across agriculture, such fungal diseases of plants include new devastating epidemics of trees and jeopardize food security worldwide by causing epidemics in staple and commodity crops that feed billions. Further, ingestion of mycotoxins contributes to ill health and causes cancer. Coordinated international research efforts, enhanced technology translation, and greater policy outreach by scientists are needed to more fully understand the biology and drivers that underlie the emergence of fungal diseases and to mitigate against their impacts. Here, we focus on poignant examples of emerging fungal threats in each of three areas: human health, wildlife biodiversity, and food security.

mBio↗

USGS1996

The Fox River PCB transport study: Stepping stone to a healthy Great Lakes ecosystem

Polychlorinated Biphenyls (PCBs) in the Great Lakes Despite being banned since the 1970's, polychlorinated biphenyls (PCBs) continue to pose a threat to the environment because of their persistence and toxicity to organisms ranging from minute algae to fish, waterfowl, and human beings. PCBs, a set of 209 related chlorinated organic compounds, had various industrial uses such as in hydraulic fluids, cutting oils, sealants, and pesticides. Despite the manufacturing ban in the mid-1970's, PCBs remain ubiquitous in the environment. In the Laurentian Great Lakes of the Midwest. PCBs and other toxic compounds contaminate bottom sediments at almost all designated "areas of concern" (AOC)(figure 1, upper left inset). The International Joint Commission, a binational group from Canada and the United States, has identified these AOCs in their efforts to restore and protect Great Lakes ecosystems. One such area, the Fox River which flows into Green Bay, has been the focus of much scientific study in an effort to improve not only that river but to apply lessons learned to other AOCs. The final goal is a healthy Great Lakes food chain with fish and waterfowl that are safe to consume.

Fox River, Great Lakes, Lake Winnebago↗

USGS2003

Survival, transport, and sources of fecal bacteria in streams and survival in land-applied poultry litter in the upper Shoal Creek basin, southwestern Missouri, 2001–2002

Densities of fecal coliform bacteria along a 5.7-mi (mile) reach of Shoal Creek extending upstream from State Highway 97 (site 3) to State Highway W (site 2) and in two tributaries along this reach exceeded the Missouri Department of Natural Resources (MDNR) standard of 200 col/100 mL (colonies per 100 milliliters) for whole-body contact recreation. A combination of techniques was used in this report to provide information on the source, transport, and survival of fecal bacteria along this reach of Shoal Creek. Results of water-quality samples collected during dye-trace and seepage studies indicated that at summer low base-flow conditions, pastured cattle likely were a substantial source of fecal bacteria in Shoal Creek at the MDNR monitoring site (site 3) at State Highway 97. Using repeat element Polymerase Chain Reaction (rep-PCR), cattle were the presumptive source of about 50 percent of the Escherichia coli ( E. coli ) isolates in water samples from site 3. Cattle, horses, and humans were the most common presumptive source of E. coli isolates at sites further upstream. Poultry was identified by rep-PCR as a major source of E. coli in Pogue Creek, a tributary in the upper part of the study area. Results of the rep-PCR were in general agreement with the detection and distribution of trace concentrations of organic compounds commonly associated with human wastewater, such as caffeine, the antimicrobial agent triclosan, and the pharmaceutical compounds acetaminophen and thiabendazole (a common cattle anthelmintic). Significant inputs of fecal bacteria to Shoal Creek occurred along a 1.6-mi reach of Shoal Creek immediately upstream from site 3. During a 36-hour period in July 2001, average densities of fecal coliform and E. coli bacteria increased from less than or equal to 500 col/100 mL upstream from this stream reach (sample site 2c) to 2,100 and 1,400 col/100 mL, respectively, at the MDNR sampling site. Fecal bacteria densities exhibited diurnal variability at all five sampling sites along the 5.7-mi study reach of Shoal Creek, but the trends at successive downstream sites were out of phase and could not be explained by simple advection and dispersion. At base-flow conditions, the travel time of bacteria in Shoal Creek along the 5.7-mi reach between State Highway W (site 2) and the MDNR sampling site (site 3) was about 26 hours. Substantial dispersion and dilution occurs along the upper 4.1 mi of this reach because of inflows from a number of springs and tributaries and the presence of several long pools and channel meanders. Minimal dispersion and dilution occurs along the 1.6-mi reach immediately upstream from the MDNR sampling site. Measurements of fecal bacteria decay in Shoal Creek during July 2001 indicated that about 8 percent of fecal coliform and E. coli bacteria decay each hour with an average first-order decay constant of 0.084 h -1 (per hour). Results of field test plots indicated that substantial numbers of fecal bacteria present in poul try litter can survive in fields for as much as 8 weeks after the application of the litter to the land surface. Median densities of fecal coliform and E. coli in slurry-water samples collected from fields increased from less than 60 col/100 mL before the application of turkey and broiler litter, to as large as 420,000 and 290,000 col/100 mL after the application of litter. Bacteria densities in the test plots generally decreased in a exponential manner over time with decay rates ranging from 0.085 to 0.185 d -1 (per day) for fecal coliform to between 0.100 and 0.250 d -1 for E. coli . The apparent survival of significant numbers of fecal bacteria on fields where poultry litter has been applied indicates that runoff from these fields is a potential source of fecal bacteria to vicinity streams for many weeks following litter application.

Water-Resources Investigations Report↗

USGS2019

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships between intermediate host snails (abundance, density, and prevalence) and human urogenital schistosomiasis reinfection (prevalence and intensity in schoolchildren after drug administration). However, we also found that snail distributions were so patchy in space and time that obtaining useful data required effort that exceeds what is feasible in standard monitoring and control campaigns. Instead, we identified several environmental proxies that were more effective than snail variables for predicting human infection: the area covered by suitable snail habitat (i.e., floating, nonemergent vegetation), the percent cover by suitable snail habitat, and size of the water contact area. Unlike snail surveys, which require hundreds of person-hours per site to conduct, habitat coverage and site area can be quickly estimated with drone or satellite imagery. This, in turn, makes possible large-scale, high-resolution estimation of human urogenital schistosomiasis risk to support targeting of both mass drug administration and snail control efforts.

PNAS↗

USGS2015

Human activities and climate variability drive fast-paced change across the world's estuarine-coastal ecosystems

Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2–5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine–coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine–coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.

Global Change Biology↗

USGS2024

Microplastic-mediated new mechanism of liver damage: From the perspective of the gut-liver axis

Microplastics (MPs) are environmental contaminants that are present in all environments and can enter the human body, accumulate in various organs, and cause harm through the ingestion of food, inhalation, and dermal contact. The connection between bowel and liver disease and the interplay between gut, liver, and flora has been conceptualized as the “gut-liver axis”. Microplastics can alter the structure of microbial communities in the gut and the liver can also be a target for microplastic invasion. Numerous studies have found that when MPs impair human health, they not only promote dysbiosis of the gut microbiota and disruption of the gut barrier but also cause liver damage. For this reason, the gut-liver axis provides a new perspective in understanding this toxic response. The cross-talk between MPs and the gut-liver axis has attracted the attention of the scientific community, but knowledge about whether MPs cause gut-liver interactions through the gut-liver axis is still very limited, and the effect of MPs on liver injury is not well understood. MPs can directly induce microbiota disorders and gut barrier dysfunction. As a result, harmful bacteria and metabolites in the gut enter the blood through the weak intestinal barrier (portal vein channel along the gut-liver axis) and reach the liver, causing liver damage (inflammatory damage, metabolic disorders, oxidative stress, etc.). This review provides an integrated perspective of the gut-liver axis to help conceptualize the mechanisms by which MP exposure induces gut microbiota dysbiosis and hepatic injury and highlights the connection between MPs and the gut-liver axis. Therefore, from the perspective of the gut-liver axis, targeting intestinal flora is an important way to eliminate microplastic liver damage.

Science of the Total Environment↗

USGS2011

Status and understanding of groundwater quality in the Santa Clara River Valley, 2007-California GAMA Priority Basin Project

Groundwater quality in the approximately 460-square-mile Santa Clara River Valley study unit was investigated from April through June 2007 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project is conducted by the U.S. Geological Survey (USGS) in collaboration with the California State Water Resources Control Board and the Lawrence Livermore National Laboratory. The Santa Clara River Valley study unit contains eight groundwater basins located in Ventura and Los Angeles Counties and is within the Transverse and Selected Peninsular Ranges hydrogeologic province. The Santa Clara River Valley study unit was designed to provide a spatially unbiased assessment of the quality of untreated (raw) groundwater in the primary aquifer system. The assessment is based on water-quality and ancillary data collected in 2007 by the USGS from 42 wells on a spatially distributed grid, and on water-quality data from the California Department of Public Health (CDPH) database. The primary aquifer system was defined as that part of the aquifer system corresponding to the perforation intervals of wells listed in the CDPH database for the Santa Clara River Valley study unit. The quality of groundwater in the primary aquifer system may differ from that in shallow or deep water-bearing zones; for example, shallow groundwater may be more vulnerable to surficial contamination. Eleven additional wells were sampled by the USGS to improve understanding of factors affecting water quality.The status assessment of the quality of the groundwater used data from samples analyzed for anthropogenic constituents, such as volatile organic compounds (VOCs) and pesticides, as well as naturally occurring inorganic constituents, such as major ions and trace elements. The status assessment is intended to characterize the quality of untreated groundwater resources in the primary aquifers of the Santa Clara River Valley study unit, not the quality of treated drinking water delivered to consumers. Relative-concentrations (sample concentration divided by health- or aesthetic-based benchmark concentration) were used for evaluating groundwater quality for those constituents that have Federal and (or) California benchmarks. A relative-concentration greater than 1.0 indicates a concentration greater than a benchmark. For organic and special interest constituents, relative-concentrations were classified as high (greater than 1.0); moderate (greater than 0.1 and less than or equal to 1.0); and low (less than or equal to 0.1). For inorganic constituents, relative-concentrations were classified as high (greater than 1.0); moderate (greater than 0.5 and less than or equal to 1.0); and low (less than or equal to 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 is defined as the areal percentage of the primary aquifer system with relative-concentrations greater than 1.0. Moderate and low aquifer-scale proportions are defined as the areal 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 Santa Clara River Valley study unit (within 90 percent confidence intervals). The status assessment showed that inorganic constituents were more prevalent and relative-concentrations were higher than for organic constituents. For inorganic constituents with human-health benchmarks, relative-concentrations (of one or more constituents) were high in 21 percent of the primary aquifer system areally, moderate in 30 percent, and low or not detected in 49 percent. Inorganic constituents with human-health benchmarks with high aquifer-scale proportions were nitrate (15 percent of the primary aquifer system), gross alpha radioactivity (14 percent), vanadium (3.4 percent), boron (3.2 percent), and arsenic (2.3 percent). For inorganic constituents with aesthetic benchmarks, relative-concentrations (of one or more constituents) were high in 54 percent of the primary aquifer system, moderate in 41 percent, and low or not detected in 4 percent. The inorganic constituents with aesthetic benchmarks with high aquifer-scale proportions were total dissolved solids (35 percent), sulfate (22 percent), manganese (38 percent), and iron (22 percent). In contrast, the results of the status assessment for organic constituents with human-health benchmarks showed that relative-concentrations were high in 0 percent (not detected above benchmarks) of the primary aquifer system, moderate in 2.4 percent, and low or not detected in 97 percent. Relative-concentrations of the special interest constituent, perchlorate, were moderate in 12 percent of the primary aquifer system and low or not detected in 88 percent. Relative-concentrations of two VOCs-carbon tetrachloride and trichloroethene (TCE)-were moderate in 2.4 percent of the primary aquifer system. One VOC-chloroform (water disinfection byproduct)-was detected in more than 10 percent of the primary aquifer system but at low relative-concentrations. Of the 88 VOCs and gasoline oxygenates analyzed, 71 were not detected. Pesticides were low or not detected in 100 percent of the primary aquifer system. Of the 118 pesticides and pesticide degradates analyzed, 13 were detected and 5 of those had human-health benchmarks. Two of these five pesticides-simazine and atrazine-were detected in more than 10 percent of the primary aquifer system. The second component of this study, the understanding assessment, was to identify the natural and human factors that affect groundwater quality on the basis of the evaluation of land use, physical characteristics of the wells, and geochemical conditions of the aquifer. Results from these analyses are used to explain the occurrence and distribution of selected constituents in the primary aquifer system of the Santa Clara River Valley study unit. The understanding assessment indicated that water quality varied spatially primarily in relation to depth, groundwater age, reduction-oxidation conditions, pH, and location in the regional groundwater flow system. High and moderate relative-concentrations of nitrate and low relative-concentrations of pesticides were correlated with shallow depths to top-of-perforation, and with high dissolved oxygen. Groundwater of modern and mixed ages had higher nitrate than pre-modern-age groundwater. Decreases in concentrations of total dissolved solids (TDS) and sulfate were correlated with increases in pH. This relationship probably indicates relations of these constituents with increasing depth across most of the Santa Clara River Valley study unit. Previous studies have indicated multiple sources of high concentrations of TDS and sulfate and multiple geochemical processes affecting these constituents in the Santa Clara River Valley study unit. Manganese and iron concentrations were highest in pre-modern-age groundwater at depth and in the downgradient area of the Santa Clara River Valley study unit (closest to the coastline), indicating the prevalence of reducing groundwater conditions in these aquifer zones.

Scientific Investigations Report↗

USGS2012

Status and understanding of groundwater quality in the two southern San Joaquin Valley study units, 2005-2006 - California GAMA Priority Basin Project

Groundwater quality in the southern San Joaquin Valley was investigated from October 2005 through March 2006 as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project is conducted by the U.S. Geological Survey (USGS) in collaboration with the California State Water Resources Control Board and the Lawrence Livermore National Laboratory. There are two study units located in the southern San Joaquin Valley: the Southeast San Joaquin Valley (SESJ) study unit and the Kern County Subbasin (KERN) study unit. The GAMA Priority Basin Project in the SESJ and KERN study units was designed to provide a statistically unbiased, spatially distributed assessment of untreated groundwater quality within the primary aquifers. The status assessment is based on water-quality and ancillary data collected in 2005 and 2006 by the USGS from 130 wells on a spatially distributed grid, and water-quality data from the California Department of Public Health (CDPH) database. Data was collected from an additional 19 wells for the understanding assessment. The aquifer systems (hereinafter referred to as primary aquifers) were defined as that part of the aquifer corresponding to the perforation interval of wells listed in the CDPH database for the SESJ and KERN study units. The status assessment of groundwater quality used data from samples analyzed for anthropogenic constituents such as volatile organic compounds (VOCs) and pesticides, as well as naturally occurring inorganic constituents such as major ions and trace elements. The status assessment is intended to characterize the quality of untreated groundwater resources within the primary aquifers in the SESJ and KERN study units, not the quality of drinking water delivered to consumers. Although the status assessment applies to untreated groundwater, Federal and California regulatory and non-regulatory water-quality benchmarks that apply to drinking water are used to provide context for the results. Relative-concentrations (sample concentration divided by benchmark concentration) were used for evaluating groundwater. A relative-concentration greater than 1.0 indicates a concentration greater than the benchmark and is classified as high. The relative-concentration threshold for classifying inorganic constituents as moderate or low was 0.5; for organic constituents the threshold between moderate and low was 0.1. Aquifer-scale proportion was used as the primary metric for assessing the quality of untreated groundwater for the study units. High aquifer-scale proportion is defined as the areal percentage of the primary aquifers with a high relative-concentration for a particular constituent or class of constituents. Moderate and low aquifer-scale proportions were defined as the areal percentage of the primary aquifers 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 for the two study units in the southern San Joaquin Valley (within 90 percent confidence intervals). The status assessment showed that inorganic constituents were more prevalent than organic constituents and that relative-concentrations were higher for inorganic constituents than for organic constituents. For inorganic constituents with human-health benchmarks, the relative-concentration of at least one constituent in the SESJ study unit was high in 30 percent of the primary aquifers. In the KERN study unit, the relative-concentration of at least one constituent was high in 23 percent of the primary aquifers. In the SESJ and KERN study units, the inorganic constituents with human-health benchmarks detected at high relative-concentrations in more than 2 percent of the primary aquifers were arsenic, boron, vanadium, nitrate, uranium, and gross alpha radioactivity. Additional constituents with human-health benchmarks—antimony, radium, and fluoride—were detected at high relative-concentrations in the KERN study unit. For inorganic constituents with aesthetic benchmarks (secondary maximum contaminant levels, SMCLs), the relative-concentration of at least one constituent in the SESJ study unit was high in 6.6 percent of the primary aquifers. In the KERN study unit, the relative-concentration of at least one constituent was high in 22 percent of the primary aquifers. Inorganic constituents with aesthetic benchmarks detected at high relative-concentrations in the primary aquifers in the SESJ and KERN study units were iron and manganese. Additional constituents with aesthetic benchmarks—total dissolved solids (TDS), sulfate, and chloride—were detected at high relative-concentrations in the KERN study unit. In contrast, the status assessment for organic constituents with human-health benchmarks showed that relative-concentrations were high in 4.8 percent and 2.1 percent of the primary aquifers in the SESJ and KERN study units, respectively. The special-interest constituent, perchlorate, was detected at high relative-concentrations in 1.2 percent of the primary aquifers in the SESJ study unit. Twenty-eight of the 78 VOCs (not including fumigants) analyzed were detected. Of these 28 VOCs, benzene had high relative-concentrations in the SESJ study unit, and relative-concentrations for the other 27 VOCs were moderate and low. Five of the 10 fumigants were detected; 1,2-dibromo-3-chloropropane (DBCP) was the only fumigant with high relative-concentrations in the SESJ and KERN study units. Of the 136 pesticides and pesticide degradates analyzed, 33 were detected. Human-health benchmarks were established for eighteen of the detected pesticides. Dieldrin was detected at moderate relative-concentrations in the SESJ and KERN study units. All other pesticides detected with human-health benchmarks were present at low relative-concentrations. The detection frequencies for two of these pesticides—simazine and atrazine—were greater than or equal to 10 percent in the SESJ and KERN study units. The understanding assessment of groundwater quality included an analysis of correlations of selected water-quality constituents or classes of constituents with potential explanatory factors. The understanding assessment indicated that the concentrations of many trace elements and major ions were correlated to well depth, groundwater age, and/or geochemical conditions. Many trace elements were positively correlated with depth. Arsenic, boron, vanadium, fluoride, manganese, and iron concentrations increased with well depth or depth to top-of-perforations. The concentrations for these trace elements also were higher in older (pre-modern) groundwater. In contrast, uranium concentrations decreased with increasing depth and groundwater age. Most trace elements were correlated to geochemical conditions. Arsenic, antimony, boron, fluoride, manganese, and iron concentrations generally were higher wherever the pH of the groundwater was greater than 7.6. Concentrations for these constituents generally were higher at low concentrations of dissolved oxygen (DO). Uranium was the exception; uranium concentrations generally were lower at high pH and at high concentrations of DO. Nitrate concentrations generally were lower in deeper wells. Nitrate concentrations also were higher in groundwater with higher DO. Total dissolved solids, sulfate, and chloride concentrations were higher in the KERN study unit than in the SESJ study unit. Total dissolved solids were negatively correlated with pH in the KERN study unit. Total dissolved solids and sulfate were higher in areas with more agricultural land use. Chloride concentrations increased with depth to top-of-perforations in the KERN study unit. Organic constituents and constituents of special interest, like many inorganic constituents, were correlated with well depth, groundwater age, and DO. Unlike most trace elements, however, solvent and pesticide detections, and total trihalomethanes (THM), DBCP, and perchlorate concentrations decreased with increasing well depth. Volatile organic compound, solvent, and pesticide detections, and THM concentrations also were lower in older (pre-modern) groundwater than in modern-age groundwater. Solvent detections and total THM, DBCP, and perchlorate concentrations increased with increasing DO concentrations.

California↗

USGS2018

Human Bacteroides and total coliforms as indicators of recent combined sewer overflows and rain events in urban creeks

Combined sewer overflows (CSOs) are a known source of human fecal pollution and human pathogens in urban water bodies, which may present a significant public health threat. To monitor human fecal contamination in water, bacterial fecal indicator organisms (FIOs) are traditionally used. However, because FIOs are not specific to human sources and do not correlate with human pathogens, alternative fecal indicators detected using qPCR are becoming of interest to policymakers. For this reason, this study measured correlations between the number and duration of CSOs and mm of rainfall, concentrations of traditional FIOs and alternative indicators, and the presence of human pathogens in two urban creeks. Samples were collected May–July 2016 and analyzed for concentrations of FIOs (total coliforms and E . coli ) using membrane filtration as well as for three alternative fecal indicators (human Bacteroides HF183 marker, human polyomavirus (HPoV), pepper mild mottle virus (PMMoV)) and nine human pathogens using qPCR. Four of the nine pathogens analyzed were detected at these sites including adenovirus, Enterohemorrhagic E . coli , norovirus, and Salmonella . Among all indicators studied, human Bacteroides and total coliforms were significantly correlated with recent CSO and rainfall events, while E . coli, PMMoV, and HPoV did not show consistent significant correlations. Further, human Bacteroides were a more specific indicator, while total coliforms were a more sensitive indicator of CSO and rainfall events. Results may have implications for the use and interpretation of these indicators in future policy or monitoring programs.

Pennsylvania↗

USGS2010

Nodeomics: Pathogen detection in vertebrate lymph nodes using meta-transcriptomics

The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.

PLoS↗

USGS2023

Modeling, mapping, and measuring the risk of freshwater invasive species across Alaska

Freshwater ecosystems of the Alaskan Arctic and Subarctic provide resources that are culturally, ecologically, and economically invaluable. Presently, these regions are relatively free of the impacts from invasive species compared to southern latitudes. To date, there have been relatively few verified introductions of aquatic invasive species (AIS) to freshwater ecosystems in Alaska. The expanding list and distribution of AIS has led to significant negative ecological and economic impacts (e.g., waterweed Elodea nuttalli ; E. canadensis and northern pike Esox Lucius introduced outside its native range in Alaska). Escalating human activity across Alaskan lands and waters, coupled with rapidly shifting environmental conditions, increases the potential for new species introductions and subsequent establishment. Creating a proactive framework for well-informed decision-making and action can improve the effectiveness of prevention efforts and bolster decision support tools that help resource managers direct limited resources. Prioritizing AIS that may be introduced and become established, as well as the locations at highest risk of invasion, is foundational to building a proactive invasive species management framework in Alaska. This project sought to identify and prioritize AIS known to be invasive in the contiguous United States, evaluate current and future habitat suitability for AIS in Alaska, and assess potential for AIS to be transported to habitats across Alaska, utilizing similar assessment methods as implemented for Bering Sea marine invasive species and non-native plants in Alaska. To accomplish this goal, the objectives of the project were to: 1) develop a formal ranked list of potential AIS to freshwater systems of Alaska; 2) assess the level of establishment risk for potential AIS by developing habitat suitability models for waterbodies across Alaska; and 3), identify potential pathways and specific vectors for high-risk AIS to invade Alaska and develop a framework for how vector analysis will be completed to understand transport risk. Overall, our goal is horizon scanning which is defined by Roy et al. (2019) as “a systematic examination of potential threats and opportunities, within a given context, and likely future developments, which are at the margin of current thinking and planning.” The scans include pathway analyses and risk screening of species present at pathway origin points, with a focus on identifying species at high risk of being introduced, becoming established, spreading, and causing harm. We refined a list of 28 AIS from a list of hundreds based on characterizations of species’ invasiveness and species’ proximity to Alaska (USGS 2020; GBIF 2022). Next, we evaluated the relative invasiveness of individual species to create an initial AIS ranking. We sought to characterize habitat suitability of AIS by selecting variables that were continental in scale, covering North America to include Alaska as well as the lower 48 states comparing natural discharge, sub-basin average terrain slope (degrees), average silt fraction, average organic carbon, lithological class, and human footprint in sub-basin in 2009. We estimated AIS habitat suitability across the entire state of Alaska using the physiological tolerances of the AIS (Appendix 2). We also evaluated pathways and vectors for the introduction of AIS (Appendix 2). Many pathways and vectors considered did not meet the criteria for Alaska or freshwater systems. Of the 28 ranked species that we categorized as very high, high, and moderate levels of invasiveness; all three risk groups included fish and mollusks (Appendix 2). One commonality of the very high-invasiveness-ranked species was the availability of Ecological Risk Screening Summary documents (USFWS, 2022) produced by U.S. Fish and Wildlife Service (USFWS), except for the goldfish ( Carassius auratus ) and the New Zealand mudsnail ( Potamopyrgus antipodarum ). The Ecological Risk Screening Summary is now available for New Zealand mudsnails. In general, fish species often ranked very high or high in invasiveness and included sportfish and aquarium fish, suggesting the importance of pathways such as aquarium trade, fishing industry, intentional (but illegal) introductions of sportfishes and aquarium fishes for establishment. The technique we used for habitat suitability models necessitated aquatic environmental datasets that were continental in scale, which was often interpolated from very coarse resolution source data layers, particularly in Alaska. Better spatial data representing aquatic environments would likely improve this approach. While the lack of introductions in Alaska and nearby provinces and states is encouraging, the lack of occurrence data for the focal species also created complications for habitat suitability modeling. Despite the challenges, the habitat suitability models indicated limited suitability for warmwater species while some species, such as Brook trout (S alvelinus fontinalis ), have high habitat suitability across Alaska no matter what threshold approach is taken. Some environmental predictors were more important than others. Specifically, the most important predictor variable, ‘frost free days,’ was critical for 15 out of 28 species as expected due to harsh winter conditions in Arctic and Subarctic regions. The second most important predictor was ‘subbasin land surface runoff’, a variable that indicates the amount of discharge and runoff, while the third most important predictor was ‘snow cover’ another indication of winter conditions. Overall, the ability to understand the effect of future climate scenarios on the establishment of AIS was challenging. A detailed dataset of freshwater temperatures and water chemistry (e.g., pH, calcium) would greatly improve the ability to predict invasiveness of freshwater species to Alaska’s ecosystems on a regional basis. Future studies may benefit from a more focused geographic scope examining a group of subbasins or a regional basin rather than the entire state. These drainages could be selected based upon the mostly likely locations of introduction pathways. The two most prevalent pathway risks for AIS are in-state transfer and stowaways/contaminants. Although there are examples of introductions from other pathways, the risk is somewhat mitigated by Alaska’s climate and regulations. However, variable application of protocols for inspection and cleaning of fishing gear, watercraft, and other similar items while traveling into Alaska as well as transferring from waterbody to waterbody within the state creates a substantial risk in introducing invasive species. We plot cumulative invasive vulnerability for all subbasins and for the top 10% of subbasins (Appendix 3).

Alaska↗

USGS2018

Macrobenthic infaunal communities associated with deep‐sea hydrocarbon seeps in the northern Gulf of Mexico

There are thousands of seeps in the deep ocean worldwide; however, many questions remain about their contributions to global biodiversity and the surrounding deep‐sea environment. In addition to being globally distributed, seeps provide several benefits to humans such as unique habitats, organisms with novel genes, and carbon regulation. The purpose of this study is to determine whether there are unique seep macrobenthic assemblages, by comparing seep and nonseep environments, different seep habitats, and seeps at different depths and locations. Infaunal community composition, diversity, and abundance were examined between seep and nonseep background environments and among three seep habitats (i.e., microbial mats, tubeworms, and soft‐bottom seeps). Abundances were higher at seep sites compared to background areas. Abundance and diversity also differed among microbial mat, tubeworm, and soft‐bottom seep habitats. Although seeps contained different macrobenthic assemblages than nonseep areas, infaunal communities were also generally unique for each seep. Variability was 75% greater within communities near seeps compared to communities in background areas. Thus, high variability in community structure characterized seep communities rather than specific taxa. The lack of similarity among seep sites supports the idea that there are no specific infauna that can be used as indicators of seepage throughout the northern Gulf of Mexico, at least at higher taxonomic levels.

Marine Ecology↗