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USGS2012

USGS Environmental health science strategy: providing environmental health science for a changing world: Public review release

America has an abundance of natural resources. We have bountiful clean water, fertile soil, and unrivaled national parks, wildlife refuges, and public lands. These resources enrich our lives and preserve our health and wellbeing. These resources have been maintained because of our history of respect for their value and an enduring commitment to their vigilant protection. Awareness of the social, economic, and personal value of the health of our environment is increasing. The emergence of environmentally driven diseases caused by environmental exposure to contaminants and pathogens is a growing concern worldwide. New health threats and patterns of established threats are affected by both natural and anthropogenic changes to the environment. Human activities are key drivers of emerging (new and re-emerging) health threats. Societal demands for land and natural resources, a better quality of life, improved economic prosperity, and the environmental impacts associated with these demands will continue to increase. Natural earth processes, climate trends, and related climatic events will add to the environmental impact of human activities. These environmental drivers will influence exposure to disease agents, including viral, bacterial, prion, and fungal pathogens, parasites, natural earth materials, toxins and other biogenic compounds, and synthetic chemicals and substances. The U.S. Geological Survey (USGS) defines environmental health science broadly as the interdisciplinary study of relations among the quality of the physical environment, the health of the living environment, and human health. The interactions among these three spheres are driven by human activities, ecological processes, and natural earth processes; the interactions affect exposure to contaminants and pathogens and the severity of environmentally driven diseases in animals and people. This definition provides USGS with a framework for synthesizing natural science information from across the Bureau and providing it to environmental, natural resource, agricultural, and public-health managers. The USGS is a Federal science agency with a broad range of natural science expertise relevant to environmental health. USGS provides scientific information and tools as a scientific basis for management and policy decision making. USGS specializes in science at the environment-health interface, by characterizing the processes that affect the interaction among the physical environment, the living environment, and people, and the resulting factors that affect ecological and human exposure to disease agents. This report describes a 10-year strategy that encompasses the portfolio of USGS environmental health science. It summarizes national environmental health priorities that USGS is best suited to address, and will serve as a strategic framework for USGS environmental health science goals, actions, and outcomes for the next decade. Implementation of this strategy is intended to aid coordination of USGS environmental health activities and to provide a focal point for disseminating information to stakeholders. The "One Health" paradigm advocated by the World Health Organization (WHO, 2011), and the American Veterinary Medicine Association (AVMA, 2008), among others, is based on a general recognition that the health of humans, animals, and the environment are inextricably linked. Thus, successful efforts to protect that health will require increased interdisciplinary research and increased communication and collaboration among the broader scientific and health community. This strategy is built upon that paradigm. The vision, mission, and five cornerstone goals of the USGS Environmental Health Science Strategy were developed with significant input from a wide range of stakeholders. Vision - The USGS is a premier source of the environmental health science needed to safeguard the health of the environment, fish, wildlife, and people. Mission - The mission of USGS in environmental health science is to contribute scientific information to environmental, natural resource, agricultural, and public-health managers, who use that science to support sound decision making. USGS provides the science to: - Goal 1: Identify, prioritize, and detect contaminants and pathogens of emerging environmental concern. - Goal 2: Reduce the impact of contaminants on the environment, fish, wildlife, and people. - Goal 3: Reduce the impact of pathogens on the environment, fish, wildlife, and people. - Goal 4: Discover the complex interactions and combined effects of exposure to contaminants and pathogens. - Goal 5: Prepare for and respond to environmental impacts and related health threats of natural and anthropogenic disasters. Goals 1 through 4 are intended to provide science to address environmental health threats in a logical order, from informing prevention and preparedness, to supporting systematic management response to environmental health issues. Goal 4 addresses the interaction among contaminants and pathogens, an issue of emerging concern in environmental health science. Goal 5 acknowledges the fact that natural and anthropogenic disasters can cause immediate and prolonged adverse environmental health threats. This strategy proposes that USGS take the following strategic science actions to achieve each of the five goals of this strategy: Goal 1: Identify, prioritize, and detect contaminants and pathogens of emerging environmental concern. - Strategic Science Action 1. - Prioritize contaminants and pathogens of emerging concern to guide research, detection, and management activities. - Strategic Science Action 2. - Conduct surveillance and monitoring to provide early warning of emerging health threats. - Strategic Science Action 3. - Develop approaches and tools that identify vulnerable environmental settings, ecosystems, and species. Goal 2: Reduce the impact of contaminants on the environment, fish, wildlife, and people. - Strategic Science Action 1. - Systematically characterize the sources, occurrence, transport and fate of environmental contaminants to guide efforts to manage and mitigate contamination. - Strategic Science Action 2. - Evaluate the threats of contamination on the health of the environment, fish, wildlife, and people, and inform the associated management and protection efforts. - Strategic Science Action 3. - Characterize potential human exposure to support establishment of health-based standards or guidelines and contamination-reduction efforts. Goal 3: Reduce the impact of pathogens on the environment, fish, wildlife, and people. - Strategic Science Action 1. - Determine the biotic and abiotic factors that control the ecology of infectious diseases affecting natural populations of aquatic and terrestrial species and potential transmission to other animals and humans. - Strategic Science Action 2. - Establish how natural and anthropogenic environmental changes affect the distribution and severity of infectious diseases in natural populations of aquatic and terrestrial species and potential transmission to other animals and humans. - Strategic Science Action 3. - Develop surveillance systems to identify changing patterns of disease activity in priority geographic areas. Goal 4: Discover the complex interactions and combined effects of exposure to contaminants and pathogens. - Strategic Science Action 1. - Identify how exposure to one class of disease agents (contaminants or pathogens) can make an organism more susceptible to effects from exposure to the other class of disease agents. - Strategic Science Action 2. - Implement interdisciplinary studies that characterize the effects of combined exposure to pathogens and contaminants. Goal 5: Prepare for and respond to the environmental impacts and related health threats of natural and anthropogenic disasters. - Strategic Science Action 1. - Establish a formal interdisciplinary science capability to rapidly assess the environmental health risks associated with disasters. - Strategic Science Action 2. - Enhance methods to anticipate, prepare for, and identify environmental, ecological, and related health impacts of future disasters. This strategy is one of seven USGS science strategies developed concurrently: - Climate and Land Use Change - Core Science Systems - Ecosystems - Energy and Mineral Resources - Environmental Health - Natural Hazards - Water. This strategy describes how USGS will address the highest priority environmental health issues facing the Nation. The ultimate intended outcome of this science strategy is prevention and reduction of adverse impacts to the quality of the environment, the health of our living resources, and human health. Communication with, and receiving input from, partners and stakeholders regarding their science needs is essential for successful implementation of this strategy. It is incumbent on USGS to reach out to all stakeholders to ensure that USGS efforts are focused on the highest priority environmental health issues and that products are provided in the most timely and usable form to all those who can use them. USGS must reach out to the scientific community, internally and externally, to ensure that our efforts are integrated with and take full advantage of the activities of others.

Open-File Report↗
USGS2018

Faunal and vegetation monitoring in response to harbor dredging in the Port of Miami

Seagrasses are highly productive ecosystems. A before-after-control-impact (BACI) design was used to examine effects of dredging on seagrasses and the animals that inhabit them. The control site North Biscayne Bay and the affected site Port of Miami had seagrass densities decrease during both the before, Fish and Invertebrate Assessment Network 2006-2011, and after, Faunal Monitoring in Response to Harbor Dredging 2014-2016, studies. Turbidity levels increased at North Biscayne Bay and Port of Miami basins during the Faunal Monitoring in Response to Harbor Dredging study, especially in 2016. Animal populations decreased significantly in North Biscayne Bay and Port of Miami in the Faunal Monitoring in Response to Harbor Dredging study compared to the Fish and Invertebrate Assessment Network study. Predictive modeling shows that numbers of animal populations will likely continue to decrease if the negative trends in seagrass densities continue unabated. There could be effects on several fisheries vital to the south Florida economy. Additional research could determine if animal populations and seagrass densities have rebounded or continued to decrease.

Florida↗
USGS2006

Occurrence of organic wastewater compounds in drinking water, wastewater effluent, and the Big Sioux River in or near Sioux Falls, South Dakota, 2001-2004

The U.S. Geological Survey (USGS) in cooperation with the city of Sioux Falls conducted several rounds of sampling to determine the occurrence of organic wastewater compounds (OWCs) in the city of Sioux Falls drinking water and waste-water effluent, and the Big Sioux River in or near Sioux Falls during August 2001 through May 2004. Water samples were collected during both base-flow and storm-runoff conditions. Water samples were collected at 8 sites, which included 4 sites upstream from the wastewater treatment plant (WWTP) discharge, 2 sites downstream from the WWTP discharge, 1 finished drinking-water site, and 1 WWTP effluent (WWE) site. A total of 125 different OWCs were analyzed for in this study using five different analytical methods. Analyses for OWCs were performed at USGS laboratories that are developing and/or refining small-concentration (less than 1 microgram per liter (ug/L)) analytical methods. The OWCs were classified into six compound classes: human pharmaceutical compounds (HPCs); human and veterinary antibiotic compounds (HVACs); major agricultural herbicides (MAHs); household, industrial,and minor agricultural compounds (HIACs); polyaromatic hydrocarbons (PAHs); and sterol compounds (SCs). Some of the compounds in the HPC, MAH, HIAC, and PAH classes are suspected of being endocrine-disrupting compounds (EDCs). Of the 125 different OWCs analyzed for in this study, 81 OWCs had one or more detections in environmental samples reported by the laboratories, and of those 81 OWCs, 63 had acceptable analytical method performance, were detected at concentrations greater than the study reporting levels, and were included in analyses and discussion related to occurrence of OWCs in drinking water, wastewater effluent, and the Big Sioux River. OWCs in all compound classes were detected in water samples from sampling sites in the Sioux Falls area. For the five sampling periods when samples were collected from the Sioux Falls finished drinking water, only one OWC was detected at a concentration greater than the study reporting level (metolachlor; 0.0040 ug/L). During base-flow conditions, Big Sioux River sites upstream from the WWTP discharge had OWC contributions that primarily were from nonpoint animal or crop agriculture sources or had OWC concentrations that were minimal. The influence of the WWTP discharge on OWCs at downstream river sites during base-flow conditions ranged from minimal influence to substantial influence depending on the sampling period. During runoff conditions, OWCs at sites upstream from the WWTP discharge probably were primarily contributed by nonpoint animal and/or crop agriculture sources and possibly by stormwater runoff from nearby roads. OWCs at sites downstream from the WWTP discharge probably were contributed by sources other than the WWTP effluent discharge, such as stormwater runoff from urban and/or agriculture areas and/or resuspension of OWCs adsorbed to sediment deposited in the Big Sioux River. OWC loads generally were substantially smaller for upstream sites than downstream sites during both base-flow and runoff conditions.discharge had OWC contributions that primarily were from nonpoint animal or crop agriculture sources or had OWC concentrations that were minimal. The influence of the WWTP discharge on OWCs at downstream river sites during base-flow conditions ranged from minimal influence to substantial influence depending on the sampling period. During runoff conditions, OWCs at sites upstream from the WWTP discharge probably were primarily contributed by nonpoint animal and/or crop agriculture sources and possibly by stormwater runoff from nearby roads. OWCs at sites downstream from the WWTP discharge probably were contributed by sources other than the WWTP effluent discharge, such as stormwater runoff from urban and/or agriculture areas and/or resuspension of OWCs adsorbed to sediment deposited in the Big Sioux River. OWC loads generally were substantially smaller for

South Dakota↗
USGS2009

Method for Estimating Water Withdrawals for Livestock in the United States, 2005

Livestock water use includes ground water and surface water associated with livestock watering, feedlots, dairy operations, and other on-farm needs. The water may be used for drinking, cooling, sanitation, waste disposal, and other needs related to the animals. Estimates of water withdrawals for livestock are needed for water planning and management. This report documents a method used to estimate withdrawals of fresh ground water and surface water for livestock in 2005 for each county and county equivalent in the United States, Puerto Rico, and the U.S. Virgin Islands. Categories of livestock included dairy cattle, beef and other cattle, hogs and pigs, laying hens, broilers and other chickens, turkeys, sheep and lambs, all goats, and horses (including ponies, mules, burros, and donkeys). Use of the method described in this report could result in more consistent water-withdrawal estimates for livestock that can be used by water managers and planners to determine water needs and trends across the United States. Water withdrawals for livestock in 2005 were estimated by using water-use coefficients, in gallons per head per day for each animal type, and livestock-population data. Coefficients for various livestock for most States were obtained from U.S. Geological Survey water-use program personnel or U.S. Geological Survey water-use publications. When no coefficient was available for an animal type in a State, the median value of reported coefficients for that animal was used. Livestock-population data were provided by the National Agricultural Statistics Service. County estimates were further divided into ground-water and surface-water withdrawals for each county and county equivalent. County totals from 2005 were compared to county totals from 1995 and 2000. Large deviations from 1995 or 2000 livestock withdrawal estimates were investigated and generally were due to comparison with reported withdrawals, differences in estimation techniques, differences in livestock coefficients, or use of livestock-population data from different sources. The results of this study were distributed to U.S. Geological Survey water-use program personnel in each State during 2007. Water-use program personnel are required to submit estimated withdrawals for all categories of use in their States to the National Water-Use Information Program for inclusion in a national report describing water use in the United States during 2005. Water-use program personnel had the option of submitting these estimates, a modified version of these estimates, or their own set of estimates or reported data. Estimated withdrawals resulting from the method described in this report are not presented herein to avoid potential inconsistencies with estimated withdrawals for livestock that will be presented in the national report, as different methods used by water-use personnel may result in different withdrawal estimates. Estimated withdrawals also are not presented to avoid potential disclosure of data for individual livestock operations.

Scientific Investigations Report↗
USGS2010

Demography of the Pryor Mountain wild horses, 1993-2007

Wild horses (Equus caballus) at Pryor Mountain were studied by direct observation from 1993 through 2007. All horses present were individually identifiable on the basis of coat coloration, head and leg markings, gender, and band associations. Of the 609 horses either present prior to foaling in 1993 or born since, ages were precisely known for 491 (observed as a foal). Ages for 52 horses were estimated through tooth eruption and wear patterns, and for the remaining 66 horses through body size, morphology, and anecdotal evidence concerning when they were present on the range. At varying intensities, never less than 30 days per year, all horses were inventoried and their band associations noted. Foals were paired with dams based on observations of attachment during the early days and weeks of life. Year of death was determined by identification of the carcass where possible. In the absence of finding a carcass, an animal that was not observed for 2 years was considered to have died in the year that it went missing. Animals that were removed from the herd and mares that were part of a contraception study were excluded from calculations of survival and foaling rates, respectively, as appropriate. The average prefoaling population over the 15 years of the study was 148.8 animals (range = 120-187), and the annual foal crop averaged 32.1 (range = 23-40). Large removals (19-60 animals) in four years helped maintain the herd at this level; apparent growth rate (calculated as though removals had not occurred) was 9.6 percent annually (? = 1.096, range = 0.977-1.220). This annual growth rate is relatively low compared to that for many western horse herds, at least in part because of a decline in foal survival. Sex ratio of the foal crop varied widely among years, but pooled across years did not differ from 50:50. Sex ratio in the herd changed mostly as a result of removals. The average age of both males and females in the herd increased during the course of the study. Annual survival of males did not differ from that of females, nor did gender affect annual survival of foals. Pooled across years, ages, and sexes, the annual survival rate was 0.899. Annual foal survival rate was 0.697 and declined through time, with a tendency toward recovery in 2005-2007. Foal survival was higher in larger bands, but did not differ between foals born to primiparous and multiparous mares. A few 2-year-old mares produced foals; foaling rate (excluding contracepted mares and foals they produced) increased through age 10, remained high through age 15, and declined thereafter. Overall foaling rate for mares =3 years of age was 0.576 foals per mare, with no apparent trend during the period of our study. Foaling rate in years following gathers was somewhat lower than in other years. There was a positive relation between foaling rate and band size. Primiparous mares were somewhat less likely to foal in the following year than were multiparous mares. Most stallions that acquired a harem did so at age 5 or 6, and the average age of harem stallions increased during our study. Most harems had 1-3 mares =2 years of age, but harem size varied with age of the stallion, increasing through about age 11 and declining thereafter. About 6 percent of bands had a satellite stallion (=5 years of age), but the mean number of mares did not differ between single- and multistallion bands. Most stallions left their natal band at age 2 or 3, but 17 percent remained with their natal band until age 4 or 5. Foal survival rate was positively related to precipitation, suggesting a possible link to forage production and availability mediated through mare fitness. There also was evidence for density-dependent population regulation, as both population growth rate and survival rate were negatively correlated with population size from the previous year. These and other factors were not sufficient to stabilize the population during our period of study, however, as evidenced by the necess

Scientific Investigations Report↗
USGS2011

Trends in sea otter population abundance in western Prince William Sound, Alaska: Progress toward recovery following the 1989 Exxon Valdez oil spill

Sea otters in western Prince William Sound (WPWS) and elsewhere in the Gulf of Alaska suffered widespread mortality as a result of oiling following the 1989 T/V Exxon Valdez oil spill. Following the spill, extensive efforts have been directed toward identifying and understanding long-term consequences of the spill and the process of recovery. We conducted annual aerial surveys of sea otter abundance from 1993 to 2009 (except for 2001 and 2006) in WPWS. We observed an increasing trend in population abundance at the scale of WPWS through 2000 at an average annual rate of 4 percent: however, at northern Knight Island where oiling was heaviest and sea otter mortality highest, no increase in abundance was evident by 2000. We continued to see significant increase in abundance at the scale of WPWS between 2001 and 2009, with an average annual rate of increase from 1993 to 2009 of 2.6 percent. We estimated the 2009 population size of WPWS to be 3,958 animals (standard error=653), nearly 2,000 animals more than the first post-spill estimate in 1993. Surveys since 2003 also have identified a significant increasing trend at the heavily oiled site in northern Knight Island, averaging about 25 percent annually and resulting in a 2009 estimated population size of 116 animals (standard error=19). Although the 2009 estimate for northern Knight Island remains about 30 percent less than the pre-spill estimate of 165 animals, we interpret this trend as strong evidence of a trajectory toward recovery of spill-affected sea otter populations in WPWS.

Alaska↗
USGS2000

Reconnaissance of the hydrology, water quality, and sources of bacterial and nutrient contamination in the Ozark Plateaus aquifer system and Cave Springs Branch of Honey Creek, Delaware County, Oklahoma, March 1999-March 2000

A reconnaissance investigation of hydrology and water quality was conducted to evaluate possible sources of bacteria and nutrient contamination in the Cave Springs Branch basin and the underlying karstic Ozark Plateau aquifer system. Objectives were to: (1) determine the directions of ground-water flow in the basin and determine whether Cave Springs Branch interacts with ground water, (2) compare water quality in Cave Springs Branch with water quality in nearby wells to determine whether the stream is contaminating nearby wells, and (3) determine sources of fecal coliform bacteria and nitrate contamination in Cave Springs Branch and ground water. Potential sources of bacteria and nitrate in the area include cultivated agriculture, cow and horse on pasture, poultry production, households, and wildlife. Presence of fecal coliform and fecal streptococcal bacteria directly indicate fecal contamination and the potential for the presence of other pathogenic organisms in a water supply. Nitrate in drinking water poses health risks and may indicate the presence of additional contaminants. Fecal coliform bacteria colony counts were least in wells, intermediate in the poultry-processing plant wastewater outfall and Honey Creek above the confluence with Cave Springs Branch, and greatest in Cave Springs Branch. Bacteria strains and resistance to antibiotics by some bacteria indicate that livestock may have been sources of some bacteria in the water samples. Multiple antibiotic resistances were not present in the isolates from the water samples, indicating that the bacteria may not be from human or poultry sources. Ribotyping indicates that Escherichia coli bacteria in water samples from the basin were from bird, cow, horse, dog, deer, and human sources. The presence of multiple ribotypes from each type of animal source except bird indicates that most of the bacteria are from multiple populations of source animals. Identifiable sources of bacteria in Cave Springs Branch at the state line were dominantly cow and horse with one ribotype from bird. Escherichia coli was detected in only one well sample. Bacterial ribotypes in water from that upgradient well indicated human and dog feces as sources for bacteria, and that on site wastewater treatment may not always be adequate in these highly permeable soils. Greater concentrations of nitrate in Cave Springs Branch and O'Brien Spring relative to the poultry-processing plant wastewater outfall may be due, in part, to conversion of ammonia from poultry processing plant wastewater. The poultry-processing plant wastewater outfall sample collected in March 2000 contained greater concentrations of ammonia and total organic nitrogen plus ammonia than the spring, stream, and well samples collected during August 1999. Cave Springs Branch and Honey Creek contributed approximately equal loads of nitrogen to Honey Creek below the confluence and the greatest loads of nitrogen were introduced to Cave Springs Branch by the poultry processing plant wastewater outfall and O'Brien Spring. Nitrate concentrations in upgradient well samples ranged from 0.38 to 4.60 milligrams per liter, indicating that there are sources of ground-water nitrogen other than Cave Springs Branch, such as animal waste, fertilizer, or human waste. Nitrogen compounds in water from wells downgradient of Cave Springs Branch may be from Cave Springs Branch, fertilizers, animal waste, or human waste.

Oklahoma↗
USGS1999

Sources and chronology of nitrate contamination in spring waters, Suwannee River basin, Florida

A multi-tracer approach, which consisted of analyzing water samples for n aturally occurring chemical and isotopic indicators, was used to better understand sources and chronology of nitrate contamination in spring wate rs discharging to the Suwannee and Santa Fe Rivers in northern Florida. Dur ing 1997 and 1998, as part of a cooperative study between the Suwannee River Water Management District and the U.S. Geological Survey, water samples were collected and analyzed from 24 springs and two wells for major ions, nutrients, dissolved organic carbon, and selected environmental isotopes [18O/16O, D/H, 13C/12C, 15N/14N]. To better understand when nitrate entered the ground-water system, water samples were analyzed for chlorofluorocarbons (CFCs; CCl3F, CCl2F2, and C2Cl3F3) and tritium (3H); in this way, the apparent ages and residence times of spring waters and water from shallow zones in the Upper Floridan aquifer were determined. In addition to information obtained from the use of isotopic and other chemical tracers, information on changes in land-use activities in the basin during 1954-97 were used to estimate nitrogen inputs from nonpoint sources for five counties in the basin. Changes in nitrate concentrations in spring waters with time were compared with estimated nitrogen inputs for Lafayette and Suwannee Counties. Agricultural activities [cropland farming, animal farming operations (beef and dairy cows, poultry, and swine)] along with atmospheric deposition have contributed large quantities of nitrogen to ground water in the Suwannee River Basin in northern Florida. Changes in agricultural land use during the past 40 years in Alachua, Columbia, Gilchrist, Lafayette, and Suwannee Counties have contributed variable amounts of nitrogen to the ground-water system. During 1955-97, total estimated nitrogen from all nonpoint sources (fertilizers, animal wastes, atmospheric deposition, and septic tanks) increased continuously in Gilchrist and Lafayette Counties. In Suwannee, Alachua, and Columbia Counties, estimated nitrogen inputs from all nonpoint sources peaked in the late 1970's corresponding to the peak use in fertilizer during this time. Fertilizer use in Columbia, Gilchrist, Lafayette, and Suwannee Counties increased substantially during 1993-97. The heavy use of fertilizers in the basin is corroborated by nitrogen isotope data. Values of d15N of nitrate (d15N-NO3) in spring waters range from 2.7 per mil (SUW718971) to 10.6 per mil (Poe Spring) with a median of 5.4 per mil. The range of values indicates that nitrate in the sampled spring waters most likely originates from a mixture of inorganic (fertilizers) and organic (animal wastes) sources; however, higher d15N values for Poe and Lafayette Blue Springs indicate that an organic source of nitrogen probably is contributing nitrate to these spring waters. Water samples from two wells sampled in Lafayette County have high d15N-NO3 values of 11.0 and 12.1 per mil, indicating the predominance of an organic source of nitrate. These two wells are located near dairy and poultry farms, where leachate from animal wastes may contribute nitrate to ground water. Dissolved-gas data (nitrogen, argon, and oxygen) indicate that denitrification has not removed large amounts of nitrate from the ground-water system. Thus, variations in d15N-NO3 values of spring waters can be attributed to variations in d15N-NO3 values of ground-water recharge, and can be used to obtain information about source(s) of nitrate. Extending the use of age-dating techniques (CFCs and 3H) to spring waters in complex karst systems required the use of several different approaches for estimating age and residence time of ground water discharging to springs. These approaches included the use of a simple reservoir model, a piston-flow model, an exponential model, and a binary-mixing model. When age data (CFC-11, CFC-113, and 3H) are combined for all springs, models that incorporate exponential mixtures seem to provide reliable estimates of average residence times of ground water discharging to springs. Whereas, data for some individual springs fit a binary-mixing model with more than 50 percent young water (recharged within the past 5 years), data from other individual springs fit a piston-flow model with a water age of about 25 years. The young ages of several spring waters (such as SUW718971, SUW725971, and Ginnie Spring) indicate the high vulnerability of the springs to contamination. For most springs, CFCs suggest that a large fraction of the water is more than 20 years old. Springs with lower flows tend to have young ages (shallow ground-water flow systems), whereas springs with higher flows tend to have older ages (deep ground-water flow systems). The chemical composition of spring waters can be used as a qualitative indicator of age and ground-water residence time. Nitrate-nitrogen concentrations and dissolved oxygen in spring waters are inversely related to the apparent ages of spring waters and ground-water residence time in the basin. Silica concentrations increase as the age of spring waters increase. Long-term trends in nitrate concentrations in selected spring waters were compared with estimated inputs of nitrogen from various sources in Suwannee and Lafayette Counties. In both counties, trends in nitrate concentrations in spring waters closely followed the estimated contribution of nitrogen from fertilizers. Decreasing nitrate concentrations in spring waters from Suwannee County followed the decrease in estimated fertilizer use from the mid-1970's to the early 1990's. Increasing nitrate concentrations in sprin g waters from Lafayette County followed the steady increase in fertilizer use from the early 1960's to the mid-1990's The relation between the concentration of nitrate in ground water and the amount of nitrogen that is added to a ground-water contributing area for a spring is controlled by complex interactions among hydrogeologic, land-use, and climatic factors, as well as several other land-management factors. Spring waters represent mixtures of converging flow paths that contain ground water with a range of ages. Even if nitrogen inputs were reduced substantially, it may take decades for nitrate concentrations in the ground-water system to return to near background levels.

Florida↗
USGS2015

Health condition of juvenile Chelonia mydas related to fibropapillomatosis in southeast Brazil

Packed cell volume (PCV), plasma biochemistry, visual body condition (BC), and calculated body condition index (BCI) were evaluated in 170 wild juvenile green sea turtles Chelonia mydas from an aggregation in the effluent canal of a steel mill in Brazil. Occurrence of cutaneous fibropapillomatosis (FP) was observed in 44.1% of the animals examined. BCI alone did not differ significantly between healthy animals and those afflicted with FP. However, all turtles with low BCI were severely afflicted and were uremic, hypoglycemic, and anemic in relation to healthy animals. Severe FP was not always reflected by a poor health condition of the individual. Clinical evaluation and plasma biochemistry indicated that most animals afflicted with FP were in good health condition. Differences in FP manifestations and associated health conditions in different geographic regions must be assessed by long-term health monitoring programs to help define priorities for conservation efforts.

Diseases of Aquatic Organisms↗
USGS1994

Humic and fulvic acids: sink or source in the availability of metals to the marine bivalves Macoma balthica and Potamocorbula amurensis ?

Humic acids (HA) and fulvic acids (FA) are common forms of organic matter in marine sediments, and are routinely ingested by deposit- and suspension-feeding animals. These compounds may be a sink for metals, implying that once metals are bound to humic substances they are no longer available to food webs. A series of experiments was conducted to quantitatively examine this premise using 2 estuarine bivalves from San Francisco Bay, USA: the suspension feeder Potarnocorbula arnurensis and the facultative deposit feeder Macoma balthica . HA and FA, isolated from marine sediments, were bound as organic coatings to either hydrous ferric oxides (HFO) or silica particles. Cd and Cr(II1) were adsorbed to the organic coatings or directly to uncoated HFO and silica particles. Pulse-chase laboratory feeding expenments using 109 Cd and 51 Cr(III) were then conducted to determine absorption efficiencies of Cd and Cr for individual specimens using each of the particle types. The results demonstrated that: (1) absorption of Cr(I1I) from all types of non-living particles was consistently low (< 11%). Ingested Cd showed greater bioavailability than Cr(IIl), perhaps due to differences in metal chemistry. (2) Bivalves absorbed Cd bound to uncoated HFO or silica particles (i.e. with no HA or FA present). (3) The presence of organic coatings on particles reduced Cd bioavailabhty compared with uncoated particles. (4) Both geochemical and biological conditions affected the food chain transfer of Cd. The data suggest that in marine systems inorganic and organic-coated particles are predominantly a sink for Cr in sediments. In the transfer of Cd to consumer animals, inorganic particles and humic substances can act as a link (although not a highly efficient one) under oxidized conditions.

Marine Ecology Progress Series↗
USGS2018

Spatial and temporal patterns in population trends and burrow usage of burrowing owls in North America

Many researchers have suggested that abundance of Burrowing Owls ( Athene cunicularia ) has declined in many portions of their breeding range, but a thorough review of their population trends over time is lacking. Published population trends from the North American Breeding Bird Survey program suggested that Burrowing Owl populations in the US have declined over the past 60 yr, but the declines were not considered significant until 2014. However, accurate trend estimates and the statistical significance of those estimates were hampered by low relative abundance of owls. Moreover, many authors have suggested that eradication of burrowing animals is a major cause of Burrowing Owl declines, because burrows dug by burrowing animals are a critical resource for Western Burrowing Owls ( A. cunicularia hypugaea ). Despite this, we currently lack a range-wide summary of the burrowing animals on which Western Burrowing Owls depend. To help fill these two information gaps, my objectives were to: (1) use Breeding Bird Survey (BBS) data to examine geographic patterns in population trends of Burrowing Owls throughout their breeding range in the USA, and (2) use past studies to provide the first summary of the spatial extent to which Western Burrowing Owls rely on the suite of burrowing animals throughout their breeding range. Significantly more BBS routes in the US show declining counts of owls than show increasing or stable counts, and the declines were most apparent prior to 1995. Counts of Burrowing Owls declined most precipitously on the northern edge and southern edge of the owl's US breeding range. Western Burrowing Owls primarily use black-tailed prairie dog ( Cynomys ludovicianus ) burrows in the eastern portion of their breeding range, whereas the diversity of burrowing species on which the owls depend is much greater in the western and central portions of their breeding range. Burrowing owl declines have been most apparent in portions of their range where they rely primarily on Richardson's ground squirrels ( Urocitellus richardsonii ), California ground squirrels ( Otospermophilus beecheyi ), black-tailed prairie dogs, and American badgers ( Taxidea taxus ).

Journal of Raptor Research↗
USGS2019

Putative mitochondrial sex determination in the Bivalvia: Insights from a hybrid transcriptome assembly in freshwater mussels

Bivalves exhibit an astonishing diversity of sexual systems, with genetic and environmental determinants of sex, and possibly the only example of mitochondrial genes influencing sex determination pathways in animals. In contrast to all other animal species in which strict maternal inheritance (SMI) of mitochondria is the rule, bivalves possess a system known as doubly uniparental inheritance (DUI) of mitochondria in which maternal and paternal mitochondria (and their corresponding female-transmitted or F mtDNA and male-transmitted or M mtDNA genomes) are transmitted within a species. Species with DUI also possess sex-associated mtDNA-encoded proteins (in addition to the typical set of 13), which have been hypothesized to play a role in sex determination. In this study, we analyzed the sex-biased transcriptome in gonads of two closely-related freshwater mussel species with different reproductive and mitochondrial transmission modes: the gonochoric, DUI species, Utterbackia peninsularis , and the hermaphroditic, SMI species, Utterbackia imbecillis . Through comparative analysis with other DUI and non-DUI bivalve transcriptomes already available, we identify common male and female-specific genes, as well as SMI and DUI-related genes, that are probably involved in sex determination and mitochondrial inheritance in this animal group. Our results contribute to the understanding of what could be the first animal sex determination system involving the mitochondrial genome

Florida↗
USGS2022

Immunogenicity, safety, and anti-viral efficacy of a subunit SARS-CoV-2 vaccine candidate in captive black-footed ferrets (Mustela nigripes) and their susceptibility to viral challenge

A preliminary vaccination trial against the emergent pathogen, SARS-CoV-2, was completed in captive black-footed ferrets ( Mustela nigripes; BFF) to assess safety, immunogenicity, and anti-viral efficacy. Vaccination and boosting of 15 BFF with purified SARS-CoV-2 S1 subunit protein produced a nearly 150-fold increase in mean antibody titers compared to pre-vaccination titers. Serum antibody responses were highest in young animals, but in all vaccinees, antibody response declined rapidly. Anti-viral activity from vaccinated and unvaccinated BFF was determined in vitro, as well as in vivo with a passive serum transfer study in mice. Transgenic mice that received BFF serum transfers and were subsequently challenged with SARS-CoV-2 had lung viral loads that negatively correlated ( p < 0.05) with the BFF serum titer received. Lastly, an experimental challenge study in a small group of BFF was completed to test susceptibility to SARS-CoV-2. Despite viral replication and shedding in the upper respiratory tract for up to 7 days post-challenge, no clinical disease was observed in either vaccinated or naive animals. The lack of morbidity or mortality observed indicates SARS-CoV-2 is unlikely to affect wild BFF populations, but infected captive animals pose a potential risk, albeit low, for humans and other animals.

Viruses↗
USGS2015

Estimating bighorn sheep (Ovis canadensis) abundance using noninvasive sampling at a mineral lick within a National Park Wilderness Area

Conservation of species requires accurate population estimates. We used genetic markers from feces to determine bighorn sheep abundance for a herd that was hypothesized to be declining and in need of population status monitoring. We sampled from a small but accessible portion of the population's range where animals naturally congregate at a natural mineral lick to test whether we could accurately estimate population size by sampling from an area where animals concentrate. We used mark-recapture analysis to derive population estimates, and compared estimates from this smaller spatial sampling to estimates from sampling of the entire bighorn sheep range. We found that estimates were somewhat comparable; in 2009, the mineral lick sample and entire range sample differed by 20 individuals, and in 2010 they differed by only one individual. However, we captured 13 individuals in the entire range sample that were not captured at the mineral lick, and thus violated a model assumption that all individuals had an equal opportunity of being captured. This eliminated the possibility of inferring a total population estimate from just animals visiting the mineral lick, but because estimates were relatively similar, monitoring at the mineral lick can provide a useful index for management and conservation. We compared our results to a radio-collar study conducted in 2003–2004 and confirmed that the population remained stable since 2004. Our population estimates were 78 (CI 62–114) in 2009 and 95 (CI 77–131) in 2010. Between 7 and 11 sampling dates were needed to achieve a CV of 20% for population estimates, assuming a capture probability between 0.09 and 0.13. We relied on citizen science volunteers to maximize data collection and reduce costs; 71% of all fecal samples were collected by volunteers, compared to 29% collected by paid staff. We conclude that our technique provides a useful monitoring tool for managers. The technique could be tested and applied in similar populations where animals congregate with high fidelity at a mineral lick or other area.

Colorado↗
USGS2020

The effect of size on postrelease survival of head-started Mojave desert tortoises

Captive-rearing conservation programs focus primarily on maximizing postrelease survival. Survival increases with size in a variety of taxa, often leading to the use of enhanced size as a means to minimize postrelease losses. Head-starting is a specific captive-rearing approach used to accelerate growth in captivity prior to release in the wild. We explored the effect of size at release, among other potential factors, on postrelease survival in head-started Mojave desert tortoises Gopherus agassizii . Juvenile tortoises were reared for different durations of captivity (2–7 y) and under varying husbandry protocols, resulting in a wide range of juvenile sizes (68–145 mm midline carapace length) at release. We released all animals ( n = 78) in the Mojave National Preserve, California, United States, on 25 September 2018. Release size and surface activity were the only significant predictors of fate during the first year postrelease. Larger sized head-starts had higher predicted survival rates when compared with smaller individuals. This trend was also observed in animals of the same age but reared under different protocols, suggesting that accelerating the growth of head-started tortoises may increase efficiency of head-starting programs without decreasing postrelease success. Excluding five missing animals, released head-starts had 82.2% survival in their first year postrelease (September 2018–September 2019), with all mortalities resulting from predation. No animals with >90-mm midline carapace length were predated by ravens. Our findings suggest the utility of head-starting may be substantially improved by incorporating indoor rearing to accelerate growth. Target release size for head-started chelonians will vary among head-start programs based on release site conditions and project-specific constraints.

California↗
USGS2014

Lichens: Unexpected anti-prion agents?

The prion diseases sheep scrapie and cervid chronic wasting disease are transmitted, in part, via an environmental reservoir of infectivity; prions released from infected animals persist in the environment and can cause disease years later. Central to controlling disease transmission is the identification of methods capable of inactivating these agents on the landscape. We have found that certain lichens, common, ubiquitous, symbiotic organisms, possess a serine protease capable of degrading prion protein (PrP) from prion-infected animals. The protease functions against a range of prion strains from various hosts and reduces levels of abnormal PrP by at least two logs. We have now tested more than 20 lichen species from several geographical locations and from various taxa and found that approximately half of these species degrade PrP. Critical next steps include examining the effect of lichens on prion infectivity and cloning the protease responsible for PrP degradation. The impact of lichens on prions in the environment remains unknown. We speculate that lichens could have the potential to degrade prions when they are shed from infected animals onto lichens or into environments where lichens are abundant. In addition, lichens are frequently consumed by cervids and many other animals and the effect of dietary lichens on prion disease transmission should also be considered.

Arkansas, California, Michigan, Missouri, Oregon, ↗
USGS2025

Estimating disease prevalence from preferentially sampled, pooled data

After the onset of the COVID-19 pandemic, scientific interest in coronaviruses endemic in animal populations has increased dramatically. However, investigating the prevalence of disease in animal populations across the landscape, which requires finding and capturing animals can be difficult. Spatial random sampling over a grid could be extremely inefficient because animals can be hard to locate, and the total number of samples may be small. Alternatively, preferential sampling, using existing knowledge to inform sample location, can guarantee larger numbers of samples, but estimates derived from this sampling scheme may exhibit bias if there is a relationship between higher probability sampling locations and the disease prevalence. Sample specimens are commonly grouped and tested in pools which can also be an added challenge when combined with preferential sampling. Here we present a Bayesian method for estimating disease prevalence with preferential sampling in pooled presence-absence data motivated by estimating factors related to coronavirus infection among Mexican free-tailed bats ( Tadarida brasiliensis ) in California. We demonstrate the efficacy of our approach in a simulation study, where a naive model, not accounting for preferential sampling, returns biased estimates of parameter values; however, our model returns unbiased results regardless of the degree of preferential sampling. Our model framework is then applied to data from California to estimate factors related to coronavirus prevalence. After accounting for preferential sampling impacts, our model suggests small prevalence differences between male and female bats.

California↗
USGS2020

Antibiotic resistant bacteria in wildlife: Perspectives on trends, acquisitions and dissemination, data gaps, and future directions

The proliferation of antibiotic resistant bacteria in the environment has potential negative economic and health consequences. Thus, previous investigations have targeted wild animals to understand the occurrence of antibiotic resistance in diverse environmental sources. In this critical review and synthesis, we summarize important concepts learned through the sampling of wildlife for antibiotic resistant indicator bacteria. These concepts are helpful for understanding dissemination of resistance through environmental pathways and helping to guide future research efforts. Our review is comprised of six sections. The first section briefly introduces antibiotic resistance as it pertains to bacteria harbored in environmental sources such as wild animals. Next, we differentiate wildlife from other animals in the context of how diverse taxa provide different information on antibiotic resistance in the environment. In the third section, we identify representative research and seminal works that illustrate important associations between the occurrence of antibiotic resistant bacteria in wildlife and anthropogenic inputs into the environment. For example, we highlight numerous investigations that support the premise that anthropogenic inputs into the environment drive the occurrence of antibiotic resistance in bacteria harbored by free-ranging wildlife. Additionally, we summarize previous research demonstrating foraging as a mechanism by which wildlife may be exposed to anthropogenic antibiotic resistance contamination in the environment. In the fourth section of our review, we summarize molecular evidence for the acquisition and dissemination of resistance among bacteria harbored by wildlife. In the fifth section, we identify what we believe to be important data gaps and potential future directions that other researchers may find useful towards the development of efficient, informative, and impactful investigations of antibiotic resistant bacteria in wildlife. Finally, we conclude our review by highlighting the need to move from surveys that simply identify antibiotic resistant bacteria in wildlife towards hypothesis-driven investigations that: (1) identify point sources of antibiotic resistance; (2) provide information on risk to human and animal health; (3) identify interventions that may interrupt environmentally mediated pathways of antibiotic resistance acquisition/transmission; and (4) evaluate whether management practices are leading to desirable outcomes.

Journal of Wildlife Diseases↗