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USGS2001

Characterization of surface-water quality based on real-time monitoring and regression analysis, Quivira National Wildlife Refuge, south-central Kansas, December 1998 through June 2001

Because of the considerable wildlife benefits offered by the Quivira National Wildlife Refuge in south-central Kansas, there is a desire to ensure suitable water quality. To assess the quality of water flowing from Rattlesnake Creek into the refuge, the U.S. Geological Survey collected periodic water samples from December 1998 through June 2001 and analyzed the samples for physical properties, dissolved solids, total suspended solids, suspended sediment, major ions, nutrients, metals, pesticides, and indicator bacteria. Concentrations of 10 of the 125 chemicals analyzed did not meet water-quality criteria to protect aquatic life and drinking water in a least one sample. These were pH, turbidity, dissolved oxygen, dissolved solids, sodium, chloride, phosphorus, total coliform bacteria, E. coli bacteria, and fecal coliform bacteria. No metal or pesticide concentrations exceeded water-quality criteria. Twenty-two of the 43 metals analyzed were not detected, and 36 of the 46 pesticides analyzed were not detected. Because dissolved solids, sodium, chloride, fecal coliform bacteria, and other chemicals that are a concern for the health and habitat of fish and wildlife at the refuge cannot be measured continuously, regression equations were developed from a comparison of the analytical results of periodic samples and in-stream monitor measurements of specific conductance, pH, water temperature, turbidity, and dissolved oxygen. A continuous record of estimated chemical concentrations was developed from continuously recorded in-stream measurements. Annual variation in water quality was evaluated by comparing 1999 and 2000 sample data- the 2 years for which complete data sets were available. Median concentrations of alkalinity, fluoride, nitrate, and fecal coliform bacteria were smaller or did not change from 1999 to 2000. Dissolved solids, total suspended solids, sodium, chloride, sulfate, total organic nitrogen, and total phosphorus had increases in median concentrations from 1999 to 2000. Increases in the median concentrations of the major ions were expected due to decreased rainfall in 2000 and very low streamflow late in the year. Increases for solids and nutrients may have been due to the unusually high streamflow in the early spring of 2000. This was the time of year when fields were tilled, exposing solids and nutrients that were transported with runoff to Rattlesnake Creek. Load estimates indicate the chemical mass transported into the refuge and can be used in the development of total maximum daily loads (as specified by the U.S. Environmental Protection Agency) for water-quality contaminants in Rattlesnake Creek. Load estimates also were used to evaluate seasonal variation in water quality. Seasonal variation was most pronounced in the estimates of nutrient loads, and most of the nutrient load transported to the refuge occurred during just a few periods of surface runoff in the spring and summer. This information may be used by resource managers to determine when water-diversion strategies would be most beneficial. Load estimates also were used to calculate yields, which are useful for site comparisons. The continuous and real-time nature of the record of estimated concentrations, loads, and yields may be important for resource managers, recreationalists, or others for evaluating water-diversion strategies, making water-use decisions, or assessing the environmental effects of chemicals in time to prevent adverse effects on fish or other aquatic life at the refuge.

Kansas↗

USGS2005

Surface water-quality and water-quantity data from selected urban runoff-monitoring sites at the Rocky Mountain Arsenal, Commerce City, Colorado, water years 1988-2004

The U.S. Geological Survey has monitored the quality and quantity of streamflow at the Rocky Mountain Arsenal (RMA) northeast of Denver, Colorado, since the early 1990s in cooperation with the U.S. Army. This report, prepared in cooperation with the U.S. Fish and Wildlife Service, documents existing surface-water-quality conditions on the RMA. All RMA water-quality data for the Irondale Gulch and First Creek Basins adjacent to and on the RMA were reviewed. Where applicable, water-quality data were compared to State standards established by the Colorado Department of Public Health and Environment. At both the Havana Interceptor below 56th Avenue gaging station and the Uvalda Interceptor below 56th Avenue gaging station, all of the dissolved-oxygen concentrations met the State standard requiring at least 5.0 milligrams per liter (mg/L) of dissolved oxygen for the protection of aquatic life. In contrast, the dissolved-oxygen concentrations at the Peoria Interceptor below 56th Avenue gage commonly were less than 5.0 mg/L. Excluding one suspect concentration of 1.6 mg/L, the dissolved-oxygen concentrations for the First Creek Basin ranged from 4.2 to 12.6 mg/L. Excluding the one suspect value, three dissolved-oxygen concentrations failed to meet the State standard of 5.0 mg/L at the First Creek below Buckley Road site. At the Peoria Interceptor below 56th Avenue site, all pH values were within the range specified by the State standard (6.50-8.99). Results of seven sampling events at the Havana Interceptor below 56th Avenue gaging station indicated a pH greater than or equal to 9 (pH values of 9 or greater exceed the upper limit of the standard). No sampling events indicated a pH less than 6.50. Results from one sampling event at the Uvalda Interceptor below 56th Avenue indicated pH values outside the range specified by the State standard. The concentrations obtained for chloride, magnesium, and sodium generally were below 200 mg/L at all three Irondale Gulch monitoring stations for the entire period of record, but there were a few sampling events at each of these sites where much higher concentrations for these analytes were obtained. The median concentrations for calcium, magnesium, and sodium generally were higher at the First Creek below Buckley Road site than in the three Irondale Gulch sites, while the 90th percentile and maximum concentrations for magnesium and sodium generally were higher at the three Irondale Gulch sites than at the First Creek below Buckley Road site. The urban runoff flowing onto the RMA had low concentrations and few, if any, detections for most organic contaminants. Part of the reason for low detections of organic contaminants may be in how the samples are collected. The existing surface-water sampling program was not designed specifically to target storm runoff and therefore does not characterize water quality for all hydrologic regimes, most notably storm runoff. As a result, the existing data may not adequately represent potential contaminant transport onto the RMA. In addition, during stormwater-runoff events, the sites examined for this report frequently are subject to sharp increases in discharge, and just as quickly the discharge rapidly recedes. These types of transient flow events make water-quality sampling difficult, and none of the sites have a safe place to sample the higher flows that occur in any given year. As a result, most of the surface-water-quality samples were collected after the flow had decreased substantially from the peak flow, which may have transported much of the chemical contaminant load through the system. Thus, little is known about the water quality during the critical initial stormwater-runoff period when contaminants are most likely to be mobilized and transported through the stormwater conveyances past the locations where gaging stations are located.

Colorado↗

USGS2010

Occurrence of antibiotic compounds in source water and finished drinking water from the upper Scioto River Basin, Ohio, 2005-6

The occurrence of antibiotics in surface water and groundwater in urban basins has become a topic of increasing interest in recent years. Little is known about the occurrence, fate, or transport of these compounds and the possible health effects in humans and aquatic life. The U.S. Geological Survey, in cooperation with the City of Columbus, Division of Power and Water, did a study to provide a synoptic view of the occurrence of antibiotics in source and finished waters in the upper Scioto River Basin. Water samples were collected seasonally-winter (December 2005), spring (May 2006), summer (August 2006) and fall (October 2006)-at five surface-water sites, one groundwater site, and three water-treatment plants (WTPs). Within the upper Scioto River Basin, sampling at each WTP involved two sampling sites: a source-water intake site and a finished-water site. One or more antibiotics were detected at 11 of the 12 sampling sites. Of the 49 targeted antibiotic compounds, 12 (24 percent) were detected at least one time for a total of 61 detections overall. These compounds were azithromycin, tylosin, erythromycin-H2O, erythromycin, roxithromycin, ciprofloxacin, ofloxacin, sulfamethazine, sulfamethoxazole, iso-chlorotetracycline, lincomycin, and trimethoprim. Detection results were at low levels, with an overall median of 0.014 (u or mu)g/L. Hap Cremean WTP had the fewest detections, with two source-water detections of sulfamethoxazole and azithromycin and no detections in the finished water. Of the total of 61 detections, 31 were in the winter sample run. Sulfamethoxazale and azithromycin detections represent 41 percent of all antibiotic detections. Azithromycin was detected only in the winter sample. Some antibiotics, such as those in the quinoline and tetracycline families, dissipate more quickly in warm water, which may explain why they were detected in the cool months (winter, spring, and fall) and not in the summer. Antibiotic data collected during this study were compared to antibiotic data collected in previous national, regional, and local studies. Many of the same antibiotic compounds detected in the upper Scioto River Basin also were detected in those investigations.

Ohio↗

USGS2025

Assessment of treated wastewater infiltration in Bright Angel Wash and the potential for contaminants of emerging concern influencing spring water quality along the South Rim of the Grand Canyon in Grand Canyon National Park, Arizona

In April 2021, a synoptic study conducted by the U.S. Geological Survey (USGS) and National Park Service (NPS) identified wastewater-related contaminants of emerging concern (CECs) in springs along the South Rim of the Grand Canyon. These springs are located north of Bright Angel Wash, an ephemeral channel that receives treated effluent from the South Rim Wastewater Treatment Plant (SRWTP). Although water flows southwest and away from the canyon, there is evidence that treated wastewater is finding a flow path along fractures associated with the Bright Angel Fault back to water sources along the South Rim. The CECs identified during the April 2021 sampling included several per- and polyfluoroalkyl substances (PFAS) and pharmaceutical compounds. The PFAS compounds detected only consisted of perfluoroalkyl acids, and these were only detected at Bright Angel Wash (treated wastewater), Monument Spring, and upper Horn Bedrock Spring. The other five sampled springs (the Salt Creek, Horn East Alluvium, Garden, Pumphouse, and Pipe Springs) had no detections of PFAS compounds. The five perfluoroalkyl acids detected at Monument Spring (in descending order of concentration) were perfluorobutanesulfonic acid (PFBS), perfluoropentanoic acid, perfluorooctanoic acid, perfluorohexanoic acid, and perfluorooctanesulfonic acid. Only the short-chained PFBS and perfluorobutanoic acid compounds were detected at the upper Horn Bedrock Spring. All the same perfluoroalkyl acids were found at Bright Angel Wash, except for PFBS. Monument Spring was the only spring to have detections of pharmaceuticals. The two pharmaceuticals detected at the highest concentrations at Monument Spring were diphenhydramine (antihistamine) and carbamazepine (anticonvulsant or anti-epileptic drug). The other detected pharmaceuticals included (in descending order of concentration) fluconazole (antifungal), sulfamethoxazole (antibiotic), metformin (diabetes drug), tramadol (opioid analgesic), and venlafaxine (antidepressant and nerve pain medication). The same pharmaceuticals were detected in the wastewater at Bright Angel Wash but in greater concentrations. No CEC concentrations measured at Monument Spring exceeded any drinking water standards or human health benchmarks; however, most of the compounds detected have no regulatory standards. Studies of the ecological effects of these compounds show that some of the compounds detected can have endocrine and physiological effects, but generally, effects were observed at concentrations multiple orders of magnitude greater than what was measured during the April 2021 study. Data from 1980 through 2022 retrieved from the Water Quality Portal were combined with data from the one-time synoptic sampling in April 2021 to assess the usefulness of other analytes for identifying a wastewater connection to South Rim springs. Most of the historical water chemistry data showed a statistical difference between samples collected within and east of the Garden Creek watershed and samples collected from locations in watersheds to the west of Garden Creek, including the Horn Creek, Salt Creek, Monument Creek, and Hermit Creek watersheds, which roughly align with the Bright Angel Fault. Most of the historical analytes were inconclusive as potential wastewater tracers, but nitrate, chloride, and gadolinium data possibly support the historical contribution of wastewater to Monument Spring.

Arizona↗

USGS2023

Green turtle fibropapillomatosis: Tumor morphology and growth rate in a rehabilitation setting

Fibropapillomatosis (FP) is a neoplastic disease most often found in green turtles ( Chelonia mydas ). Afflicted turtles are burdened with potentially debilitating tumors concentrated externally on the soft tissues, plastron, and eyes and internally on the lungs, kidneys, and the heart. Clinical signs occur at various levels, ranging from mild disease to severe debilitation. Tumors can both progress and regress in affected turtles, with outcomes ranging from death due to the disease to complete regression. Since its official description in the scientific literature in 1938, tumor growth rates have been rarely documented. In addition, FP tumors come in two very different morphologies; yet, to our knowledge, there have been no quantified differences in growth rates between tumor types. FP tumors are often rugose in texture, with a polypoid to papillomatous morphology, and may or may not be pedunculated. In other cases, tumors are smooth, with a skin-like surface texture and little to no papillose structures. In our study, we assessed growth-rate differences between rugose and smooth tumor morphologies in a rehabilitation setting. We measured average biweekly tumor growth over time in green turtles undergoing rehabilitation at the University of Florida Whitney Laboratory Sea Turtle Hospital in St. Augustine, Florida, and compared growth between rugose and smooth tumors. Our results demonstrate that both rugose and smooth tumors follow a similar active growth progression pattern, but rugose tumors grew at significantly faster rates ( p = 0.013) than smooth ones. We also documented regression across several examined tumors, ranging from −0.19% up to −10.8% average biweekly negative growth. Our study offers a first-ever assessment of differential growth between tumor morphologies and an additional diagnostic feature that may lead to a more comprehensive understanding and treatment of the disease. We support the importance of tumor morphological categorization (rugose versus smooth) being documented in future FP hospital- and field-based health assessments.

Veterinary Sciences↗

USGS2006

Advances in recreational water quality monitoring at Indiana Dunes National Lakeshore

Indiana Dunes has improved its ability to protect the health of swimmers through better science-based management and increased understanding of contaminants. Most research has focused on Escherichia coli and its nature, sources, and distribution because it is widely accepted as an indicator of potential pathogens. Though research on E. coli and recreational water quality is continually generating new information, public beach managers may gain valuable insight into this management issue from our experience at Indiana Dunes. This article reviews one of the longest maintained indicator bacteria monitoring programs in the National Park System, highlights lessons learned, and summarizes research findings that may be of interest to public beach managers.

Park Science↗

USGS2008

Effects of forest harvesting on ecosystem health in the headwaters of the New York City Water Supply, Catskill Mountains, New York

The effects of forest clearcutting and selective harvesting on forest soils, soil and stream water chemistry, forest regrowth, and aquatic communities were studied in four small headwater catchments. This research was conducted to identify the sensitivity of forested ecosystems to forest disturbance in the northeastern United States. The study area was in the headwaters of the Neversink Reservoir watershed, part of the New York City water supply system, in the Catskill Mountains of southeastern New York. Two sub-catchments of the Shelter Creek watershed were selectively harvested, one in its northern half and one more heavily in its southern half in 1995?96, the Dry Creek watershed was clearcut in the winter of 1996?97, and the Clear Creek watershed was left undisturbed and monitored as a control site. Monitoring was conducted from 4 years before the harvests until 4 years after the harvests. Clearcutting caused a large release of nitrate (NO3-) from watershed soils and a concurrent release of inorganic monomeric aluminum (Alim), which is toxic to some aquatic biota. The increased soil NO3- concentrations measured after the harvest could be completely accounted for by the decrease in nitrogen (N) uptake by watershed trees, rather than an increase in N mineralization and nitrification. The large increase in stream water NO3- and Alim concentrations caused 100-percent mortality of caged brook trout (Salvelinus fontinalis) during the first year after the clearcut and adversely affected macroinvertebrate communities for 2 years after the harvest. Nutrient uptake and biomass accumulation increased in uncut mature trees after the two selective harvests. There was no increase in stream-water NO3- or Alim concentrations, and so there were no adverse affects on macroinvertebrate or trout communities. The amount of tree biomass that can be removed without causing a sharp increase in stream-water NO3- and Alim stream-water concentrations is unknown, but probably depends on the history of forest-disturbance and acid deposition and the level of soil acidification. Results of this study indicate that macroinvertebrate and brook trout communities were sensitive to clearcutting and that deer browsing may affect water quality by suppressing forest regeneration and nutrient uptake. Further studies of selective harvests could identify the harvesting threshold below which changes in water quality and soil chemistry are minimized, and nutrient retention is maximized, thus reducing the damage that logging can inflict on stream and aquatic communities.

New York↗

USGS2005

Biomonitoring of Environmental Status and Trends (BEST) Program: Environmental contaminants and their effects on fish in the Columbia River Basin

This project examined and analyzed 560 fish representing eight species from 16 sites in the Columbia River Basin (CRB) from September 1997 to April 1998. Ten of the 16 sampling locations were historical National Contaminant Biomonitoring Program (NCBP) sites where organochlorine and elemental contaminants in fish had been monitored from 1969 through 1986. Five sites were co-located at U.S. Geological Survey (USGS)-National Stream Quality Accounting Network (NASQAN) stations at which water quality is monitored. The sampling location at Marine Park in Vancouver, Washington did not correspond to either of the established monitoring programs. Eight of the sampling locations were located on the Columbia River; three were on the Snake River; two were on the Willamette River, and one site was on each of the Yakima, Salmon and Flathead Rivers. Common carp ( Cyprinus carpio ), black basses ( Micropterus sp. ), and largescale sucker ( Catostomus macrocheilus ) together accounted for 80% of the fish sampled during the study. Fish were weighed and measured then field-examined for external and internal lesions, and liver, spleen, and gonads were weighed to compute somatic indices. Selected tissues and fluids were obtained and preserved for analysis of fish health and reproductive biomarkers. Composite samples of whole fish from each station were grouped by species and gender and analyzed for persistent organic and inorganic contaminants and for dioxin-like activity using H4IIE rat hepatoma cell bioassay.

Columbia River Basin↗

USGS2012

Status and understanding of groundwater quality in the Tahoe-Martis, Central Sierra, and Southern Sierra study units, 2006-2007--California GAMA Priority Basin Project

Groundwater quality in the Tahoe-Martis, Central Sierra, and Southern Sierra study units was investigated as part of the Priority Basin Project of the California Groundwater Ambient Monitoring and Assessment (GAMA) Program. The three study units are located in the Sierra Nevada region of California in parts of Nevada, Placer, El Dorado, Madera, Tulare, and Kern Counties. The GAMA Priority Basin Project is being conducted by the California State Water Resources Control Board, in collaboration with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory. The project was designed to provide statistically robust assessments of untreated groundwater quality within the primary aquifer systems used for drinking water. The primary aquifer systems (hereinafter, primary aquifers) for each study unit are defined by the depth of the screened or open intervals of the wells listed in the California Department of Public Health (CDPH) database of wells used for municipal and community drinking-water supply. The quality of groundwater in shallower or deeper water-bearing zones may differ from that in the primary aquifers; shallower groundwater may be more vulnerable to contamination from the surface. The assessments for the Tahoe-Martis, Central Sierra, and Southern Sierra study units were based on water-quality and ancillary data collected by the USGS from 132 wells in the three study units during 2006 and 2007 and water-quality data reported in the CDPH database. Two types of assessments were made: (1) status, assessment of the current quality of the groundwater resource, and (2) understanding, identification of the natural and human factors affecting groundwater quality. The assessments characterize untreated groundwater quality, not the quality of treated drinking water delivered to consumers by water purveyors. Relative-concentrations (sample concentrations divided by benchmark concentrations) were used for evaluating groundwater quality for those constituents that have Federal or California regulatory or non-regulatory benchmarks for drinking-water quality. A relative-concentration (RC) greater than (>) 1.0 indicates a concentration above a benchmark. RCs for organic constituents (volatile organic compounds and pesticides) and special-interest constituents were classified as "high" (RC > 1.0), "moderate" (1.0 ≥ RC > 0.1), or "low" (RC ≤ 0.1). For inorganic constituents (major ions, trace elements, nutrients, and radioactive constituents), the boundary between low and moderate RCs was set at 0.5. A new metric, aquifer-scale proportion, was used in the status assessment as the primary metric for evaluating regional-scale groundwater quality. High aquifer-scale proportion is defined as the percentage of the area of the primary aquifers with RC > 1.0 for a particular constituent or class of constituents; moderate and low aquifer-scale proportions are defined as the percentages of the area of the primary aquifer with moderate and low RCs, respectively. Percentages are based on an areal rather than a volumetric basis. Two statistical approaches—grid-based, which used one value per grid cell, and spatially weighted, which used multiple values per grid cell—were used to calculate aquifer-scale proportions for individual constituents and classes of constituents. The spatially weighted estimates of high aquifer-scale proportions were within the 90-percent (%) confidence intervals of the grid-based estimates in all cases. The status assessment showed that inorganic constituents had greater high and moderate aquifer-scale proportions than did organic constituents in all three study units. In the Tahoe-Martis study unit, RCs for inorganic constituents with health-based benchmarks (primarily arsenic) were high in 20% of the primary aquifer, moderate in 13%, and low in 67%. In the Central Sierra study unit, aquifer-scale proportions for inorganic constituents with health-based benchmarks (primarily arsenic, uranium, fluoride, and molybdenum) were 41% high, 36% moderate, and 23% low. In the Southern Sierra study unit, 32, 34, and 34% of the primary aquifer had high, moderate, and low RCs of inorganic constituents with health-based benchmarks (primarily arsenic, uranium, fluoride, boron, and nitrate). The high aquifer-scale proportions for inorganic constituents with non-health-based benchmarks were 14, 34, and 24% for the Tahoe-Martis, Central Sierra, and Southern Sierra study units, respectively, and the primary constituent was manganese for all three study units. Organic constituents with health-based benchmarks were not present at high RCs in the primary aquifers of the Central Sierra and Southern Sierra study units, and were present at high RCs in only 1% of the Tahoe-Martis study unit. Moderate aquifer-scale proportions for organic constituents were < 5% in all three study units. Of the 173 organic constituents analyzed, 22 were detected, and of those 22, 17 have health-based benchmarks. Organic constituents were detected in 20, 27, and 40% of the primary aquifers in the Tahoe-Martis, Central Sierra, and Southern Sierra study units, respectively. Four organic constituents had study-unit detection frequencies of > 10%: the trihalomethane chloroform in the Tahoe-Martis study unit; chloroform and the herbicide simazine in the Central Sierra study unit; and chloroform, simazine, the herbicide atrazine, and the solvent perchloroethene in the Southern Sierra study unit. The second component of this study, the understanding assessment, identified the natural and human factors that may have affected groundwater quality in the three study units by evaluating statistical correlations between water-quality constituents and potential explanatory factors. The potential explanatory factors evaluated were land use, septic tank density, climate, relative position in the regional flow system, aquifer lithology, geographic location, well depth and depth to the top of the screened or open interval in the well, groundwater age distribution, pH, and dissolved oxygen concentration. Results of the statistical evaluations were used to explain the occurrence and distribution of constituents in the study units. Aquifer lithology (granitic, metamorphic, sedimentary, or volcanic rocks), groundwater age distribution [modern (recharged since 1952), pre-modern (recharged before 1952), or mixed (containing both modern and pre-modern recharge)], geographic location, pH, and dissolved oxygen were the most significant factors explaining the occurrence patterns of most inorganic constituents. High and moderate RCs of arsenic were associated with pre-modern and mixed-age groundwater and two distinct sets of geochemical conditions: (1) oxic, high-pH conditions, particularly in volcanic rocks, and (2) low-oxygen to anoxic conditions and low- to neutral-pH conditions, particularly in granitic rocks. In granitic and metamorphic rocks, high and moderate RCs of uranium were associated with pre-modern and mixed-age groundwater, low-oxygen to anoxic conditions, and location within parts of the Central Sierra and Southern Sierra study units known to have rocks with anomalously high uranium content compared to other parts of the Sierra Nevada. High and moderate RCs of uranium in sedimentary rocks were associated with pre-modern-age groundwater, oxic and high-pH conditions, and location in the Tahoe Valley South subbasin within the Tahoe-Martis study unit. Land use within 500 meters of the well and groundwater age were the most significant factors explaining occurrence patterns of organic constituents. Herbicide detections were most strongly associated with modern- and mixed-age groundwater from wells with agricultural land use. Trihalomethane detections were most strongly associated with modern- and mixed-age groundwater from wells with > 10% urban land use and (or) septic tank density > 7 tanks per square kilometer. Solvent detections were not significantly related to groundwater age. Eighty-three percent of the wells with modern- or mixed-age groundwater, and 86% of wells with detections of herbicides and (or) THMs had depths to the top of the screened or open interval of < 170 feet. These observations suggest that modern groundwater has infiltrated to depths of approximately 170 feet below land surface. Land use and occurrence of herbicides and solvents were the most significant factors explaining the occurrence of nitrate. Wells with > 5% agricultural land use and detection of a herbicide or solvent had the highest nitrate concentrations. Comparison between observed and predicted detection frequencies of perchlorate suggests that the perchlorate detected at concentrations < 1 microgram per liter likely reflects the distribution of perchlorate under natural conditions, and that the perchlorate detected at higher concentrations may reflect redistribution of originally natural perchlorate salts by irrigation in the agricultural areas of the Southern Sierra study unit.

California↗

USGS2002

Elevated temperature exacerbates Ichthyophonus infections in buffalo sculpin

High incidences of Ichthyophonus hoferi, a parasite primarily of marine and estuarine fishes, have recently been reported in rockfishes and Pacific herring from the eastern North Pacific (Kent et al 2001, Hershberger et al 2002). Taxonomic position of I. hoferi remains unresolved, but recent phylogenetic studies have grouped the organism with Dermocystidium, Psorospermium, the rosette agent of salmonids, and Rhinosporidium in the Mesomycetozoa, a novel clade of protists near the animal-fungal divergence (Herr et al 1999). Genetic differences among isolates from the east coast of North America indicate that more than one species of Ichthyophonus exist (Rand et al 2000), and different species have likely been assigned the same name based on morphological characteristics. Therefore, hereafter in this manuscript, the organism will be referred to as Ichthyophonus .

Fish Health Newsletter↗

USGS2017

Investigation of plastic debris ingestion by four species of sea turtles collected as bycatch in pelagic Pacific longline fisheries

Ingestion of marine debris is an established threat to sea turtles. The amount, type, color and location of ingested plastics in the gastrointestinal tracts of 55 sea turtles from Pacific longline fisheries from 2012 to 2016 were quantified, and compared across species, turtle length, body condition, sex, capture location, season and year. Six approaches for quantifying amounts of ingested plastic strongly correlated with one another and included: number of pieces, mass, volume and surface area of plastics, ratio of plastic mass to body mass, and percentage of the mass of gut contents consisting of plastic. All olive ridley (n = 37), 90% of green (n = 10), 80% of loggerhead (n = 5) and 0% of leatherback (n = 3) turtles had ingested plastic; green turtles ingested significantly more than olive ridleys. Most debris was in the large intestines. No adverse health impacts (intestinal lesions, blockage, or poor body condition) due directly to plastic ingestion were noted.

Marine Pollution Bulletin↗

USGS2013

Status and understanding of groundwater quality in the Madera, Chowchilla Study Unit, 2008: California GAMA Priority Basin Project

Groundwater quality in the approximately 860-square-mile Madera and Chowchilla Subbasins (Madera-Chowchilla study unit) of the San Joaquin Valley Basin was investigated as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The study unit is located in California's Central Valley region in parts of Madera, Merced, and Fresno Counties. The GAMA Priority Basin Project is being conducted by the California State Water Resources Control Board in collaboration with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory. The Project was designed to provide statistically robust assessments of untreated groundwater quality within the primary aquifer systems in California. The primary aquifer system within each study unit is defined by the depth of the perforated or open intervals of the wells listed in the California Department of Public Health (CDPH) database of wells used for municipal and community drinking-water supply. The quality of groundwater in shallower or deeper water-bearing zones may differ from that in the primary aquifer system; shallower groundwater may be more vulnerable to contamination from the surface. The assessments for the Madera-Chowchilla study unit were based on water-quality and ancillary data collected by the USGS from 35 wells during April-May 2008 and water-quality data reported in the CDPH database. Two types of assessments were made: (1) status , assessment of the current quality of the groundwater resource, and (2) understanding , identification of natural factors and human activities affecting groundwater quality. The primary aquifer system is represented by the grid wells, of which 90 percent (%) had depths that ranged from about 200 to 800 feet (ft) below land surface and had depths to the top of perforations that ranged from about 140 to 400 ft below land surface. Relative-concentrations (sample concentrations divided by benchmark concentrations) were used for evaluating groundwater quality for those constituents that have Federal or California regulatory or non-regulatory benchmarks for drinking-water quality. A relative-concentration (RC) greater than 1.0 indicates a concentration above a benchmark. RCs for organic constituents (volatile organic compounds and pesticides) and special-interest constituents (perchlorate) were classified as "high" (RC is greater than 1.0), "moderate" (RC is less than or equal to 1.0 and greater than 0.1), or "low" (RC is less than or equal to 0.1). For inorganic constituents (major and minor ions, trace elements, nutrients, and radioactive constituents), the boundary between low and moderate RCs was set at 0.5. The assessments characterize untreated groundwater quality, not the quality of treated drinking water delivered to consumers by water purveyors; drinking-water benchmarks, and thus relative-concentrations, are used to provide context for the concentrations of constituents measured in groundwater. Aquifer-scale proportion was used in the status assessment as the primary metric for evaluating regional-scale groundwater quality. High aquifer-scale proportion is defined as the percentage of the area of the primary aquifer system with RCs greater than 1.0 for a particular constituent or class of constituents; moderate and low aquifer-scale proportions are defined as the percentages of the area of the primary aquifer system with moderate and low RCs, respectively. Percentages are based on an areal, rather than a volumetric basis. Two statistical approaches--grid-based, which used one value per grid cell, and spatially weighted, which used multiple values per grid cell--were used to calculate aquifer-scale proportions for individual constituents and classes of constituents. The spatially weighted estimates of high aquifer-scale proportions were within the 90% confidence intervals of the grid-based estimates for all constituents except iron. The status assessment showed that inorganic constituents had greater high and moderate aquifer-scale proportions in the Madera-Chowchilla study unit than did organic constituents. RCs for inorganic constituents with health-based benchmarks were high in 37% of the primary aquifer system, moderate in 30%, and low in 33%. The inorganic constituents contributing most to the high aquifer-scale proportion were arsenic (13%), uranium (17%), gross alpha particle activity (20%), nitrate (6.7%), and vanadium (3.3%). RCs for inorganic constituents with non-health-based benchmarks were high in 6.7% of the primary aquifer system, and the constituent contributing most to the high aquifer-scale proportion was total dissolved solids (TDS). RCs for organic constituents with health-based benchmarks were high in 10% of the primary aquifer system, moderate in 3.3%, and low in 40%; organic constituents were not detected in 47% of the primary aquifer system. The fumigant 1,2-dibromo-3-chloropropane (DBCP) was the only organic constituent detected at high RCs. Seven organic constituents were detected in 10% or more of the primary aquifer system: DBCP; the fumigant additive 1,2,3-trichloropropane; the herbicides simazine, atrazine, and diuron; the trihalomethane chloroform; and the solvent tetrachloroethene (PCE). RCs for the special-interest constituent perchlorate were moderate in 20% of the primary aquifer system. The second component of this study, the understanding assessment , identified the natural and human factors that may affect groundwater quality by evaluating statistical correlations between water-quality constituents and potential explanatory factors, such as land use, position relative to important geologic features, groundwater age, well depth, and geochemical conditions in the aquifer. Results of the statistical evaluations were used to explain the distribution of constituents in the study unit. Depth to the top of perforations in the well and groundwater age were the most important explanatory factors for many constituents. High and moderate RCs of nitrate, uranium, and TDS and the presence of herbicides, trihalomethanes, and solvents were all associated with depths to the top of perforations less than 235 ft and modern- and mixed-age groundwater. Positive correlations between uranium, bicarbonate, TDS, and the proportion of calcium and magnesium in the total cations suggest that downward movement of recharge from irrigation water contributed to the elevated concentrations of these constituents in the primary aquifer system. High and moderate RCs of arsenic were associated with depths to the top of perforations greater than 235 ft, mixed- and pre-modern-age groundwater, and location in sediments from the Chowchilla River alluvial fan, suggesting that increased residence time and appropriate aquifer materials were needed for arsenic to accumulate in the groundwater. High and moderate RCs of fumigants were associated with depths to the top of perforations of less than 235 ft and location south of the city of Madera; low RCs of fumigants were detected in wells dispersed across the study unit with a range of depths to top of perforations.

California↗

USGS2006

Sedimentation and Occurrence and Trends of Selected Chemical Constituents in Bottom Sediment, Empire Lake, Cherokee County, Kansas, 1905-2005

For about 100 years (1850-1950), the Tri-State Mining District in parts of southeast Kansas, southwest Missouri, and northeast Oklahoma was one of the primary sources of lead and zinc ore in the world. The mining activity in the Tri-State District has resulted in substantial historical and ongoing input of cadmium, lead, and zinc to the environment including Empire Lake in Cherokee County, southeast Kansas. The environmental contamination caused by the decades of mining activity resulted in southeast Cherokee County being listed on the U.S. Environmental Protection Agency's National Priority List as a superfund hazardous waste site in 1983. To provide some of the information needed to support efforts to restore the ecological health of Empire Lake, a 2-year study was begun by the U.S. Geological Survey in cooperation with the U.S. Fish and Wildlife Service and the Kansas Department of Health and Environment. A combination of sediment-thickness mapping and bottom-sediment coring was used to investigate sediment deposition and the occurrence of cadmium, lead, zinc, and other selected constituents in the bottom sediment of Empire Lake. The total estimated volume and mass of bottom sediment in Empire Lake were 44 million cubic feet and 2,400 million pounds, respectively. Most of the bottom sediment was located in the main body and the Shoal Creek arm of the reservoir. Minimal sedimentation was evident in the Spring River arm of the reservoir. The total mass of cadmium, lead, and zinc in the bottom sediment of Empire Lake was estimated to be 78,000 pounds, 650,000 pounds, and 12 million pounds, respectively. In the bottom sediment of Empire Lake, cadmium concentrations ranged from 7.3 to 76 mg/kg (milligrams per kilogram) with an overall median concentration of 29 mg/kg. Compared to an estimated background concentration of 0.4 mg/kg, the historical mining activity increased the median cadmium concentration by about 7,200 percent. Lead concentrations ranged from 100 to 950 mg/kg with an overall median concentration of 270 mg/kg. Compared to an estimated background concentration of 33 mg/kg, the median lead concentration was increased by about 720 percent as a result of mining activities. The range in zinc concentrations was 1,300 to 13,000 mg/kg with an overall median concentration of 4,900 mg/kg. Compared to an estimated background concentration of 92 mg/kg, the median zinc concentration was increased by about 5,200 percent. Within Empire Lake, the largest sediment concentrations of cadmium, lead, and zinc were measured in the main body of the reservoir. Within the Spring River arm of the reservoir, increased concentrations in the downstream direction likely were the result of tributary inflow from Short Creek, which drains an area that has been substantially affected by historical lead and zinc mining. Compared to nonenforceable sediment-quality guidelines, all Empire Lake sediment samples (representing 21 coring sites) had cadmium concentrations that exceeded the probable-effects guideline (4.98 mg/kg), which represents the concentration above which toxic biological effects usually or frequently occur. With one exception, cadmium concentrations exceeded the probable-effects guideline by about 180 to about 1,400 percent. With one exception, all sediment samples had lead concentrations that exceeded the probable-effects guideline (128 mg/kg) by about 10 to about 640 percent. All sediment samples had zinc concentrations that exceeded the probable-effects guideline (459 mg/kg) by about 180 to about 2,700 percent. Overall, cadmium, lead, and zinc concentrations in the bottom sediment of Empire Lake have decreased over time following the end of lead and zinc mining in the area. However, the concentrations in the most recently deposited bottom sediment (determined for 4 of 21 coring sites) still exceeded the probable-effects guideline by about 440 to 640 percent for cadmium, about 40 to 80 percent for lead, and about 580

Scientific Investigations Report↗

USGS1978

Influence of laying on lead accumulation in bone of mallard ducks

Paired mallard ducks (Anas platyrhynchos) were given No. 4 lead shot, and bone lead concentrations were compared in drakes and in laying and nonlaying hens. Lead accumulation was significantly greater in bones with a high medullary content (femur and sternum) compared with bones with a lower medullary content (ulna-radius or wingbones). In dosed groups, hens always contained higher bone lead residues than drakes. After dosage with one shot (approximately 200 mg lead), lead in femurs of laying hens averaged 488.4 ppm compared with 113.6 ppm in nonlaying hens. Femurs of drakes averaged 9.4 ppm lead. Dosage with the second lead shot did not result in further accumulation of bone lead in hens, but increased bone lead concentrations threefold in drakes, suggesting that saturation levels for bone lead had already been reached in the hens after ingestion of one shot. There was no demonstrable relationship between egg production and bone lead residues. The high lead residues, found in medullary bones of laying hens indicate that sex and physiological condition are major factors influencing lead absorption by bone.

Journal of Toxicology and Environmental Health↗

USGS2014

Urban ecosystem services and decision making for a green Philadelphia

Traditional approaches to urban development often do not account for, or recognize, the role of ecosystem services and the benefits these services provide to the health and well-being of city residents. Without such accounting, urban ecosystem services are likely to be degraded over time, with negative consequences for the sustainability of cities and the well-being of their residents (Millennium Ecosystem Assessment, 2005; Hirsch, 2008). On May 23, 2013, the Spatial Integration Laboratory for Urban Systems (SILUS), a collaboration between the U.S. Geological Survey (USGS) Science and Decisions Center and the Wharton GIS Lab, convened a one-day symposium—Urban Ecosystem Services and Decision Making: A Green Philadelphia—at the University of Pennsylvania in Philadelphia, Pennsylvania, to examine the role of green infrastructure in the environmental, economic, and social well-being of cities. Cosponsored by the USGS and the Penn Institute for Urban Research (Penn IUR), the symposium brought together policymakers, practitioners, and researchers from a range of disciplines to advance a research agenda on the use of science in public decision making to inform investment in green infrastructure and ecosystem services in urban areas. The city of Philadelphia has recently implemented a program designed to sustain urban ecosystem services and advance the use of green infrastructure. In 2009, the Philadelphia Mayor’s Office of Sustainability launched its Greenworks plan, establishing a citywide sustainability strategy. Major contributions towards its goals are being implemented in coordination with the Philadelphia Water Department (PWD). The Green City, Clean Waters initiative, the city’s nationally recognized stormwater management plan, was signed into action with the U.S. Environmental Protection Agency (EPA) in April 2012. The plan outlines a 25-year strategy to use green infrastructure to protect and improve the city’s watershed. Widespread support for the plan marks a citywide effort to factor environmental quality concerns into the city’s strategic planning, choosing to replace expensive and aging grey infrastructure, with innovative and resilient green infrastructure. The symposium focused on these city of Philadelphia initiatives and also on two new Federal- local partnership programs: America’s Great Outdoors, initiated to promote conservation and recreation, and the Urban Waters Federal Partnership, a multiagency effort to reconnect urban communities to their waterways. A second goal of the symposium was to advance a research agenda on urban ecosystem services. While there has been considerable work on ecosystem services, the discussion of the benefits provided by urban ecosystems is not as developed. Benefits range from improved water and air quality to quality of life gains, including aesthetic and recreational considerations. There is also need for additional focused research toward furthering the understanding of the multiple indirect benefits provided by urban ecosystem services (Bolund and Hunhammar, 1999). Moreover, there is a need for a greater understanding of how best to inform local decision making in this area, as local decision makers in cities across the country are increasingly recognizing the importance of developing sustainability measures for their immediate and long-term planning (United States Conference of Mayors, 2005). Approaching these local and regional plans from a holistic perspective has become a guiding principle of sustainability and resiliency. Therefore, there is a need to better understand the gains that have been achieved and to advance a research agenda on ecosystem services going forward. The day’s program included presentations on greening initiatives from the Philadelphia’s Mayor’s Office of Sustainability, as well as discussion about using an urban ecosystem services framework to evaluate these initiatives. Panel sessions included discussion of the Green City, Clean Waters initiative; a dialogue about the management of urban trees and green space; and a conversation addressing the needs for future research.

Pennsylvania↗

USGS2020

Novel circoviruses detected in feces of Sonoran felids

Sonoran felids are threatened by drought and habitat fragmentation. Vector range expansion and anthropogenic factors such as habitat encroachment and climate change are altering viral evolutionary dynamics and exposure. However, little is known about the diversity of viruses present in these populations. Small felid populations with lower genetic diversity are likely to be most threatened with extinction by emerging diseases, as with other selective pressures, due to having less adaptive potential. We used a metagenomic approach to identify novel circoviruses, which may have a negative impact on the population viability, from confirmed bobcat ( Lynx rufus ) and puma ( Puma concolor ) scats collected in Sonora, Mexico. Given some circoviruses are known to cause disease in their hosts, such as porcine and avian circoviruses, we took a non-invasive approach using scat to identify circoviruses in free-roaming bobcats and puma. Three circovirus genomes were determined, and, based on the current species demarcation, they represent two novel species. Phylogenetic analyses reveal that one circovirus species is more closely related to rodent associated circoviruses and the other to bat associated circoviruses, sharing highest genome-wide pairwise identity of approximately 70% and 63%, respectively. At this time, it is unknown whether these scat-derived circoviruses infect felids, their prey, or another organism that might have had contact with the scat in the environment. Further studies should be conducted to elucidate the host of these viruses and assess health impacts in felids

Sonoran Desert↗

USGS2010

Assessment and management of ecological integrity: Chapter 12

Assessing and understanding the impacts of human activities on aquatic ecosystems has long been a focus of ecologists, water resources managers, and fisheries scientists. While traditional fisheries management focused on single-species approaches to enhance fish stocks, there is a growing emphasis on management approaches at community and ecosystem levels. Of course, as fisheries managers shift their attention from narrow (e.g., populations) to broad organizational scales (e.g., communities or ecosystems), ecological processes and management objectives become more complex. At the community level, fisheries managers may strive for a fish assemblage that is complex, persistent, and resilient to disturbance. Aquatic ecosystem level objectives may focus on management for habitat quality and ecological processes, such as nutrient dynamics, productivity, or trophic interactions, but a long-term goal of ecosystem management may be to maintain ecological integrity. However, human users and social, economic, and political demands of fisheries management often result in a reduction of ecological integrity in managed systems, and this conflict presents a principal challenge for the modern fisheries manager. The concepts of biotic integrity and ecological integrity are being applied in fisheries science, natural resource management, and environmental legislation, but explicit definitions of these terms are elusive. Biotic integrity of an ecosystem may be defined as the capability of supporting and maintaining an integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of a natural habitat of the region (Karr and Dudley 1981). Following that, ecological integrity is the summation of chemical, physical, and biological integrity. Thus, the concept of ecological integrity extends beyond fish and represents a holistic approach for ecosystem management that is especially applicable to aquatic systems. The more general term, ecological condition, refers to the state of the physical, chemical, and biological characteristics of the environment and the processes and interactions that connect them. While the concept of ecological integrity may appear unambiguous, its assessment and practice are much less clear. Ecological integrity made its debut in the USA with the Clean Water Act (CWA) of 1972 (Federal Water Pollution Control Act, as amended through Public Law 107–303, November 27, 2002), which states only one objective, “to restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.” This legislation compelled resource managers to focus on chemical pollution from point effluent sources, such as industrial and municipal outflows, as well as give attention to diffuse, chronic, and watershed effects on ecological integrity. Further, the CWA allowed pursuit of restoration programs in degraded water bodies and catalyzed the science and practice of restoration ecology. The term ecosystem health is often raised in discussions of ecological integrity. Perhaps it is natural to anthropomorphize our concern for personal health to ecosystems, so it becomes a useful metaphor for understanding the concept of ecological integrity. However, whether or not an ecosystem should be considered an entity, such as a superorganism, is a debate without end that began with early ecologists and continues today (Clements 1916; Suter 1993; Simon 1999a). Regardless, the ecosystem is indeed a natural unit with a level of organization and properties beyond the collection of those species that occupy it and presents the most appropriate spatial and organizational scale in which to assess and study ecological integrity. Streams and rivers serve as integrators of chemical, physical, and biological conditions across the landscape, and while the theory and practice associated with ecological integrity of aquatic systems is easily applied to flowing waters and is emphasized in this chapter, they are broadly applicable among all aquatic systems.

Book chapter↗

USGS2024

The National Ocean Biodiversity Strategy

President Biden has been clear that the ocean is central to life on Earth. As he has proclaimed, “the ocean powers millions of jobs; feeds and sustains us; and is a rejuvenating source of inspiration, exploration, and recreation.” The Biden-Harris Administration has worked hard to fulfill the President’s goal to protect and conserve at least 30% of U.S. waters by 2030. The ocean faces increased threats from warming, overfishing, increased acidity, and loss of biodiversity. It is now more important than ever to sustain the many benefits that the ocean, coasts, and Great Lakes provide, including food, a favorable climate, recreation, physical and mental health, and for many, a sense of cultural identity. Ocean life represents an irreplaceable heritage, the foundation of a habitable planet, and a vast trove of resources. Keeping our ocean healthy requires reliable information on the changing status of these living organisms, the drivers of biodiversity change, and options for effectively addressing those drivers. Over 2 million species are estimated to live in the ocean, yet only about 240,000 species have been described by scientists. Most of the ocean’s benefits result from those diverse species interacting with one another and the environment they create. To protect and conserve the ocean, we as a nation need to make better use of existing knowledge and prioritize acquiring new biodiversity knowledge to enable better policy and management decisions. The ability to monitor ocean species and habitats has expanded dramatically over the past decade, with innovations in technology, genomics, taxonomy, big data management and sharing, artificial intelligence, and machine learning. Yet large fractions of the U.S. ocean remain almost unknown. The National Ocean Biodiversity Strategy (strategy) reflects the urgent need to leverage these advances. The goals of this strategy must be guided by the nation’s diverse voices and ways of knowing, in order to maximize effective and equitable stewardship of the ocean’s diverse life and its benefits to people. The strategy is intended as a guiding document for government to advance three overarching goals: ● Goal 1: Drive delivery of ocean biodiversity knowledge at the national scale. Objectives include developing an Implementation Plan for achieving the strategy’s three goals; establishing a coordination mechanism to manage the implementation; and documenting gaps in biodiversity knowledge and the benefits of ocean biodiversity to people and economies. ● Goal 2: Strengthen tools and institutions to deliver ocean biodiversity knowledge. Objectives include establishing a robust information pipeline to support indicators and dynamic maps of ocean biodiversity, from the coasts to the deep sea. This pipeline should include expanded observing systems and comprehensive data management; science and technology solutions to accelerate the availability of biodiversity information; and plans to leverage previous investments to rebuild and expand the nation’s human capital and infrastructure to sustain foundational taxonomy and biodiversity science. ● Goal 3: Protect, conserve, restore, and sustainably use ocean biodiversity. Objectives include expanding the collection, delivery, and use of biodiversity knowledge to inform actions that advance ocean protection, conservation, restoration, and sustainable development. Government should lead in establishing and incentivizing diverse partnerships across scales and sectors to implement those actions and should educate and involve the public to discover and value the nation’s diverse ocean life. Achieving these goals will require commitments across society: new federal and private investments, coordination across sectors to address climate and equity challenges, and engagement of Indigenous Knowledge holders and frontline communities as full partners throughout planning and implementation. The Subcommittee on Ocean Science and Technology (SOST) IWG-Biodiversity will begin developing an Implementation Plan to describe and direct specific actions to implement the strategy. Successful implementation of the strategy will harmonize and expand collection and delivery of timely knowledge on ocean life to all of society. The strategy will also enable evidence-based management and protection of the ocean. Advancing the strategy will build human and institutional capital and partnerships that support both existing mandates and new needs to rebuild and sustain biodiversity, achieve healthy ocean ecosystems, and manage living resources. Implementing the strategy will deliver knowledge for monitoring, modeling, forecasting, and assessments that support food security, public health, and cultural values, and that more effectively protect, conserve, and restore nature.

Report↗