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644 records · Page 36Linked to original sources
USGS2024

The skin I live in: Pathogenesis of white-nose syndrome of bats

The emergence of white-nose syndrome (WNS) in North America has resulted in mass mortalities of hibernating bats and total extirpation of local populations. The need to mitigate this disease has stirred a significant body of research to understand its pathogenesis. Pseudogymnoascus destructans , the causative agent of WNS, is a psychrophilic (cold-loving) fungus that resides within the class Leotiomycetes, which contains mainly plant pathogens and is unrelated to other consequential pathogens of animals. In this review, we revisit the unique biology of hibernating bats and P . destructans and provide an updated analysis of the stages and mechanisms of WNS progression. The extreme life history of hibernating bats, the psychrophilic nature of P . destructans , and its evolutionary distance from other well-characterized animal-infecting fungi translate into unique host–pathogen interactions, many of them yet to be discovered.

PLoS Pathogens↗
USGS2025

Virulence evolution of a salmonid virus following a host jump

Emergent viral diseases remain a critical obstacle to welfare across landscapes and species, encompassing humans, wildlife, and agriculture. Following a jump to a novel host, the severity of disease resulting from infection is a critical determinant of the overall emergent pathogen threat. Conventional wisdom posits that virulence, defined here as host mortality, attenuates to intermediate levels as a pathogen adapts to a novel host, but this is largely based on data from just one system, myxoma virus, which was intentionally introduced as a biocontrol agent in rabbits ( Oryctolagus cuniculus ) in mid-1900s Australia. In this study, we demonstrate that infectious hematopoietic necrosis virus (IHNV), which made a host jump from sockeye salmon ( Oncorhynchus nerka , ancestral host) to rainbow trout ( O. mykiss , novel host), has not conformed to classical theory. We quantified virulence in the ancestral and novel hosts using common garden in vivo experiments with 16 archival IHNV isolates collected from 1972-2017, which span the period from shortly after the host jump and the subsequent 45 years of host adaptation. These virus isolates also represent two distinct phylogenetic genogroups, each associated with either the ancestral or novel host. The experiments were replicated across two research facilities, two challenges dosages, and two temperatures. While isolates from the ancestral genogroup showed no temporal change in virulence in either host, isolates from the novel viral genogroup displayed a significant increase in virulence over time in the novel host. Some possible indication of a virus temperature adaption after the host jump was also present. Potential drivers of virulence evolution are discussed. This represents one of only a handful of systems in which the evolution of increased virulence has been empirically characterized after a host jump and subsequent adaptation. It contributes to a growing body of evidence that contradicts the classical case study of myxoma virus attenuation after adaptation.

PLoS Pathogens↗
USGS2023

Utilizing high-resolution genetic markers to track population-level exposure of migratory birds to renewable energy development

With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools, has been estimating the effects from such development on individual breeding populations of migratory birds. To help address this, we utilize a newly developed, high-resolution genetic tagging method to rapidly identify the breeding population of origin of carcasses recovered from renewable energy facilities and combine them with maps of genetic variation across geographic space (called ‘genoscapes’) for five species of migratory birds known to be exposed to energy development, to assess the extent of population-level effects on migratory birds. We demonstrate that most avian remains collected were from the largest populations of a given species. In contrast, those remains from smaller, declining populations made up a smaller percentage of the total number of birds assayed. Results suggest that application of this genetic tagging method can successfully define population-level exposure to renewable energy development and may be a powerful tool to inform future siting and mitigation activities associated with renewable energy programs.

PLOS Sustainability and Transformation↗
USGS2022

Effects of return flows on stream water quality and availability in the Upper Colorado, Delaware, and Illinois River Basins

Understanding effects of human water use and subsequent return flows on the availability and suitability of water for downstream uses is critical to efficient and effective watershed management. We compared spatially detailed estimates of stream chemistry within three watersheds in diverse settings to available standards to isolate effects of wastewater and irrigation return flows on the suitability of downstream waters for maintaining healthy aquatic ecosystems and for selected human uses. Mean-annual flow-weighted total and source-specific concentrations of nitrogen and phosphorus in individual stream reaches within the Upper Colorado, Delaware, and Illinois River Basins and of total dissolved solids within stream reaches of the Upper Colorado River Basin were estimated from previously calibrated regional watershed models. Estimated concentrations of both nitrogen and phosphorus in most stream reaches in all three watersheds (at least 78%, by length) exceed recommended standards for the protection of aquatic ecosystems, although concentrations in relatively few streams exceed such standards due to contributions from wastewater return flows, alone. Consequently, efforts to reduce wastewater nutrient effluent may provide important local downstream benefits but would likely have minimal impact on regional ecological conditions. Similarly, estimated mean-annual flow-weighted total dissolved solids concentrations in the Upper Colorado River Basin exceed standards for agricultural water use and (or) the secondary maximum contaminant level (SMCL) for drinking water in 52% of streams (by length), but rarely due to effects of irrigation return flows, alone. Dissolved solids in most tributaries of the Upper Colorado River are attributable primarily to natural sources.

Upper Colorado, Delaware, and Illinois River Basin↗
USGS2023

Estimated reduction of nitrogen in streams of the Chesapeake Bay in areas with agricultural conservation practices

Spatial data provided by the U.S. Department of Agriculture National Resource Conservation Service representing implementation at the field-level for a selection of agricultural conservation practices were incorporated within a spatially referenced regression model to estimate their effects on nitrogen loads in streams in the Chesapeake Bay watershed. Conservation practices classified as “high-impact” were estimated to be effective ( p = 0.017) at reducing contemporary nitrogen loads to streams of the Chesapeake Bay watershed in areas where groundwater ages are estimated to be less than 14-years old. Watershed-wide, high-impact practices were estimated to reduce nitrogen loads to streams by 1.45%, with up to 60% reductions in areas with shorter groundwater ages and larger amounts of implementation. Effects of “other-impact” practices and practices in areas with groundwater ages of 14 years or more showed less evidence of effectiveness. That the discernable impact of high-impact practices was limited to areas with a median groundwater age of less than 14 years does not imply that conservation practices are not effective in areas with older groundwater ages. A model recalibrated using high-impact agricultural conservation practice data summarized by county suggests effects may also be detectable using implementation data available at such coarser resolution. Despite increasing investment, effects of agricultural conservation practices on regional water quality remain difficult to quantify due to factors such as groundwater travel times, varying modes-of-action, and the general lack of high-quality spatial datasets representing practice implementation.

Chesapeake Bay watershed↗
USGS2023

Arsenic in groundwater in the Grand Canyon region and an evaluation of potential pathways for arsenic contamination of groundwater from breccia pipe uranium mining

The Grand Canyon in northern Arizona is an international tourist destination, a home or sacred place to many Native Americans, and hosts some of the highest-grade uranium deposits in the United States. Although potential contamination of water resources by uranium from mining activities is a concern, other elements commonly associated with these uranium deposits may pose a greater risk to human populations in the area. This study presents an assessment of arsenic in groundwater in the Grand Canyon area. First, sampling results for arsenic are presented and areas with elevated arsenic concentrations are discussed. Potential pathways of groundwater contamination by arsenic from uranium mines are then discussed to elucidate situations and conditions under which elevated concentrations of arsenic might be expected to become mobilized from breccia-pipe uranium mining activities. Results for arsenic in groundwater in the study area were available for 652 samples collected from 230 sites. Arsenic concentrations in groundwater ranged from less than reporting limits in 60 samples to a maximum concentration of 875 μg/L at Pumpkin Spring. About 88% (202) of the sites sampled had a maximum arsenic concentration below the drinking water standard of 10 μg/L. Available data from near former or current breccia-pipe uranium mines in the area indicate limited evidence to-date of mining effects on elevated arsenic in groundwater, although slow groundwater flow paths in the region may result in extended times of decades or more for groundwater to reach discharge locations. Post-mining entry of groundwater into the shaft and underground mine workings, with subsequent transport of metal-enriched groundwater offsite, may be a potential pathway of groundwater arsenic contamination from mining, although concentrations would likely be attenuated by contact with sedimentary rock units and dilution with native groundwater along flow paths. Monitoring of perched groundwater at reclaimed mine sites post-reclamation could provide data on the effectiveness of clean-closure practices on protecting groundwater quality in the area.

Arizona↗
USGS2024

Assessing potential effects of oil and gas development activities on groundwater quality near and overlying the Elk Hills and North Coles Levee Oil Fields, San Joaquin Valley, California

Groundwater resources are utilized near areas of intensive oil and gas development in California’s San Joaquin Valley. In this study, we examined chemical and isotopic data to assess if thermogenic gas or saline water from oil producing formations have mixed with groundwater near the Elk Hills and North Coles Levee Oil Fields in the southwestern San Joaquin Valley. Major ion concentrations and stable isotope compositions were largely consistent with natural processes, including mixing of different recharge sources and water-rock interactions. Trace methane concentrations likely resulted from microbial rather than thermogenic sources. Trace concentrations of benzene and other dissolved hydrocarbons in three wells had uncertain sources that could occur naturally or be derived from oil and gas development activities or other anthropogenic sources. In the mid-1990s, two industrial supply wells had increasing Cl and B concentrations likely explained by mixing with up to 15 percent saline oil-field water injected for disposal in nearby injection disposal wells. Shallow groundwater along the western margin of Buena Vista Lake Bed had elevated Cl, B, and SO 4 concentrations that could be explained by accumulation of salts during natural wetting and drying cycles or, alternatively, legacy surface disposal of saline oil-field water in upgradient ephemeral drainages. This study showed that groundwater had relatively little evidence of thermogenic gas or saline water from oil and gas sources in most parts of the study area. However, the evidence for groundwater mixing with injected disposal water, and possibly legacy surface disposal water, demonstrates produced water management practices as a potential risk factor for groundwater-quality degradation near oil and gas fields. Additional studies in the San Joaquin Valley and elsewhere could improve understanding of such risks by assessing the locations, volumes, and types of produced water disposal practices used during the life of oil fields.

California↗
USGS2024

Salinity or sum of constituents— Methods comparison for computing dissolved solids concentrations in streams of the Upper Colorado River Basin

The Colorado River is an important water source in the southwestern United States and northern Mexico. High concentrations of dissolved solids in the river, sourced mainly from the Upper Colorado River Basin (UCOL), cause hundreds of millions of dollars in damages annually to crops and infrastructure. Determinations of total dissolved solids (TDS) in river and tributary samples often rely on summed concentrations of constituents in solution reported as the sum of constituents (SOC), which includes the bicarbonate concentration converted to the equivalent carbonate mass that would be present as a residue after drying. Alternatively, salinity, similar to SOC but including the entire concentration of bicarbonate in solution, may be used as a measure of dissolved solids. Use of SOC results may under-represent actual dissolved-solids concentrations and loads in streams where bicarbonate is a substantial component of the dissolved solids in solution. The objective of this manuscript is to evaluate the differences between the SOC and salinity determinations of dissolved solids in UCOL streams and rivers. Water-quality data from the U.S. Geological Survey were used to compute salinity concentrations at UCOL stream sites for comparison with SOC determinations. Results from 8,001 samples at 418 UCOL sites indicate a median increase in dissolved solids of 20% (13% and 30%, 25th and 75th percentiles, respectively) using the salinity method compared with SOC results. Differences in dissolved solids attributable to the computational approach for handling bicarbonate at UCOL sites were significantly greater than laboratory variability based on results from 890 replicate analyses. Salinity may be a more useful indicator of water quality than SOC in systems with substantial proportions of bicarbonate in the composition of dissolved solids, including the Colorado River and UCOL sites.

Arizona, Colorado, New Mexico, Utah, Wyoming↗
USGS2025

Quantifying the success of stormwater control measure networks using effective imperviousness

The deleterious effects of directly-connected impervious surfaces on urban streams have been widely recognized. To deal with these effects, the use of stormwater control measures that aim to disconnect impervious surfaces and prevent stormwater from reaching the stream has surged. However, we lack widespread use of consistent metrics that describe how effective these stormwater control measures are for mitigating the effects of untreated stormwater. Using total impervious area neglects the effect of stormwater control measures whereas directly-connected impervious area assumes that stormwater control measures perform perfectly. Comparing the success of stormwater control measures across many watersheds and cities will require use of consistent metrics of effective imperviousness, describing actual performance of stormwater control measures in reducing impervious areas hydraulically connected to the stream. This work applies two published approaches to quantify effective imperviousness, one that measures the frequency of downstream flow disturbances and another that computes parameters from a paired rainfall-runoff regression analysis. We apply these approaches in two settings: 1) two watersheds with new low impact development in Clarksburg, Maryland, USA and 2) five watersheds with stormwater retrofits in Melbourne, Australia. These methods gave largely similar results, with differences in effective imperviousness ranging from 1%-9%. Using these approaches in Clarksburg, the effective imperviousness for the treatment watersheds was 6–12%, whereas the total imperviousness was 33–44% and the directly-connected imperviousness was 0%. In Clarksburg, effective imperviousness better described stream hydrologic and biotic outcomes compared to either total imperviousness or directly-connected imperviousness. In Melbourne, effective imperviousness was a better metric for hydrologic and water quality changes that are likely to provide ecological benefits. In both cases, new development and retrofits, we demonstrate the utility of effective imperviousness metrics for predicting stream outcomes and how these metrics may be used to understand the success of stormwater control measure using a consistent metric.

PLOS Water↗
USGS2025

Using probability difference to compare streamflow information of alternatives for efficient operation of monitoring networks

Efficient operation of streamflow monitoring networks requires investments in technology and labor that provide the greatest benefits from available resources. Economic analyses comparing the costs and benefits from different types of alternatives for monitoring have not been practical to implement. Streamflow information provides a generic measure of benefits that can be incorporated into operational decisions as an objective for monitoring networks. A methodology for comparing how accuracy, monitoring period, and monitoring instead of modeling affects streamflow information is developed from information-theoretic approaches for network design but contributes three novel features: (1) a probability-difference model for conditional probability of monotonically paired variables, (2) explicit discounting of unverified information that may exceed the accuracy of streamflow records, and (3) run analysis to account for non-stationarity in streamflow probabilities. Application of the methodology to the U.S. Geological Survey streamflow monitoring network indicates the value of monitoring period to reduce the uncertainty of streamflow probabilities and, thus, increase streamflow information. The methodology has important limitations, particularly for sites with non-perennial streamflow, but demonstrates that probability difference could be used to evaluate operational alternatives to increase the efficiency of monitoring networks.

PLOS Water↗
USGS2026

Hydrogeology, groundwater salinity distributions, and assessment of the effect of oil-production activities on groundwater in the Midway Valley area, western Kern County, San Joaquin Valley, California

This study seeks to determine the effects of oil field produced water disposal operations and well mechanical integrity issues on groundwater quality in oil fields in the southwest San Joaquin Valley, California. Whereas previous studies used groundwater wells to study shallow aquifers outside the oil fields, this study demonstrates that future approaches may use oil well geophysical logs to map groundwater head gradients, create salinity profiles and document changes in salinity over time in oil field areas with sparse groundwater well data and at depths greater than 330 m. We also incorporate an analysis of well histories to determine potential effects of compromised wellbore seals on changes in aquifer quality that cannot be explained by water disposal practices. Water quality in the aquifers is naturally brackish across most of the area, with better quality groundwater occurring in the eastern part. Geophysical logs are used to determine salinity variations within aquifers including the depth at which TDS exceeds 10,000 mg/L. This depth ranges from 366 m in the northwest to approximately 1,500 m in the southeast. Oil well porosity logs are used to determine water table elevations. These logs indicate the water table slopes south-southeast, showing the predominant groundwater flow direction is from oil field disposal areas toward better quality groundwater east of the oil fields. Geophysical logs show formation resistivity near some disposal facilities has decreased over time, indicating the salinity of the aquifer has increased due to disposal of saline produced water in injection wells and ponds. Oil well history analysis suggests that increased salinity over time in water-saturated sand intervals >1.5 km from disposal facilities may be caused by mechanical failures and/or incomplete borehole seals in poorly constructed or abandoned wellbores prevalent throughout the study area—particularly wells drilled prior to 1930.

California↗
USGS2026

Groundwater quality near an oil field in a stream-dominated recharge setting, California, USA

Alluvial valley aquifers are important sources of water supply in many areas but effects of co-located oil and gas development on these resources have not been widely reported, especially in settings where recharge is dominated by stream infiltration. Interpreting the presence of geochemical indicators in the context of hydrology, geology, and other factors provides a more complete understanding of the relations between groundwater and sources of oil-field fluids and aids in identifying risks associated with oil and gas development. Groundwater and Salinas River water samples were collected in an alluvial valley near the San Ardo Oil Field in Monterey County, California and analyzed for a wide range of dissolved chemical, gas, and isotopic constituents to determine if oil-field fluids (water and gas from oil-producing and non-producing zones) have mixed with fresh groundwater used for supply. Hydraulic gradients, age-dating tracers, and other geochemical indicators show that recharge from the Salinas River has the potential to dilute oil-field fluids that might migrate or seep into the aquifer. Groundwater and Salinas River water collected downgradient of the San Ardo Oil Field showed little or no evidence of mixing with oil-field fluids. Some samples within the oil field contained trace amounts of hydrocarbons or elevated temperatures, indicating that any potential effects from oil-field activities are minor or have been diluted by recharge from the Salinas River. The two samples with the most geochemical evidence of potential mixing with oil-field fluids (SP-18 and GW-17) were collected west of or along the Los Lobos fault, where naturally occurring hydrocarbons are near the land surface. Those samples are also near active or inactive oil-field wells, and so anthropogenic activities and pathways cannot be ruled out as a cause of trace detections of hydrocarbons and elevated temperatures in the aquifer.

California↗
USGS2026

Harmonization of aggregated freshwater biotic data to support continental and global assessment

Biodiversity loss and conservation are increasingly coming into focus in global policy fora, requiring information and assessments at wider spatial and temporal scales than previously considered. However, the monitoring framework required to support such data collection and assessment is lacking in many countries and is not harmonized across countries, hampering these efforts. Aggregation of existing freshwater data offers a solution to the problem of assessing status and trends of ecosystems and biodiversity at large spatial scales in the absence of nationally coordinated monitoring efforts. Analysis of aggregated data from different sources, collected using different protocols and with varying levels of metadata and supporting data, can be challenging and requires decisions regarding data comparability. In this paper, we identify the challenges inherent in harmonizing aggregated freshwater data for analysis, including general concerns related to research goals, spatial and temporal scale, sample selection, sampling effort, and site integrity. We also discuss the challenges related to measured parameters, sampled habitats, sample collection and processing methods, and data integrity for phytoplankton, benthic algae, macrophytes, zooplankton, benthic macroinvertebrates, fish, and supporting variables such as water and sediment chemistry. We provide a workflow to evaluate each of these challenges and make decisions about how best to work with the data. Finally, we review a case study from a large-scale analysis of freshwater data from the circumpolar Arctic region that exemplifies the encountered challenges and the chosen solutions. Through the description of the case study, we provide practical solutions to support aggregation and analysis of existing freshwater data. As global conversations about biodiversity status and trends continue, the demand for large-scale analyses of data from different sources will only grow. In the absence of globally harmonized monitoring, we are faced with the need to ensure comparability of data, making expert judgements where needed to support sound conclusions.

PLOS Water↗
USGS2010

Model-based evaluation of highly and low pathogenic avian influenza dynamics in wild birds

There is growing interest in avian influenza (AI) epidemiology to predict disease risk in wild and domestic birds, and prevent transmission to humans. However, understanding the epidemic dynamics of highly pathogenic (HPAI) viruses remains challenging because they have rarely been detected in wild birds. We used modeling to integrate available scientific information from laboratory and field studies, evaluate AI dynamics in individual hosts and waterfowl populations, and identify key areas for future research. We developed a Susceptible-Exposed-Infectious-Recovered (SEIR) model and used published laboratory challenge studies to estimate epidemiological parameters (rate of infection, latency period, recovery and mortality rates), considering the importance of age classes, and virus pathogenicity. Infectious contact leads to infection and virus shedding within 1–2 days, followed by relatively slower period for recovery or mortality. We found a shorter infectious period for HPAI than low pathogenic (LP) AI, which may explain that HPAI has been much harder to detect than LPAI during surveillance programs. Our model predicted a rapid LPAI epidemic curve, with a median duration of infection of 50–60 days and no fatalities. In contrast, HPAI dynamics had lower prevalence and higher mortality, especially in young birds. Based on field data from LPAI studies, our model suggests to increase surveillance for HPAI in post-breeding areas, because the presence of immunologically naïve young birds is predicted to cause higher HPAI prevalence and bird losses during this season. Our results indicate a better understanding of the transmission, infection, and immunity-related processes is required to refine predictions of AI risk and spread, improve surveillance for HPAI in wild birds, and develop disease control strategies to reduce potential transmission to domestic birds and/or humans.

PLoS ONE↗