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USGS2021

Spatiotemporal methane emission from global reservoirs

Inland aquatic systems, such as reservoirs, contribute substantially to global methane (CH 4 ) emissions; yet are among the most uncertain components of the total CH 4 budget. Reservoirs have received recent attention as they may generate high CH 4 fluxes. Improved quantification of these CH 4 fluxes, particularly their spatiotemporal distribution, is key to realistically incorporating them in CH 4 modeling and budget studies. Here we report on a new global, gridded (0.25° lat × 0.25° lon) study of reservoir CH 4 emissions, accounting for new knowledge regarding reservoir areal extent and distribution, and spatiotemporal emission patterns influenced by diurnal variability, temperature-dependent seasonality, satellite-derived freeze-thaw dynamics, and eco-climatic zone. The results of this new data set comprise daily CH 4 emissions throughout the full annual cycle and show that reservoirs cover 297 × 10 3 km 2 globally and emit 10.1 Tg CH 4 yr −1 (1σ uncertainty range of 7.2–12.9 Tg CH 4 yr −1 ) from diffusive (1.2 Tg CH 4 yr −1 ) and ebullitive (8.9 Tg CH 4 yr −1 ) emission pathways. This analysis of reservoir CH 4 emission addresses multiple gaps and uncertainties in previous studies and represents an important contribution to studies of the global CH 4 budget. The new data sets and methodologies from this study provide a framework to better understand and model the current and future role of reservoirs in the global CH 4 budget and to guide efforts to mitigate reservoir-related CH 4 emissions.

Journal of Geophysical Research: Biogeosciences↗

USGS2008

Summary of Survival Data from Juvenile Coho Salmon in the Klamath River, Northern California, 2007

A study to estimate the effects of Iron Gate Dam discharge on ESA-listed juvenile coho salmon during their seaward migration to the ocean was begun in 2005. Estimates of survival through various reaches of river downstream from the dam were completed in 2006 and 2007 as part of this process. This report describes the estimates of survival during 2007, and is a complement to a similar report from 2006. Further analyses will be included in a separate report. In 2007, a series of models were evaluated to determine what survival and capture probabilities of radio-tagged hatchery fish were in several reaches between Iron Gate Hatchery at river kilometer 309 and a site at river kilometer 33. The results indicate trends in survival among reaches were similar to those found in 2006, but the survival in 2007 was lower than in 2006. The differences in survivals from Iron Gate Hatchery to river kilometer 33 in 2006 (0.653 SE 0.039) and 2007 (0.497 SE 0.044) were caused primarily by differences in survivals upstream from the Scott River. This document is a brief summary of 2007 survival results.

Open-File Report↗

USGS1999

An Overview of the Factors Involved in Evaluating the Geochemical Effects of Highway Runoff on the Environment

Materials washed by rain and snowmelt from highways into adjacent surface waters, ground waters, and ecosystems can pollute water and affect biota. To understand the chemical behavior of any one of these materials and its effects on the environment requires knowledge of the chemistry of the material and how it interacts with other components in the local geochemical system. An integrated watershed approach, therefore, would be the most effective method to assess the effects of highway runoff on local receiving waters. Analysis of one or a few specific contaminants will provide limited and incomplete information and may be misleading in terms of environmental effects. This report addresses the background geochemistry required to model highway runoff and to make realistic assessments of the potential effects of runoff on the environment.

Open-File Report↗

USGS2006

Mapping ground water in three dimensions: An analysis of airborne geophysical surveys of the Upper San Pedro River Basin, Cochise County, southeastern Arizona

This report summarizes the results of two airborne geophysical surveys conducted in the upper San Pedro Valley of southeastern Arizona in 1997 and 1999. The combined surveys cover about 1,000 square kilometers and extend from the Huachuca Mountains on the west to the Mule Mountains and Tombstone Hills on the east and from north of the Babocomari River to near the Mexican border on the south. The surveys included the acquisition of high-resolution magnetic data, which were used to map depth to the crystalline basement rocks underlying the sediments filling the basin. The magnetic inversion results show a complex basement morphology, with sediment thickness in the center of the valley ranging from ~237 meters beneath the city of Sierra Vista to ~1,500 meters beneath Huachuca City and the Palominas area near the Mexican border. The surveys also included acquisition of 60-channel time-domain electromagnetic (EM) data. Extensive quality analyses of these data, including inversion to conductivity vs. depth (conductivity-depth-transform or CDT) profiles and comparisons with electrical well logs, show that the electrical conductor mapped represents the subsurface water-bearing sediments throughout most of the basin. In a few places (notably the mouth of Huachuca Canyon), the reported water table lies above where the electrical conductor places it. These exceptions appear to be due to a combination of outdated water-table information, significant horizontal displacement between the wells and the CDT profiles, and a subtle calibration issue with the CDT algorithm apparent only in areas of highly resistive (very dry) overburden. These occasional disparities appear in less than 5 percent of the surveyed area. Observations show, however, that wells drilled in the thick unsaturated zone along the Huachuca Mountain front eventually intersect water, at which point the water rapidly rises high into the unsaturated zone within the wellbore. This rising of water in a wellbore implies some sort of confinement below the thick unsaturated zone, a confinement that is not identified in the available literature. Occasional disparities notwithstanding, maps of the electrical conductor derived from the airborne EM system provide a synoptic view of the presence of water underlying the upper San Pedro Valley, including its three-dimensional distribution. The EM data even show faults previously only inferred from geologic mapping. The magnetic and electromagnetic data together appear to show the thickness of the sediments, the water in the saturated sediments down to a maximum of about 400 meters depth, and even places where the main ground-water body is not in direct contact with the San Pedro River. However, the geophysical data cannot reveal anything directly about hydraulic conductivity or ground-water flow. Estimating these characteristics requires new hydraulic modeling based in part on this report. One concern to reviewers of this report is the effect that clays may have on the electrical conductor mapped with the airborne geophysical system. Although the water in the basin is unusually conductive, averaging 338 microsiemens per centimeter, reasoning cited below suggests that the contribution of clays to the overall conductivity would be relatively small. Basic principles of sedimentary geology suggest that silts and clays should dominate the center of the basin, while sands and gravels would tend to dominate the margins. Although clay content may increase the amplitude of the observed electrical conductors somewhat, it will not affect the depths to the conductor derived from depth inversions. Further, fine-grained sediments generally have higher porosity and tend to lie toward a basin center, a fact in general agreement with the observed geophysical data.

Arizona↗

USGS1982

Population modeling for furbearer management

The management of furbearers has become increasingly complex as greater demands are placed on their populations. Correspondingly, needs for information to use in management have increased. Inadequate information leads the manager to err on the conservative side; unless the size of the 'harvestable surplus' is known, the population cannot be fully exploited. Conversely, information beyond what is needed becomes an unaffordable luxury. Population modeling has proven useful for organizing information on numerous game animals. Modeling serves to determine if information of the right kind and proper amount is being gathered; systematizes data collection, data interpretation, and decision making; and permits more effective management and better utilization of game populations. This report briefly reviews the principles of population modeling, describes what has been learned from previous modeling efforts on furbearers, and outlines the potential role of population modeling in furbearer management.

Book chapter↗

USGS2015

PRMS-IV, the precipitation-runoff modeling system, version 4

Computer models that simulate the hydrologic cycle at a watershed scale facilitate assessment of variability in climate, biota, geology, and human activities on water availability and flow. This report describes an updated version of the Precipitation-Runoff Modeling System. The Precipitation-Runoff Modeling System is a deterministic, distributed-parameter, physical-process-based modeling system developed to evaluate the response of various combinations of climate and land use on streamflow and general watershed hydrology. Several new model components were developed, and all existing components were updated, to enhance performance and supportability. This report describes the history, application, concepts, organization, and mathematical formulation of the Precipitation-Runoff Modeling System and its model components. This updated version provides improvements in (1) system flexibility for integrated science, (2) verification of conservation of water during simulation, (3) methods for spatial distribution of climate boundary conditions, and (4) methods for simulation of soil-water flow and storage.

Techniques and Methods↗

USGS2006

A guide for using the transient ground-water flow model of the Death Valley regional ground-water flow system, Nevada and California

This report is a guide for executing numerical simulations with the transient ground-water flow model of the Death Valley regional ground-water flow system, Nevada and California using the U.S. Geological Survey modular finite-difference ground-water flow model, MODFLOW-2000. Model inputs, including observations of hydraulic head, discharge, and boundary flows, are summarized. Modification of the DVRFS transient ground-water model is discussed for two common uses of the Death Valley regional ground-water flow system model: predictive pumping scenarios that extend beyond the end of the model simulation period (1998), and model simulations with only steady-state conditions.

Open-File Report↗

USGS2008

Simulation of Flow, Sediment Transport, and Sediment Mobility of the Lower Coeur d'Alene River, Idaho

A one-dimensional sediment-transport model and a multi-dimensional hydraulic and bed shear stress model were developed to investigate the hydraulic, sediment transport, and sediment mobility characteristics of the lower Coeur d?Alene River in northern Idaho. This report documents the development and calibration of those models, as well as the results of model simulations. The one-dimensional sediment-transport model (HEC-6) was developed, calibrated, and used to simulate flow hydraulics and erosion, deposition, and transport of sediment in the lower Coeur d?Alene River. The HEC-6 modeled reach, comprised of 234 cross sections, extends from Enaville, Idaho, on the North Fork of the Coeur d?Alene River and near Pinehurst, Idaho, on the South Fork of the river to near Harrison, Idaho, on the main stem of the river. Bed-sediment samples collected by previous investigators and samples collected for this study in 2005 were used in the model. Sediment discharge curves from a previous study were updated using suspended-sediment samples collected at three sites since April 2000. The HEC-6 was calibrated using river discharge and water-surface elevations measured at five U.S. Geological Survey gaging stations. The calibrated HEC-6 model allowed simulation of management alternatives to assess erosion and deposition from proposed dredging of contaminated streambed sediments in the Dudley reach. Four management alternatives were simulated with HEC-6. Before the start of simulation for these alternatives, seven cross sections in the reach near Dudley, Idaho, were deepened 20 feet?removing about 296,000 cubic yards of sediments?to simulate dredging. Management alternative 1 simulated stage-discharge conditions from 2000, and alternative 2 simulated conditions from 1997. Results from alternatives 1 and 2 indicated that about 6,500 and 12,300 cubic yards, respectively, were deposited in the dredged reach. These figures represent 2 and 4 percent, respectively, of the total volume of dredged sediments removed before the start of simulation. In alternatives 3 and 4, the incoming total sediment discharges from the South Fork of the river were decreased by one-half. Management alternative 3 simulated stage-discharge conditions from 2000, and alternative 4 simulated conditions from 1997. Reducing incoming sediment discharge from the South Fork did not affect the streambed and deposition in the Dudley and downstream reaches, probably because the distance between the South Fork and the Dudley reach is long enough for sediment supply, transport capacity, and channel geometry to be balanced before reaching the Dudley and downstream reaches. Development and calibration of a multi-dimensional hydraulic and bed shear stress model (FASTMECH) allowed simulation of water-surface elevation, depth, velocity, bed shear stress, and sediment mobility in the Dudley reach (5.3 miles). The computational grid incorporated bathymetric and Light Detection and Ranging (LIDAR) data, with a node spacing of about 2.5 meters. With the exception of the fourth FASTMECH calibration simulation, results from the FASTMECH calibration simulations indicated that flow depths, flow velocities, and bed shear stresses increased as river discharge increased. Water-surface elevations in the fourth calibration simulation were about 2 feet higher than those in the other simulations because high lake levels in Coeur d?Alene Lake caused backwater conditions. Average simulated velocities along the thalweg ranged from about 3 to 5.3 feet per second, and maximum simulated velocities ranged from 3.9 to 7 feet per second. In the dredged reach, average simulated velocity along the thalweg ranged from 3.5 to 6 feet per second. The model also simulated several back-eddies (flow reversal); the largest eddy encompassed about one-third of the river width. Average bed shear stresses increased more than 200 percent from the first to the last simulation. Simulated sediment mobility, asses

Scientific Investigations Report↗

USGS2010

Empirical models of wind conditions on Upper Klamath Lake, Oregon

Upper Klamath Lake is a large (230 square kilometers), shallow (mean depth 2.8 meters at full pool) lake in southern Oregon. Lake circulation patterns are driven largely by wind, and the resulting currents affect the water quality and ecology of the lake. To support hydrodynamic modeling of the lake and statistical investigations of the relation between wind and lake water-quality measurements, the U.S. Geological Survey has monitored wind conditions along the lakeshore and at floating raft sites in the middle of the lake since 2005. In order to make the existing wind archive more useful, this report summarizes the development of empirical wind models that serve two purposes: (1) to fill short (on the order of hours or days) wind data gaps at raft sites in the middle of the lake, and (2) to reconstruct, on a daily basis, over periods of months to years, historical wind conditions at U.S. Geological Survey sites prior to 2005. Empirical wind models based on Artificial Neural Network (ANN) and Multivariate-Adaptive Regressive Splines (MARS) algorithms were compared. ANNs were better suited to simulating the 10-minute wind data that are the dependent variables of the gap-filling models, but the simpler MARS algorithm may be adequate to accurately simulate the daily wind data that are the dependent variables of the historical wind models. To further test the accuracy of the gap-filling models, the resulting simulated winds were used to force the hydrodynamic model of the lake, and the resulting simulated currents were compared to measurements from an acoustic Doppler current profiler. The error statistics indicated that the simulation of currents was degraded as compared to when the model was forced with observed winds, but probably is adequate for short gaps in the data of a few days or less. Transport seems to be less affected by the use of the simulated winds in place of observed winds. The simulated tracer concentration was similar between model results when simulated winds were used to force the model, and when observed winds were used to force the model, and differences between the two results did not accumulate over time.

Scientific Investigations Report↗

USGS1994

Application of a Geographic Information System for regridding a ground-water flow model of the Columbia Plateau Regional Aquifer System, Walla Walla River basin, Oregon-Washington

Computerized Geographic Information Systems (GIS) have become viable and valuable tools for managing,analyzing, creating, and displaying data for three-dimensional finite-difference ground-water flow models. Three GIS applications demonstrated in this study are: (1) regridding of data arrays from an existing large-area, low resolution ground-water model to a smaller, high resolution grid; (2) use of GIS techniques for assembly of data-input arrays for a ground-water model; and (3) use of GIS for rapid display of data for verification, for checking of ground-water model output, and for the cre.ation of customized maps for use in reports. The Walla Walla River Basin was selected as the location for the demonstration because (1) data from a low resolution ground-water model (Columbia Plateau Regional Aquifer System Analysis [RASA]) were available and (2) concern for long-term use of water resources for irrigation in the basin. The principal advantage of regridding is that it may provide the ability to more precisely calibrate a model, assuming chat a more detailed coverage of data is available, and to evaluate the numerical errors associated with a particular grid design.Regridding gave about an 8-fold increase in grid-node density.Several FORTRAN programs were developed to load the regridded ground-water data into a finite-difference modular model as model-compatible input files for use in a steady-state model run.To facilitate the checking and validating of the GIS regridding process, maps and tabular reports were produced for each of eight ground-water parameters by model layer. Also, an automated subroutine that was developed to view the model-calculated water levels in cross-section will aid in the synthesis and interpretation of model results.

Water-Resources Investigations Report↗

USGS1984

Ground water in the Fresno area, California; preliminary report

The U.S. Geological Survey, in cooperation with Fresno County, is developing a computer model of the unconfined aquifer system in the Fresno area. In the area, consolidated rocks are overlain by unconsolidated deposits. The unconsolidated deposits are divided into a lower fine-grained unit and an overlying coarse-grained unit. The system is assumed to be a single unconfined unit. The top of the system is the water table and the bottom is the base of the coarse-grained deposits. The northeastern boundary is the only natural lateral hydrologic boundary. The other lateral boundaries are placed so that errors along them will not affect heads in the area of interest. Initial heads for 1943, hydraulic conductivity, and bottom elevations were used in a steady-state model that generated net flux values. It is anticipated that most of the remaining effort will center on model calibration. (USGS)

Water-Resources Investigations Report↗

USGS2020

Calibration of the U.S. Geological Survey National Crustal Model

The U.S. Geological Survey National Crustal Model (NCM) is being developed to include spatially varying estimates of site response in seismic hazard assessments. Primary outputs of the NCM are continuous velocity and density profiles from the Earth’s surface to the mantle transition zone at 410-kilometer (km) depth for each location on a 1-km grid across the conterminous United States. Datasets used to produce the NCM may have a resolution of better than 1 km near the Earth’s surface in some regions, but, with increasing depth, NCM resolution decreases to tens to hundreds of kilometers in the mantle. Basic subsurface information is provided by the NCM geologic framework, thermal model, and petrologic and mineral physics database. In this report, the velocities and densities that can be extracted from the NCM are calibrated through the development of a porosity model based on Biot-Gassmann theory and more than 2,000 compressional- and (or) shear-wave velocity profiles less than 10 km deep from across the conterminous United States and southwestern Canada. Sediment and rock porosities are derived from shear-wave velocity and are found to depend on effective pressure, rock type, and age (for sedimentary and extrusive volcanic deposits). Porosity-effective pressure functions are then estimated for each rock type (and age for sedimentary and extrusive volcanic deposits). Unconsolidated sediments are found to have higher porosities than consolidated units, which have higher porosities than unweathered igneous units; young sedimentary units (for example, Quaternary age units) tend to have higher porosities than older sedimentary units (for example, pre-Cenozoic age units); porosity decreases with increasing effective pressure; and porosities can decrease quickly through the weathered layer of intrusive rocks. Comparing two Los Angeles area velocity models and the U.S. Geological Survey Bay Area velocity model with the NCM, the NCM does a better job on average of reproducing observed shear-wave velocities below 1 km per second because it has less bias and uncertainty. Approaching and above 1 km per second, the NCM tends to underpredict observed shear-wave velocity. Whereas several factors could contribute to this, the primary factor is probably bias in the NCM geologic framework. For example, the NCM will predict lower velocities in places where the depth to bedrock and basement appear shallower in the measured velocity profiles than specified in the NCM geologic framework. With regard to observed compressional-wave velocity and density, the NCM has significantly less bias than California models for the former, especially below 2 km per second, and all models tend to overpredict density for densities less than about 2,200 kilograms per cubic meter.

Open-File Report↗

USGS2009

Groundwater-flow model of the Ozark Plateaus aquifer system, northwestern Arkansas, southeastern Kansas, southwestern Missouri, and northeastern Oklahoma

To assess the effect that increased water use is having on the long-term availability of groundwater within the Ozark Plateaus aquifer system, a groundwater-flow model was developed using MODFLOW 2000 for a model area covering 7,340 square miles for parts of Arkansas, Kansas, Missouri, and Oklahoma. Vertically the model is divided into five units. From top to bottom these units of variable thickness are: the Western Interior Plains confining unit, the Springfield Plateau aquifer, the Ozark confining unit, the Ozark aquifer, and the St. Francois confining unit. Large mined zones contained within the Springfield Plateau aquifer are represented in the model as extensive voids with orders-of-magnitude larger hydraulic conductivity than the adjacent nonmined zones. Water-use data were compiled for the period 1960 to 2006, with the most complete data sets available for the period 1985 to 2006. In 2006, total water use from the Ozark aquifer for Missouri was 87 percent (8,531,520 cubic feet per day) of the total pumped from the Ozark aquifer, with Kansas at 7 percent (727,452 cubic feet per day), and Oklahoma at 6 percent (551,408 cubic feet per day); water use for Arkansas within the model area was minor. Water use in the model from the Springfield Plateau aquifer in 2005 was specified from reported and estimated values as 569,047 cubic feet per day. Calibration of the model was made against average water-level altitudes in the Ozark aquifer for the period 1980 to 1989 and against waterlevel altitudes obtained in 2006 for the Springfield Plateau and Ozark aquifers. Error in simulating water-level altitudes was largest where water-level altitude gradients were largest, particularly near large cones of depression. Groundwater flow within the model area occurs generally from the highlands of the Springfield Plateau in southwestern Missouri toward the west, with localized flow occurring towards rivers and pumping centers including the five largest pumping centers near Joplin, Missouri; Carthage, Missouri; Noel, Missouri; Pittsburg, Kansas; and Miami, Oklahoma. Hypothetical scenarios involving various increases in groundwater-pumping rates were analyzed with the calibrated groundwater-flow model to assess changes in the flow system from 2007 to the year 2057. Pumping rates were increased between 0 and 4 percent per year starting with the 2006 rates for all wells in the model. Sustained pumping at 2006 rates was feasible at the five pumping centers until 2057; however, increases in pumping resulted in dewatering the aquifer and thus pumpage increases were not sustainable in Carthage and Noel for the 1 percent per year pumpage increase and greater hypothetical scenarios, and in Joplin and Miami for the 4 percent per year pumpage increase hypothetical scenarios. Zone-budget analyses were performed to assess the groundwater flow into and out of three zones specified within the Ozark-aquifer layer of the model. The three zones represented the model part of the Ozark aquifer in Kansas (zone 1), Oklahoma (zone 2), and Missouri and Arkansas (zone 3). Groundwater pumping causes substantial reductions in water in storage and induces flow through the Ozark confining unit for all hypothetical scenarios evaluated. Net simulated flow in 2057 from Kansas (zone 1) to Missouri (zone 3) ranges from 74,044 cubic feet per day for 2006 pumping rates (hypothetical scenario 1) to 625,319 cubic feet per day for a 4 percent increase in pumping per year (hypothetical scenario 5). Pumping from wells completed in the Ozark aquifer is the largest component of flow out of zone 3 in Missouri and Arkansas, and varies between 88 to 91 percent of the total flow out of zone 3 for all of the hypothetical scenarios. The largest component of flow into Oklahoma (zone 2) comes from the overlying Ozark confining unit, which is consistently about 45 percent of the total. Flow from the release of water in storage, from general-head boundaries, and from zones 1 and 3 is considerably smaller values that range from 3 to 22 percent of the total flow into zone 2. The largest flow out of the Oklahoma part of the model occurs from pumping from wells and ranges from 52 to 69 percent of the total.

Arkansas, Kansas, Missouri, Oklahoma↗

USGS1991

Use of the Priestley-Taylor evaporation equation for soil water limited conditions in a small forest clearcut

The Priestley-Taylor equation, a simplification of the Penman equation, was used to allow calculations of evapotranspiration under conditions where soil water supply limits evapotranspiration. The Priestley-Taylor coefficient, α, was calculated to incorporate an exponential decrease in evapotranspiration as soil water content decreases. The method is appropriate for use when detailed meteorological measurements are not available. The data required to determine the parameter for the α coefficient are net radiation, soil heat flux, average air temperature, and soil water content. These values can be obtained from measurements or models. The dataset used in this report pertains to a partially vegetated clearcut forest site in southwest Oregon with soil depths ranging from 0.48 to 0.70 m and weathered bedrock below that. Evapotranspiration was estimated using the Bowen ratio method, and the calculated Priestley-Taylor coefficient was fitted to these estimates by nonlinear regression. The calculated Priestley-Taylor coefficient (α′) was found to be approximately 0.9 when the soil was near field capacity (0.225 cm 3 cm −3 ). It was not until soil water content was less than 0.14 cm 3 cm −3 that soil water supply limited evapotranspiration. The soil reached a final residual water content near 0.05 cm 3 cm −3 at the end of the growing season.

Agricultural and Forest Meteorology↗

USGS2022

Greenhouse gas balances in coastal ecosystems: Current challenges in “blue carbon” estimation and significance to national greenhouse gas inventories

Coastal wetlands are defined herein as inundated, vegetated ecosystems with hydrology, and biogeochemistry influenced by sea levels, at timescales of tides to millennia. Coastal wetlands are necessary components of global greenhouse gas estimation and scenario modeling, both for continental and oceanic mass balances. The carbon pools and fluxes on coastal lands, especially those influenced by tidal drivers and sea level rise, are distinct in their magnitude, rates, and uncertainties. We describe herein the pathways taken for a US scale estimation of blue carbon based on annual timesteps and bottom-up modeling, as appropriate for the first effort to include coastal wetlands in the Intergovernmental Panel on Climate Change (IPCC) guidelines for a National Greenhouse Gas Inventory (NGGI). As such, we summarize multiple efforts to reconcile mapping, modeling, and measurement issues and we report the assumptions we made based on data availability. Provided as requested feedback to the IPCC. Subsidiary Body for Scientific and Technological Advice (SBSTA) evaluation of guidance criteria, these analyses synergistically point scientists, practitioners, and policy makers toward the greatest uncertainties to address in future assessments: coastal wetland methane emissions and carbon dioxide emissions associated with the fate of eroded soil. This is a story of what was learned in the 2014–2018 NASA Carbon Monitoring System project (https://carbon.nasa.gov/cgi-bin/cms_projects.pl), how it informs “good practice” (IPCC 2006) in reporting coastal wetland emissions and removals, and where it points scientifically toward data needs at different temporal and spatial scales.

Book chapter↗

USGS2021

Establishment of baseline cytology metrics in nestling American kestrels (Falco sparverius): Immunomodulatory effects of the flame retardant isopropylated triarylphosphate isomers

Avian populations must mount effective immune responses upon exposure to environmental stressors such as avian influenza and xenobiotics. Although multiple immune assays have been tested and applied to various avian species, antibody-mediated immune responses in non-model avian species are not commonly reported due to the lack of commercially available species-specific antibodies. The objectives of the present study were to advance methods for studying wild bird immune responses and to apply these to the evaluation of cytological responses after exposure of American kestrels, Falco sparverius, to a commercial flame retardant mixture containing isopropylated triarylphosphate isomers (ITP). Hatchlings were gavaged daily with safflower oil or 1.5 ug/g bw/day of ITP suspended in safflower oil, then bled on days 9, 17, and 21. The ITP treatment group ( n = 18) and a subset of controls (Poly I:C treatment group; n = 10) were injected on days 9 and 15 with a synthetic analog of viral double-stranded RNA, polyinosinic:polycytidylic acid (Poly I:C), a toll-like receptor ligand and synthetic viral mimic, and responses compared to a sham injected control group (n = 8). The hypotheses tested whether kestrels showed immunological differences among treatment groups, genetic sex, and/or white blood cell (WBC) subpopulation type over time. A flow cytometry (FCM) gating strategy categorized heterophils (H), lymphocytes (L), and monocytes (M) and their proportions, and measured relative fluorescence in response to anti-chicken CD4 binding. Fluorescent cell surfaces and some granular/vacuolar inclusions were visualized by epifluorescence microscopy. A fourth subpopulation with higher levels of granularity than M but less than H became increasingly apparent with time and was gated along with the H subpopulation; its frequency of occurrence was lowest in the ITP group ( P = 0.0023). The percentages of cells differed among treatment groups, days, and sexes ( P = 0.0001). For both sexes, percentages of H and L were higher than M in control and Poly I:C. In the ITP group, L percentages were higher than H and M ( P = 0.0457), and H and L were higher than M on days 9 and 21 ( P = 0.0001). The ratios of H:L and H:WBC, indicators of robust immunity, were also higher on days 9 and 21 than on 17 ( P = 0.0079). For each sex, the highest levels of activity measured by FCM geometric means (GEO) of fluorescence (indicative of antibody binding) were observed on day 9 ( P = 0.0001 female, and P = 0.0011 male) in H over both L and M ( P < 0.0001 for each). In males, GEO of the Poly I:C group was higher than that of the ITP group ( P = 0.0374), with no difference observed among females over all days. By using a FCM algorithm for population comparisons of fluorescence to investigate binding within H, the T(x) scores indicated higher fluorescence in control and Poly I:C groups over ITP ( P = 0.0001). Unlike chickens, Gallus gallus , which express CD4 primarily on L, kestrels bound the commercial antibody primarily within the gated H subpopulation, suggesting an immunophenotypic difference between taxa, despite a ~60% identity of Falco CD4 amino acid sequences with chicken CD4. The emergent cell subset within the gated H presented dendritic-like cell (DLC) morphological and functional properties, apparently serving as an effector cell. This study adds interpretive context to ecological investigations of infection and of potential immunomodulation by emerging compounds, whereby the early innate responses are mediated by the various cell subsets serving as useful quantitative markers of immunological condition. Data showed that dietary exposure to ITP was immunosuppressive for male and female kestrels over the course of the experiment, reducing DLC frequency compared to the Poly I:C controls. Heterophils and DLC were important in facilitating innate immunological responses.

Environment International↗

USGS2009

Thermal characteristics of amphibian microhabitats in a fire-disturbed landscape

Disturbance has long been a central issue in amphibian conservation, often regarding negative effects of logging or other forest management activities, but some amphibians seem to prefer disturbed habitats. After documenting increased use of recently burned forests by boreal toads (Bufo boreas), we hypothesized that burned habitats provided improved thermal opportunities in terrestrial habitats. We tested this hypothesis by conducting a radio telemetry study of habitat use (reported previously) and by using physical models that simulated the temperature of adult toads. We deployed 108 physical models in and adjacent to a 1-year old burn using a fully-replicated design with three burn severities (unburned, partial, high severity) and four microhabitats (open surface, under vegetation, under log, in burrow). Model temperatures were compared to a range of preferred temperatures in published studies. We found 70% more observations within the preferred temperature range of B. boreas in forests burned with high severity than in unburned areas. Burned forest was warmer than unburned forest across all microhabitats, but the largest relative difference was in burrows, which averaged 3 ??C warmer in high-severity burn areas and remained warmer though the night. More than twice as many observations were within the preferred temperature range in high-severity burrows than in unburned burrows. Areas burned with high severity were still warmer than unburned forest 3 years after the fire. Habitat use of toads during the concurrent radio telemetry study matched that predicted by the physical models. These results suggest there are fitness-linked benefits to toads using burned habitats, such as increased growth, fertility, and possibly disease resistance. However, increased soil temperatures that result from wildfire may be detrimental to other amphibian species that prefer cooler temperatures and stable environments. More broadly, our data illustrate the use of physical models to measure and interpret changes that amphibians may experience from disturbance, and highlight the need for research linking vital rates such as growth and survival to disturbance.

Forest Ecology and Management↗

USGS2013

Rapid chemical evolution of tropospheric volcanic emissions from Redoubt Volcano, Alaska, based on observations of ozone and halogen-containing gases

We report results from an observational and modeling study of reactive chemistry in the tropospheric plume emitted by Redoubt Volcano, Alaska. Our measurements include the first observations of Br and I degassing from an Alaskan volcano, the first study of O 3 evolution in a volcanic plume, as well as the first detection of BrO in the plume of a passively degassing Alaskan volcano. This study also represents the first detailed spatially-resolved comparison of measured and modeled O 3 depletion in a volcanic plume. The composition of the plume was measured on June 20, 2010 using base-treated filter packs (for F, Cl, Br, I, and S) at the crater rim and by an instrumented fixed-wing aircraft on June 21 and August 19, 2010. The aircraft was used to track the chemical evolution of the plume up to ~ 30 km downwind (2 h plume travel time) from the volcano and was equipped to make in situ observations of O 3 , water vapor, CO 2 , SO 2 , and H 2 S during both flights plus remote spectroscopic observations of SO 2 and BrO on the August 19th flight. The airborne data from June 21 reveal rapid chemical O 3 destruction in the plume as well as the strong influence chemical heterogeneity in background air had on plume composition. Spectroscopic retrievals from airborne traverses made under the plume on August 19 show that BrO was present ~ 6 km downwind (20 min plume travel time) and in situ measurements revealed several ppbv of O 3 loss near the center of the plume at a similar location downwind. Simulations with the PlumeChem model reproduce the timing and magnitude of the observed O 3 deficits and suggest that autocatalytic release of reactive bromine and in-plume formation of BrO were primarily responsible for the observed O 3 destruction in the plume. The measurements are therefore in general agreement with recent model studies of reactive halogen formation in volcanic plumes, but also show that field studies must pay close attention to variations in the composition of ambient air entrained into volcanic plumes in order to unambiguously attribute observed O 3 anomalies to specific chemical or dynamic processes. Our results suggest that volcanic eruptions in Alaska are sources of reactive halogen species to the subarctic troposphere.

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