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At least 253 records · Page 14Linked to original sources

USGS2023

Assessment of habitat use by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Willamette River Basin, 2020–21

We conducted a field study during 2020–21 to describe habitat use patterns of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) in the mainstem Willamette, McKenzie, and Santiam Rivers and to evaluate how habitat suitability criteria affected the predictive accuracy of a hydraulic habitat model. Two approaches were used to collect habitat use data: a stratified sampling design was used to ensure that a representative sample of available habitats was included in our sampling; and a targeted sampling design was used to collect additional data in habitat cells where juvenile Chinook salmon were observed. Habitat attributes and fish presence data were collected in habitat cells that were approximately 2 square meters during April, June, and July. A total of 632 cells were sampled during the study and included habitat located in the main channel (373 cells), side channels (228 cells), and in alcoves (31 cells). Juvenile Chinook salmon were observed in 42 percent of the cells located in the main channel, 38 percent of the cells located in side channels, and 7 percent of the cells located in alcoves. We used logistic regression to develop resource selection functions for April, June, and July, which produced probability-based predictions of habitat use for juvenile Chinook salmon based on water velocity and water depth. The resource selection functions revealed a habitat shift by juvenile Chinook salmon to locations with higher water velocities and greater water depths from April to July as juvenile Chinook salmon size increased. The resource selection functions that we developed are an important addition to habitat modeling in the Willamette River basin because they were developed from in-basin data, capture seasonal differences in habitat use, and facilitate probability-based estimates of habitat use for juvenile Chinook salmon. These advancements will improve habitat modeling efforts for juvenile Chinook salmon during spring and summer months within the Willamette River.

Oregon↗

USGS2018

Nearshore sediment monitoring for the Stormwater Action Monitoring (SAM) Program, Puget Sound, western Washington

Chemicals such as metals and organics (polychlorinated biphenyl [PCBs], polybrominated diphenyl ethers [PBDEs], polycyclic aromatic hydrocarbons [PAHs], and phthalates) continue to enter Puget Sound, western Washington, from point sources (such as industrial and municipal outfalls) and combined sewer outfalls and non-point sources (such as stormwater runoff). Runoff during storm events has been identified as a major source of contamination entering Puget Sound and has been implicated in the degradation of nearshore habitats and biota. Metals, organic chemicals, and other pollutants are known to accumulate in sediments such as those present along the shoreline of Puget Sound. In addition to chemical contaminants, small plastic particles (known as microplastics), found in marine waters of Puget Sound and suspected of being in aquatic sediments, are a potential concern because they can be ingested by animals and are suspected of transporting sorbed chemicals such as PCBs and metals. The Stormwater Work Group of Puget Sound (SWG) (composed of State and municipal stormwater permittees, and other stakeholders) developed a strategy to address sediment conditions in the nearshore environment of Puget Sound. As part of this strategy, the SWG developed a regional stormwater monitoring strategy designed to inform monitoring requirements in National Pollutant Discharge Elimination System (NPDES) stormwater permits issued by the Washington State Department of Ecology (Ecology). The monitoring program is referred to as the Stormwater Action Monitoring (SAM). The overall focus of the work described in this report is to address one of the goals of SAM, which is to characterize the status, spatial extent, and quality of Puget Sound sediment chemicals in the nearshore urban areas. The nearshore urban areas are defined as areas parallel to established Urban Growth Areas (UGAs) using a spatially balanced probabilistic Generalized Random Tessellation Stratified (GRTS) sampling design. One of the benefits of the GRTS sampling design used for this study is that it allows one to efficiently extrapolate from a relatively small number of sampled nearshore sites to the entire nearshore shoreline within the 2011 defined UGA boundaries of Puget Sound. In addition to characterizing nearshore sediment chemical concentrations, this study also characterized the abundance of microplastics in the nearshore sediment. A total of 41 randomly selected sites were sampled throughout Puget Sound in summer and early autumn of 2016. All sampling sites were located at 6 feet below the Mean Lower Low Water line. The top 2–3 centimeters of sediment were collected using a boat-mounted, pre-cleaned stainless-steel box corer. All chemical samples were sieved to 2 millimeters and placed in appropriate containers for chemical analysis for PCBs, PBDEs, PAHs, phthalates, metals, total organic carbon, and grain size. Pre-sieved sediment samples were stored in glass containers for microplastic analysis. Nearshore sediment chemical concentrations were summarized using numerous statistical approaches to examine the minimum, mean, and maximum concentrations for each of the compounds analyzed and to compare the results to criteria and other nearshore and marine sediment studies. The GRTS sampling design also allowed the authors to assess the percentage of the UGA nearshore environment that did not meet established standards or criteria for each chemical analyzed. Additionally, regression and machine learning statistical analyses were used to examine relations between measured chemical concentrations, and land cover and geologic features at multiple scales within the watersheds adjacent to sampling sites. The influence of marine hydrodynamic factors on nearshore sediment chemical concentrations was statistically evaluated with nonparametric methods by assigning each sampling site to one of five nearshore drift cell types based on its location. The Puget Sound shoreline can be divided into segments, referred to as drift cells, based on the movement of sediment along the shore by waves. Each drift cell type has a unique influence on nearshore sediment transport. The nearshore sediment chemical concentrations for organics and metals generally were low, and in most cases less than Washington State criteria. The concentrations of some PAHs were greater than the criteria, but these exceedances were limited to one or two sites. The results of the probabilistic study design determined that, for the PAHs examined, 96 percent or more of the 1,344 km of shoreline represented by this study had concentrations less than any established criteria. For the remaining organics (PCBs and PBDEs), the probabilistic study design indicates that more than 98 percent of shoreline examined had concentrations less than criteria or proposed standards. For the metals, the results of the study indicate that 100 percent of the nearshore sediment had concentrations less than the criteria. The relations between sediment organic and metal concentrations, and adjacent watershed land cover and the particle size of the samples, were determined to be weakly related. Although weakly related, the particle size of the sediment in a sample typically explained more of the variation in metal concentrations than organics. While the measured watershed attributes adjacent to the sampling sites and sediment size of the samples were weakly related to chemical concentrations, they were significantly related to unique drift cells along the shoreline of Puget Sound known as drift cells. Each drift cell represents a long-term directional transport of sediment from its source to its depositional zone. Sediment chemical concentrations were significantly higher in drift cells with limited sediment movement compared to those with higher sediment transport energy. Microplastics in the nearshore sediment ranged from 0.02 to 0.65 pieces per gram of sediment, with a mean of 0.19 pieces per gram of sediment, and were dominated by small fibers (355–1,000 micrometers). Like chemical concentrations, microplastics concentrations in the nearshore sediment were poorly related to watershed land cover. Although not significantly different, microplastics concentrations generally were higher in the low energy drift cells compared to the high energy drift cells. The results of this study provide a statistically valid status assessment of current nearshore sediment chemical conditions throughout Puget Sound in those areas adjacent to defined UGAs. In addition to the study findings of relatively low concentrations of PCBs, PBDEs, PAHs, phthalates, and metals, the study design provides a statistically valid tool for evaluating changes in these compounds over time if future nearshore sediment assessments are done. Furthermore, the assessment of microplastic abundance represents the first study of its kind that can be used as a benchmark for future evaluations. The results of this study will help inform Ecology in the implementation of monitoring requirements as part of its NPDES stormwater permitting process.

Washington↗

USGS2024

Distribution of yellow crazy ants (Anoplolepis gracilipes) and notes on other ant species at Wake Atoll, 6-21 October, 2023

Wake Atoll, located in the central Pacific Ocean, is a tropical coral atoll comprised of three islands totaling 696 ha of emergent land. Wake Atoll supports at least 17 species of non-native ants, but one species, the yellow crazy ant ( Anoplolepis gracilipes ), is especially harmful to ecosystems, including seabirds, which are federally protected species and nest throughout Wake Atoll. Our objective was to map the distribution of yellow crazy ants (YCA) across Wake Atoll to provide U.S. Air Force managers with information that could inform an eradication strategy for this species. In addition, we documented the presence of other ant species identified during our survey. We used a 50 x 50-m cell-based sampling grid to survey for YCA and other ant species. YCA were widespread across the atoll, occupying all three islands and were detected in 566 of the 3,675 (15.4%) cells surveyed, covering an area of about 142 ha. The highest proportion of cells containing YCA was on Wilkes Island (99 of 400 cells or 24.8%), followed by Wake Island (395 of 2,760 cells or 14.3%) and Peale Island (72 of 518 cells or 14.0%). YCA detections on Wilkes Island were restricted to Wilkes South (99 of 202 cells or 49.0%); no YCA were found on Wilkes North, an important area that supports the most diverse assemblage of nesting seabirds on Wake Atoll. Based on technologies developed to eradicate YCA from Johnston Atoll and elsewhere, eradicating YCA from Wake Atoll appears technically feasible. The occurrence of discrete populations (i.e., clusters of occupied cells separated from other clusters of occupied cells) within and among islands could allow a stepwise strategy where the short-term outcome of the treatment of one population is independent of the outcome of another treatment. Without action, the high-density YCA population on Wilkes South could breach the narrow (~50 m), sometimes dry, channel separating Wilkes North and South, posing a serious threat to nesting seabirds present on Wilkes North. Eradicating YCA from Wilkes South would create a buffer from YCA and reduce the threat of northward movement of YCA. We also detected 12 ant species other than YCA during our survey, including Lepisiota frauenfeldi , a new record for the atoll.

Hawaii Cooperative Studies Unit Technical Report↗

USGS2011

Toxic effects of dietary methylmercury on immune system development in nestling American kestrels ( Falco sparverius )

This study evaluated the effects of dietary methylmercury (MeHg) on immune system development in captive-reared nestling American kestrels ( Falco sparverius ) to determine whether T cell–mediated and antibody-mediated adaptive immunity are targets for MeHg toxicity at environmentally relevant concentrations. Nestlings received various diets, including 0 (control), 0.6, and 3.9 μg/g (dry wt) MeHg for up to 18 d posthatch. Immunotoxicity endpoints included cell-mediated immunity (CMI) using the phytohemagglutinin (PHA) skin-swelling assay and antibody-mediated immune response via the sheep red blood cell (SRBC) hemagglutination assay. T cell– and B cell–dependent histological parameters in the spleen, thymus, and bursa of Fabricius were correlated with the functional assays. For nestlings in the 0.6 and 3.9 μg/g MeHg groups, CMI was suppressed by 73 and 62%, respectively, at 11 d of age. Results of this functional assay were correlated with T cell–dependent components of the spleen and thymus. Dose-dependent lymphoid depletion in spleen tissue directly affected the proliferation of T-lymphocyte populations, insofar as lower stimulation indexes from the PHA assay occurred in nestlings with lower proportions of splenic white pulp and higher THg concentrations. Nestlings in the 3.9 μg/g group also exhibited lymphoid depletion and a lack of macrophage activity in the thymus. Methylmercury did not have a noticeable effect on antibody-mediated immune function or B cell–dependent histological correlates. We conclude that T cell–mediated immunosuppression is the primary target of MeHg toward adaptive immunity in developing kestrels. This study provides evidence that environmentally relevant concentrations of MeHg may compromise immunocompetence in a developing terrestrial predator and raises concern regarding the long-term health effects of kestrels that were exposed to dietary MeHg during early avian development.

Environmental Toxicology and Chemistry↗

USGS1982

The memory of the accreting plate boundary and the continuity of fracture zones

A detailed aeromagnetic anomaly map of the Mesozoic seafloor-spreading lineations southwest of Bermuda reveals the dominant magnetic grain of the oceanic crust and the character of the accreting boundary at the time of crustal formation. The magnetic anomaly pattern is that of a series of elongate lobes perpendicular to the fracture zone (flowline) trends. The linear sets of magnetic anomaly peaks and troughs have narrow regions of reduced amplitude anomalies associated with the fracture zones. During the period of Mesozoic geomagnetic polarity reversals (when 1200 km of central North Atlantic seafloor formed), the Atlantic accreting boundary consisted of stationary, elongate, spreading center cells that maintained their independence even though sometimes only minor spatial offsets existed between cells. Normal oceanic crustal structure was formed in the spreading center cells, but structural anomalies and discontinuities characteristic of fracture zones were formed at their boundaries, which parallel flowlines of Mesozoic relative plate motion in the central North Atlantic. We suggest that the memory for a stationary pattern of independent spreading center cells resides in the young brittle lithosphere at the accreting boundary where the lithosphere is weakest; here, each spreading center cell independently goes through its cylce of stress buildup, stress release, and crustal accretion, after which its memory is refreshed. The temporal offset between the peaks of the accretionary activity that takes place within each cell may provide the mechanism for maintaining the independence of adjacent spreading center cells through times when no spatial offset between the cells exists.

Earth and Planetary Science Letters↗

USGS2022

Hot, wet and rare: Modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad

Context: Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. Aims: We sought to model the occupancy dynamics of the Dixie Valley toad ( Anaxyrus williamsi ), a recently described species endemic to a small desert spring wetland complex in Nevada, USA. Methods: We divided the species’ range into 20 m × 20 m cells and surveyed for Dixie Valley toads at 60 cells during six primary periods from 2018 to 2021, following an occupancy study design. We analysed our survey data by using a multi-state dynamic occupancy model to estimate the probability of adult occurrence, colonisation, site survival, and larval occurrence and the relationship of each to environmental covariates. Key results: The detection probabilities of adult and larval toads were affected by survey length and time of day. Adult Dixie Valley toads were widely distributed, with detections in 75% of surveyed cells at some point during the 3-year study, whereas larvae were observed only in 20% of cells during the study. Dixie Valley toad larvae were more likely to occur in cells far from spring heads with a high coverage of surface water, low emergent vegetation cover, and water temperatures between 20°C and 28°C. Adult toads were more likely to occur in cells with a greater coverage of surface water and water depth >10 cm. Cells with more emergent vegetation cover and surface water were more likely to be colonised by adult toads. Conclusions: Our results showed that Dixie Valley toads are highly dependent on surface water in both spring and autumn. Adults and larvae require different environmental conditions, with larvae occurring farther from spring heads and in fewer cells. Implications: Disturbances to the hydrology of the desert spring wetlands in Dixie Valley could threaten the persistence of this narrowly distributed toad.

Wildlife Research↗

USGS2025

A regional model comparison between MODPATH and MT3D of groundwater travel time distributions

Groundwater quality changes in wells and streams lag behind changes to land use due to groundwater travel times. Two contaminant transport methods were compared to assess differences in their simulated travel time distributions (TTDs) to streams and wells in the Wisconsin Central Sands. MODPATH simulates advective groundwater flow with particle tracking, while MT3D simulates age-mass using a finite difference solution without dispersion to allow for direct comparison of the two methods. MODPATH appropriately simulates groundwater TTDs from the water table to surface discharge but is subject to inaccuracies at weak-sink well cells due to the flow-model grid discretization and imprecise location of well discharge within well cells. MT3D better represents weak-sink well cells since it removes mass in proportion to the prescribed pumping rate, although travel time within well cells is neglected. Conversely, MT3D's treatment of surface water boundary cells is not as accurate as MODPATH because mass should be removed from the water table rather than the full cell volume. MT3D simulations of TTDs can also be confounded by the instantaneous vertical distribution of mass introduced throughout recharge cells instead of at the water table, which initiates mass along deeper flow paths. We evaluated 9 MODPATH and 13 MT3D implementations, generating differences in median travel times of up to 18 years. Both methods have strengths and weaknesses, with MT3D better representing weak-sink well cell behavior and MODPATH better representing surficial recharge and discharge. The effect of these characteristics on simulated TTDs, along with ideas for ameliorating method weaknesses, is discussed.

Wisconsin↗

USGS2014

Geographic information system (GIS)-based maps of Appalachian basin oil and gas fields

One of the more recent maps of Appalachian basin oil and gas fields (and the adjoining Black Warrior basin) is the U.S. Geological Survey (USGS) compilation by Mast and others (1998) (see Trippi and others, this volume, chap. I.1). This map is part of a larger oil and gas field map for the conterminous United States that was derived by Mast and others (1998) from the Well History Control System (WHCS) database of Petroleum Information, Inc. (now IHS Energy Group). Rather than constructing the map from the approximately 500,000 proprietary wells in the Appalachian and Black Warrior part of the WHCS database, Mast and others (1998) subdivided the region into a grid of 1-mi 2 (square mile) cells and allocated an appropriate type of hydrocarbon production (oil production, gas production, oil and gas production, or explored but no production) to each cell. Each 1-mi 2 cell contains from 0 to 5 or more exploratory and (or) development wells. For example, if the wells in the 1-mi 2 cell consisted of three oil wells, one gas well, and one dry well, then the cell would be characterized on the map as an area of oil and gas production. The map by Mast and others (1998) accurately shows the distribution and types of hydrocarbon accumulation in the Appalachian and Black Warrior basins, but it does not show the names of individual fields. To determine the locality and name of individual oil and gas fields, one must refer to State oil and gas maps (for example, Harper and others, 1982), which are generally published at scales of 1:250,000 or 1:500,000 (see References Cited), and (or) published journal articles. Other recent USGS Appalachian basin oil and gas field maps show the distribution of oil and gas production with a cell size as small as 0.25 mi 2 , such as the maps converted by Trippi and others (this volume, chap. I.1) from proprietary well-location maps used in the USGS 2002 assessment of oil and gas resources of the Appalachian basin (Milici and others, 2003). Another set of Appalachian basin oil and gas cell maps (based on a cell size of 0.25 mi 2 ) was created for the USGS 1995 National Assessment of United States Oil and Gas Resources (Gautier and others, 1995; Beeman and others, 1996). Between 1991 and 1994, R.T. Ryder (with R.E. Mattick, J.B. Roen, and J.R. San Filipo, USGS, Reston, Va.) compiled oil and gas fields on stable-base mylar greenline base maps (scale 1:500,000) for selected plays in the Appalachian basin. These map compilations included field names and field numbers where assigned by State agencies. The purpose of the maps was to provide supporting data for the USGS 1995 National Assessment of United States Oil and Gas Resources (Gautier and others, 1995). In particular, the greenline oil and gas field maps were linked, where possible, with production data from State records and (or) published literature in order to determine ultimate sizes for conventional fields and estimated ultimate recovery (EUR) values for wells in continuous accumulations (for definitions of the conventional and continuous terminology, see USGS National Oil and Gas Assessment Team, 1995; Schmoker, 1997; Schenk and Pollastro, 2002). This approach was used in the 1995 national oil and gas assessment because ultimate field size and EUR data were unavailable in the Appalachian region from Petroleum Information, Inc., and other commercial sources. In 2006 and 2007, the greenline Appalachian basin field maps were digitized under the supervision of Scott Kinney and converted to geographic information system (GIS) files for chapter I.1 (this volume). By converting these oil and gas field maps to a digital format and maintaining the field names where noted, they are now available for a variety of oil and gas and possibly carbon-dioxide sequestration projects. Having historical names assigned to known digitized conventional fields provides a convenient classification scheme into which cumulative production and ultimate field-size databases can be organized. Moreover, as exploratory and development drilling expands across the basin, many previously named fields that were originally treated as conventional fields have evolved into large, commonly unnamed continuous-type accumulations. These new digital maps will facilitate a comparison between EUR values from recently drilled, unnamed parts of continuous accumulations and EUR values from named fields discovered early during the exploration cycle of continuous accumulations.

Appalachian basin↗

USGS2018

Volume-weighted particle-tracking method for solute-transport modeling; Implementation in MODFLOW–GWT

In the traditional method of characteristics for groundwater solute-transport models, advective transport is represented by moving particles that track concentration. This approach can lead to global mass-balance problems because in models of aquifers having complex boundary conditions and heterogeneous properties, particles can originate in cells having different pore volumes and (or) be introduced (or removed) at cells representing fluid sources (or sinks) of varying strengths. Use of volume-weighted particles means that each particle tracks solute mass. In source or sink cells, the changes in particle weights will match the volume of water added or removed through external fluxes. This enables the new method to conserve mass in source or sink cells as well as globally. This approach also leads to potential efficiencies by allowing the number of particles per cell to vary spatially—using more particles where concentration gradients are high and fewer where gradients are low. The approach also eliminates the need for the model user to have to distinguish between “weak” and “strong” fluid source (or sink) cells. The new model determines whether solute mass added by fluid sources in a cell should be represented by (1) new particles having weights representing appropriate fractions of the volume of water added by the source, or (2) distributing the solute mass added over all particles already in the source cell. The first option is more appropriate for the condition of a strong source; the latter option is more appropriate for a weak source. At sinks, decisions whether or not to remove a particle are replaced by a reduction in particle weight in proportion to the volume of water removed. A number of test cases demonstrate that the new method works well and conserves mass. The method is incorporated into a new version of the U.S. Geological Survey’s MODFLOW–GWT solute-transport model.

Techniques and Methods↗

USGS1997

Hydrologic disturbance and response of aquatic biota in Big Darby Creek basin, Ohio

Washout and recolonization of macroinvertebrates and algae associated with a spring and summer storm were measured at three sites in Ohio's Big Darby Creek Basin. Related factors, such as streamflow magnitude, shear stress, and streamed disturbance were considered when interpreting observed changes in densities and community structure of macroinvertebrates and algae. During the study, 184 macroinvertebrate taxa and 202 algal taxa were identified. The major taxonomic groups for macroinvertebrates were midges and other true flies (Diptera), caddisflies (Trichoptera), beetles (Coleoptera), mayflies (Ephemeroptera), and stoneflies (Plecoptera). Diatoms were the dominant algae (in terms of percentage of total taxa found) followed by green algae, blue-green algae, euglenoids, golden flagellates, and freshwater red algae. Streamflows associated with the storm events that occurred during April 6-16 and June 23-July 5, 1994, probably had little effect on streambed elevations, but streambed disturbance was documented in the form of shifts in the median particle-size diameters of the subsurface bed materials. The streamflow magnitudes did not correlate well with the magnitude of observed changes in macroinvertebrate and algal-cell densities, but reductions in macroinvertebrate and algal-cell densities generally did occur. Local minima of macroinvertebrate density did not generally correspond to the first sample after the storms, but instead lagged by about 1 to 3 weeks. Other biotic factors, such as emergence of Diptera, probably affected the observed mid-July depression in macroinvertebrate densities. Evaluation of pre-event macroinvertebrate community structure in terms of functional feeding groups and flow-exposure groups showed that, on the basis of percentage of total taxa found, gatherers were the dominant feeding group and flow-facultative taxa were the dominant flow-exposure group. Densities of gatherers decreased from pre-event levels following all the storm events at all sites, whereas flow-facultative and flow-avoiding taxa were significantly reduced only after the summer event at Big and Little Darby Creeks. Algal-cell densities in the first post-event samples always were lower than pre-event densities; however, the total number of taxa present generally were not statistically different. In four out of five of the first post-event samples, algal-cell densities were only 16 to 26 percent of the pre-event densities. The exception was at Little Darby Creek after the spring event, where only the density of stalked algal cells in the community were significantly reduced. The observed resistance to disturbance of the algal community at Little Darby Creek may have resulted from the relative abundance of the mat-forming blue-green algae Oscillatoria spp. The stalked cells were the most consistently reduced in the post-event-samples, whereas holdfast types (such as Audouinella hermannii) and prostrate epiphytes (such as Cocconeis spp) were the most resistant to washout. Algal recolonization rates, measured as the change in algal-cell densities over a 7-day period after the summer storm event, ranged from 0.05 to 1.51 billion cells per square meter per day. These recolonization rates are expected to be affected by factors such as nutrients, temperature, amount of canopy, initial post-event algal density, and grazing by macroinvertebrates and fish. On the basis of canopy and nutrient data, one would expect the algal recolonization rates for the three sites in this study to sort in the order observed.

Water-Resources Investigations Report↗

USGS2018

Rhizophagy cycle: An oxidative process in plants for nutrient extraction from symbiotic microbes

In this paper, we describe a mechanism for the transfer of nutrients from symbiotic microbes (bacteria and fungi) to host plant roots that we term the ‘rhizophagy cycle.’ In the rhizophagy cycle, microbes alternate between a root intracellular endophytic phase and a free-living soil phase. Microbes acquire soil nutrients in the free-living soil phase; nutrients are extracted through exposure to host-produced reactive oxygen in the intracellular endophytic phase. We conducted experiments on several seed-vectored microbes in several host species. We found that initially the symbiotic microbes grow on the rhizoplane in the exudate zone adjacent the root meristem. Microbes enter root tip meristem cells—locating within the periplasmic spaces between cell wall and plasma membrane. In the periplasmic spaces of root cells, microbes convert to wall-less protoplast forms. As root cells mature, microbes continue to be subjected to reactive oxygen (superoxide) produced by NADPH oxidases (NOX) on the root cell plasma membranes. Reactive oxygen degrades some of the intracellular microbes, also likely inducing electrolyte leakage from microbes—effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation and as hairs elongate bacteria exit at the hair tips, reforming cell walls and cell shapes as microbes emerge into the rhizosphere where they may obtain additional nutrients. Precisely what nutrients are transferred through rhizophagy or how important this process is for nutrient acquisition is still unknown.

Microorganisms↗

USGS2012

Patterns of surface burrow plugging in a colony of black-tailed prairie dogs occupied by black-footed ferrets

Black-tailed prairie dogs ( Cynomys ludovicianus ) can surface-plug openings to a burrow occupied by a black-footed ferret ( Mustela nigripes ). At a coarse scale, surface plugs are more common in colonies of prairie dogs occupied by ferrets than in colonies without ferrets. However, little is known about spatial and temporal patterns of surface plugging in a colony occupied by ferrets. In a 452-ha colony of black-tailed prairie dogs in South Dakota, we sampled burrow openings for surface plugs and related those data to locations of ferrets observed during spotlight surveys. Of 67,574 burrow openings in the colony between June and September 2007, 3.7% were plugged. In a colony-wide grid of 80 m × 80 m cells, the occurrence of surface plugging (≥1 opening plugged) was greater in cells used by ferrets (93.3% of cells) than in cells not observably used by ferrets (70.6%). Rates of surface plugging (percentages of openings plugged) were significantly higher in cells used by ferrets (median = 3.7%) than in cells without known ferret use (median = 3.2%). Also, numbers of ferret locations in cells correlated positively with numbers of mapped surface plugs in the cells. To investigate surface plugging at finer temporal and spatial scales, we compared rates of surface plugging in 20-m-radius circle-plots centered on ferret locations and in random plots 1–4 days after observing a ferret (Jun–Oct 2007 and 2008). Rates of surface plugging were greater in ferret-plots (median = 12.0%) than in random plots (median = 0%). For prairie dogs and their associates, the implications of surface plugging could be numerous. For instance, ferrets must dig to exit or enter plugged burrows (suggesting energetic costs), and surface plugs might influence microclimates in burrows and consequently influence species that cannot excavate soil (e.g., fleas that transmit the plague bacterium Yersinia pestis ).

South Dakota↗

USGS1996

In vivo/in vitro comparison of pharmacokinetics and pharmacodynamics of 3,3',4,4'-tetrachlorobiphenyl (PCB77)

The rat hepatoma cell line, H4IIE, serves as a useful tool to assess potential biological effects such as induction of cytochrome P4501A1 expression. The objectives of this study were twofold: to investigate the kinetic time course and dosimetry of PCB77 in rat hepatoma cells dosed with PCB77 and in liver of rats given ip doses of PCB77, and to compare in vitro and in vivo P4501A1 enzyme induction responses. For the 4-day time–course study, H4IIE cells were exposed with two doses of [ 14 C]PCB77 (0.9 and 3 μg/plate) and harvested at 15 and 30 min, 1, 2, 4, 8, and 12 hr, and 1, 2, 3, and 4 days. PCB77-derived radioactivity was detected in the cells as early as 15 min postdosing. For the dose–response study, the cells were dosed with various concentrations of PCB77 (0.00316–5.37 μg/plate) and harvested on Day 3 since ethoxyresorufin O -deethylase (EROD) activity in vitro reached its maximum on the third day postdosing. Time–course and dose–response studies revealed that only 1–3% of the total delivered dose was found in the cells, with the remainder in the media and adhering to the culture plates. For the dose–response study in vivo, male Fischer rats were dosed with a single ip injection of various concentrations of PCB77 (0.1–50 mg/kg body wt) and euthanized on Day 3. PCB77-derived radioactivity and EROD induction in vivo were measured. When EROD activity and PCB77-derived radioactivity in the rat hepatoma cells and in the rat liver were compared on an equivalent weight basis, there was a significant correlation ( r 2 = 0.985) between them. Prior to this study, no information on quantitative dosimetry and EROD activities of PCB77 has been reported to validate the in vitro assay with in vivo data.

Toxicology and Applied Pharmacology↗

USGS2010

A methodology for the assessment of unconventional (continuous) resources with an application to the Greater Natural Buttes gas field, Utah

The Greater Natural Buttes tight natural gas field is an unconventional (continuous) accumulation in the Uinta Basin, Utah, that began production in the early 1950s from the Upper Cretaceous Mesaverde Group. Three years later, production was extended to the Eocene Wasatch Formation. With the exclusion of 1100 non-productive (“dry”) wells, we estimate that the final recovery from the 2500 producing wells existing in 2007 will be about 1.7 trillion standard cubic feet (TSCF) (48.2 billion cubic meters (BCM)). The use of estimated ultimate recovery (EUR) per well is common in assessments of unconventional resources, and it is one of the main sources of information to forecast undiscovered resources. Each calculated recovery value has an associated drainage area that generally varies from well to well and that can be mathematically subdivided into elemental subareas of constant size and shape called cells. Recovery per 5-acre cells at Greater Natural Buttes shows spatial correlation; hence, statistical approaches that ignore this correlation when inferring EUR values for untested cells do not take full advantage of all the information contained in the data. More critically, resulting models do not match the style of spatial EUR fluctuations observed in nature. This study takes a new approach by applying spatial statistics to model geographical variation of cell EUR taking into account spatial correlation and the influence of fractures. We applied sequential indicator simulation to model non-productive cells, while spatial mapping of cell EUR was obtained by applying sequential Gaussian simulation to provide multiple versions of reality (realizations) having equal chances of being the correct model. For each realization, summation of EUR in cells not drained by the existing wells allowed preparation of a stochastic prediction of undiscovered resources, which range between 2.6 and 3.4 TSCF (73.6 and 96.3 BCM) with a mean of 2.9 TSCF (82.1 BCM) for Greater Natural Buttes. A second approach illustrates the application of multiple-point simulation to assess a hypothetical frontier area for which there is no production information but which is regarded as being similar to Greater Natural Buttes.

Utah↗

USGS2011

Use of upscaled elevation and surface roughness data in two-dimensional surface water models

In this paper, we present an approach that uses a combination of cell-block- and cell-face-averaging of high-resolution cell elevation and roughness data to upscale hydraulic parameters and accurately simulate surface water flow in relatively low-resolution numerical models. The method developed allows channelized features that preferentially connect large-scale grid cells at cell interfaces to be represented in models where these features are significantly smaller than the selected grid size. The developed upscaling approach has been implemented in a two-dimensional finite difference model that solves a diffusive wave approximation of the depth-integrated shallow surface water equations using preconditioned Newton–Krylov methods. Computational results are presented to show the effectiveness of the mixed cell-block and cell-face averaging upscaling approach in maintaining model accuracy, reducing model run-times, and how decreased grid resolution affects errors. Application examples demonstrate that sub-grid roughness coefficient variations have a larger effect on simulated error than sub-grid elevation variations.

Advances in Water Resources↗

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↗

USGS2006

Semianalytical computation of path lines for finite-difference models

A semianalytical particle tracking method was developed for use with velocities generated from block centered finite-difference ground-water flow models. The method is based on the assumption that each directional velocity component varies linearly within a grid cell in its own coordinate directions. This assumption allows an analytical expression to be obtained describing the flow path within an individual grid cell. Given the initial position of a particle anywhere in a cell, the coordinates of any other point along its path line within the cell, and the time of travel between them, can be computed directly. For steady-state systems, the exit point for a particle entering a cell at any arbitrary location can be computed in a single step. By following the particle as it moves from cell to cell, this method can be used to trace the path of a particle through any multidimensional flow field generated from a block-centered finite-difference flow model.

Ground Water↗

USGS2015

Mercury, monomethyl mercury, and dissolved organic carbon concentrations in surface water entering and exiting constructed wetlands treated with metal-based coagulants, Twitchell Island, California

Coagulation with metal-based salts is a practice commonly employed by drinking-water utilities to decrease particle and dissolved organic carbon concentrations in water. In addition to decreasing dissolved organic carbon concentrations, the effectiveness of iron- and aluminum-based coagulants for decreasing dissolved concentrations both of inorganic and monomethyl mercury in water was demonstrated in laboratory studies that used agricultural drainage water from the Sacramento–San Joaquin Delta of California. To test the effectiveness of this approach at the field scale, nine 15-by-40 ‑ meter wetland cells were constructed on Twitchell Island that received untreated water from island drainage canals (control) or drainage water treated with polyaluminum chloride or ferric sulfate coagulants. Surface-water samples were collected approximately monthly during November 2012–September 2013 from the inlets and outlets of the wetland cells and then analyzed by the U.S. Geological Survey for total concentrations of mercury and monomethyl mercury in filtered (less than 0.3 micrometers) and suspended-particulate fractions and for concentrations of dissolved organic carbon. In the control wetland cells, total mercury concentrations in filtered water samples ranged from 0.94 to 2.47 nanograms per liter (ng/L) at the control inlets and from 0.84 to 2.63 ng/L at the control outlets, and particulate total mercury concentrations in water ranged from 0.27 to 1.49 ng/L at the control inlets and from 0.17 to 1.11 ng/L at the control outlets. Monomethyl mercury concentrations in filtered water ranged from 0.16 to 0.88 ng/L at the control inlets and from 0.13 to 1.30 ng/L at the control outlets; particulate monomethyl mercury concentrations in water ranged from 0.03 to 0.24 ng/L at the control inlets and from 0.03 to 0.23 ng/L at the control outlets. Dissolved organic carbon concentrations in water ranged from 7.9 to 26.7 milligrams per liter at the control inlets and from 8.5 to 28.0 milligrams per liter at the control outlets. Following coagulation, but prior to passage through the wetland cells, coagulation treatments transferred dissolved mercury and carbon to the particulate fraction relative to untreated source water: at the wetland cell inlets, the coagulation treatments decreased concentrations of filtered total mercury by 59–76 percent, filtered monomethyl mercury by 40–70 percent, and dissolved organic carbon by 65–86 percent. Passage through the wetland cells decreased the particulate fraction of mercury in wetland cells that received coagulant-treated water. Changes in total mercury, monomethyl mercury, and dissolved organic carbon concentrations resulting from wetland passage varied both by treatment and season. Despite increased monomethyl mercury in the filtered fraction during wetland passage between March and August, the coagulation-wetland systems generally decreased total mercury (filtered plus particulate) and monomethyl mercury (filtered plus particulate) concentrations relative to source water. Coagulation—either alone or in association with constructed wetlands—could be an effective way to decrease concentrations of mercury and dissolved organic carbon in surface water as well as the bioavailability of mercury in the Sacramento–San Joaquin Delta.

California↗