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At least 343 records · Page 19Linked to original sources

Ultrastructure of the spleen and head kidney of striped bass

The spleen and head kidney of striped bass Morone saxatilis were examined by electron microscopy, including examination of ultrastructural localization of peroxidase. The spleen is composed of a loosely organized reticulum that supports the red and white pulp. The principal hematopoietic and mature blood cells observed were erythrocytes, erythroblasts, lymphocytes, macrophages, thrombocytes, and aggregates of pigmented macrophages. In addition, limited numbers of neutrophils, neutrophilic myelocytes (immature neutrophils), plasma cells, eosinophils and monocytes were identified. Reticular cells and fibers appeared to provide a structural framework for both cells and blood sinuses in the spleen. Like the spleen, the head kidney contained erythrocytes, macrophages, monocytes, lymphocytes, and other less frequently observed cell types. A distinct difference in the cytologic composition of the two organs, however, was in the greater number of neutrophilic myelocytes found in the head kidney, where these cells were often arranged in groups. Positive peroxidase reactions were observed for neutrophils, neutrophilic myelocytes, macrophage phagolysosomes, and pigmented macrophages in both the spleen and head kidney.

Journal of Aquatic Animal Health↗

Plasma chloride and gill epithelial response of channel catfish to infection with Ichthyophthirius multifillis

Because infection with Ichthyophthirius multifiliis has been reported to result in osmotic stress, genesis of the plasma chloride and chloride cell response of channel catfish Ictalurus punctatus to the infection was studied from day 0 to day 7 postexposure (PE). Parasite population densities ranged from 0.08 to 0.22 trophonts per gill filament during days 1–5 PE and increased to 2.1 at day 7 PE. Population increases were the result of infection by a new generation of infective theronts and reproduction by the parasite on the host. Mean plasma chloride concentrations of fish were not significantly different among days 0–5 PE (range of means, 93.01–97.87 meq/L), but by day 7 PE the mean had declined significantly, to 83.73 meq/L. Maintenance of relatively stable plasma chloride concentrations for 5 d was associated with chloride cell proliferation. The number of interlamellar filament chloride cells had significantly increased by day 1 PE, and the number of chloride cells in the lamellae had significantly increased by day 5 PE. No further increase had occurred by day 7 PE. Vacuolization of chloride cells, examined by electron microscopy, became more common as infection progressed, and many chloride cells appeared to be degenerating by day 5 PE.

Journal of Aquatic Animal Health↗

Evaluating the effect of stressors on thiaminase activity in alewife

No consistent explanation has been found for the variability in the thiaminase activity of alewives Alosa pseudoharengus despite the role of alewife thiaminase in large-scale salmonine mortality in the Laurentian Great Lakes. We conducted experiments to evaluate the effect of two stressors, reduced salt content in the water and food limitation, on alewife thiaminase activity. Alewives were subjected to treatments in replicated tanks in which conductivity was lowered (<100 ??S/cm) for 8 d and feeding was limited for 39 d. Circulating white blood cells, plasma cortisol, plasma glucose, and whole-body thiaminase were measured in individual alewives to assess their response to these experimental treatments. Alewives from the controls had significantly larger numbers of circulating white blood cells than those in the salt-reduced and food-limited treatments (24,000 and 19,000 cells/??L and 11,000 and 9,000 cells/??L for alewives from the two control and salt-reduced treatment tanks, respectively, and 34,000 and 30,000 cells/??L and 21,000 and 16,000 cells/??L for alewives from the two control and food-limited treatment tanks). No significant differences in alewife thiaminase activity were found between treatment fish and their controls. The mean thiaminase activity in the alewives studied increased from 6,900 to 16,000 pmol??g -1??min-1 from the time of their collection in Cayuga Lake to the start of laboratory experiments 1.5-2.5 years later; the latter value was more than twice that of previously reported levels of thiaminase activity from alewives collected in the wild. These data suggest that the variability in alewife thiaminase is not related to stress from salt reduction or food limitation, but laboratory holding conditions significantly increased thiaminase through a mechanism not evaluated by our experimental treatments. ?? Copyright by the American Fisheries Society 2008.

Journal of Aquatic Animal Health↗

Evidence for an amoeba-like infectious stage of ichthyophonus sp. and description of a circulating blood stage: a probable mechanism for dispersal within the fish host

Small amoeboid cells, believed to be the infectious stage of Ichthyophonus sp., were observed in the bolus (stomach contents) and tunica propria (stomach wall) of Pacific staghorn sculpins and rainbow trout shortly after they ingested Ichthyophonus sp.–infected tissues. By 24–48 hr post-exposure (PE) the parasite morphed from the classically reported multinucleate thick walled schizonts to 2 distinct cell types, i.e., a larger multinucleate amoeboid cell surrounded by a narrow translucent zone and a smaller spherical cell surrounded by a “halo” and resembling a small schizont. Both cell types also appeared in the tunica propria, indicating that they had recently penetrated the columnar epithelium of the stomach. No Ichthyophonus sp. pseudo-hyphae (“germination tubes”) were observed in the bolus or penetrating the stomach wall. Simultaneously, Ichthyophonus sp. was isolated in vitro from aortic blood, which was consistently positive from 6 to 144 hr PE, then only intermittently for the next 4 wk. Small PAS-positive cells observed in blood cultures grew into colonies consisting of non-septate tubules (pseudo-hyphae) terminating in multinucleated knob-like apices similar to those seen in organ explant cultures. Organ explants were culture positive every day; however, typical Ichthyophonus sp. schizonts were not observed histologically until 20–25 days PE. From 20 to 60 days PE, schizont diameter increased from ≤25 μm to ≥82 μm. Based on the data presented herein, we are confident that we have resolved the life cycle of Ichthyophonus sp. within the piscivorous host.

Journal of Parasitology↗

FORSPAN Model Users Guide

The USGS FORSPAN model is designed for the assessment of continuous accumulations of crude oil, natural gas, and natural gas liquids (collectively called petroleum). Continuous (also called ?unconventional?) accumulations have large spatial dimensions and lack well defined down-dip petroleum/water contacts. Oil and natural gas therefore are not localized by buoyancy in water in these accumulations. Continuous accumulations include ?tight gas reservoirs,? coalbed gas, oil and gas in shale, oil and gas in chalk, and shallow biogenic gas. The FORSPAN model treats a continuous accumulation as a collection of petroleumcontaining cells for assessment purposes. Each cell is capable of producing oil or gas, but the cells may vary significantly from one another in their production (and thus economic) characteristics. The potential additions to reserves from continuous petroleum resources are calculated by statistically combining probability distributions of the estimated number of untested cells having the potential for additions to reserves with the estimated volume of oil and natural gas that each of the untested cells may potentially produce (total recovery). One such statistical method for combination of number of cells with total recovery, used by the USGS, is called ACCESS.

Open-File Report↗

Pallid sturgeon in the Lower Mississippi Region: Hematology and genome information

This project (Project 1448-43270-2M-002) has been coordinated through the Natchitoches National Fish Hatchery (NNFH) and the U.S. Geological Survey’s National Wetlands Research Center (NWRC). From November 2001 to April 2002, over 280 sturgeon of the genus Scaphirhynchus (including pallid sturgeon, shovelnose, and their hybrids) were sampled from the outflow channel of the Old River Control Structure Complex (ORCC) in Concordia Parish, La. In the overall project, several datasets were collected (see Appendix), including species identification by using microsatellites and morphometric characters, food habits, physical anomalies, information on blood cells, and pathologic evidence of iridovirus – the first indication in the lower Mississippi population of pallid sturgeon. In this study, data on blood cells were obtained from the sturgeon collected monthly from approximately 20 different animals at each sampling time. This report presents preliminary information on differential blood cell identifications in sturgeon, data on comparative genomic DNA content and DNA degradation, and summaries and interpretations of data collected in light of available scientific literature addressing blood parameters of fish and sturgeon, in particular. Results obtained from collection and examination of blood and body fluids are often essential in establishing the health of fish (Blaxhall, 1972; Fange, 1992). Blood cells and sperm cells can be obtained nondestructively from fishes, even from small specimens that weigh less than 100 g (Stoskopf, 1992a). For flow cytometry assays, whereby cells are analyzed individually in a fluid stream, less than 1 :L of blood is needed. Examinations of blood by microscopy and flow cytometry were performed at NWRC in assisting in the efforts directed at recovery of the pallid sturgeon population in the Lower Mississippi River Basin.

Open-File Report↗

California State Waters Map Series — Monterey Canyon and vicinity, California

Introduction In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath bathymetry data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology. The Monterey Canyon and Vicinity map area lies within Monterey Bay in central California. Monterey Bay is one of the largest embayments along the west coast of the United States, spanning 36 km from its northern to southern tips (in Santa Cruz and Monterey, respectively) and 20 km along its central axis. Not only does it contain one of the broadest sections of continental shelf along California’s coast, it also contains Monterey Canyon, one of the largest and deepest submarine canyons in the world. Note that the California’s State Waters limit extends farther offshore between Santa Cruz and Monterey so that it encompasses all of Monterey Bay. The coastal area within the map area is lightly populated. The community of Moss Landing (population, 204) hosts the largest commercial fishing fleet in Monterey Bay in its harbor. The map area also includes parts of the cities of Marina (population, about 20,000) and Castroville (population, about 6,500). Fertile lowlands of the Salinas River and Pajaro River valleys largely occupy the inland part of the map area, and land use is primarily agricultural. The offshore part of the map area lies completely within the Monterey Bay National Marine Sanctuary. The map area also includes Portuguese Ledge and Soquel Canyon State Marine Conservation Areas. Designated conservation and (or) recreation areas in the onshore part of the map area include Salinas River National Wildlife Refuge, Elkhorn Slough State Marine Conservation Area, Elkhorn Slough State Marine Reserve, Moss Landing Wildlife Area, Zmudowski and Salinas River State Beaches, and Marina Dunes Preserve. Monterey Bay, a geologically complex area within a tectonically active continental margin, lies between two major, converging strike-slip faults. The northwest-striking San Andreas Fault lies about 34 km east of Monterey Bay; this section of the fault ruptured in both the 1989 M6.9 Loma Prieta earthquake and the 1906 M7.8 great California earthquake. The northwest-striking San Gregorio Fault crosses Monterey Canyon west of Monterey Bay. Between these two regional faults, strain is accommodated by the northwest-striking Monterey Bay Fault Zone. Deformation associated with these major regional faults and related structures has resulted in uplift of the Santa Cruz Mountains, as well as the granitic highlands of the Monterey peninsula. Monterey Canyon begins in the nearshore area directly offshore of Moss Landing and Elkhorn Slough, and it can be traced for more than 400 km seaward, out to water depths of more than 4,000 m. Within the map area, the canyon can be traced for about 42 km to a water depth of about 1,520 m. The head of the canyon consists of three branches that begin about 150 m offshore of Moss Landing Harbor. At 500 m offshore, the canyon is already 70 m deep and 750 m wide. Large sand waves, which have heights from 1 to 3 m and wavelengths of about 50 m, are present along the channel axis in the upper 4 km of the canyon. Soquel Canyon is the most prominent tributary of Monterey Canyon within the map area. The head of Soquel Canyon is isolated from coastal watersheds and, thus, is considered inactive as a conduit for coarse sediment transport. North and south of Monterey and Soquel Canyons, the relatively flat continental shelf contains only a few rocky outcrop exposures. Bedrock is covered largely by sediment derived from the Salinas and Pajaro Rivers. North of Monterey Canyon, the broad and flat continental shelf dips gently seaward, to water depths of about 95 m. To the south, the shelf also dips slightly, to water depths of as much as 150 m along the canyon edge. In the map area, Monterey Canyon splits the Santa Cruz littoral cell (north of the canyon) and the southern Monterey littoral cell (south of the canyon). It is estimated that about 400,000 m 3 /yr of sand on average enters Monterey Canyon from both of these littoral cells. In the Santa Cruz littoral cell, sand generally travels east and south. Sand is supplied through sea cliff erosion, as well as from the San Lorenzo River, the Pajaro River, and several other smaller coastal watersheds. About 152,911 m 3 /yr of sand is dredged from the entrance channel of the Santa Cruz Small Craft Harbor north of the map area and then placed on beaches to the east (downdrift) of it. This sand feeds the beaches in the southeastern reach of the Santa Cruz littoral cell and (or) is eventually trapped and lost by Monterey Canyon. The southern Monterey Bay littoral cell in the map area consists of two subcells. From the head of Monterey Canyon to the Salinas River, littoral drift is dominantly to the north; sand entering the ocean from the Salinas River either is deposited offshore or travels north in the littoral zone, nourishing the beaches until it is transported down Monterey Canyon. From south of the Salinas River to the southern extent of the map area, coastal sediment is moved mainly to the south; dune erosion is the only significant source of sand in this subcell.

California↗

Ground-water flow model of the Boone formation at the Tar Creek superfund site, Oklahoma and Kansas

Extensive mining activities conducted at the Tar Creek Superfund site, one of the largest Superfund sites in the United States, pose substantial health and safety risks. Mining activities removed a total of about 6,000,000 tons of lead and zinc by 1949. To evaluate the effect of this mining on the ground-water flow, a MODFLOW 2000 digital model has been developed to simulate ground-water flow in the carbonate formations of Mississippian age underlying the Tar Creek Superfund site. The model consists of three layers of variable thickness and a grid of 580 rows by 680 columns of cells 164 feet (50 meters) on a side. Model flux boundary conditions are specified for rivers and general head boundaries along the northern boundary of the Boone Formation. Selected cells in layer 1 are simulated as drain cells. Model calibration has been performed to minimize the difference between simulated and observed water levels in the Boone Formation. Hydraulic conductivity values specified during calibration range from 1.3 to 35 feet per day for the Boone Formation with the larger values occurring along the axis of the Miami Syncline where horizontal anisotropy is specified as 10 to 1. Hydraulic conductivity associated with the mine void is set at 50,000 feet per day and a specific yield of 1.0 is specified to represent that the mine void is filled completely with water. Residuals (the difference between measured and simulated ground-water altitudes) has a root-mean-squared value of 8.53 feet and an absolute mean value of 7.29 feet for 17 observed values of water levels in the Boone Formation. The utility of the model for simulating and evaluating the possible consequences of remediation activities has been demonstrated. The model was used to simulate the emplacement of chat (mine waste consisting of fines and fragments of chert) back into the mine. Scenarios using 1,800,000 and 6,500,000 tons of chat were run. Hydraulic conductivity was reduced from 50,000 feet per day to 35 feet per day in the model cells corresponding to chat emplacement locations. A comparison of the simulated baseline conditions and conditions after simulated chat emplacement revealed little change in water levels, drainage and stream flux, and ground-water flow velocity. Using the calibrated flow model, particle tracks were simulated using MODPATH to evaluate the simultaneous movement of particles with water in the vicinity of four potential sites at which various volumes of chat might be emplaced in the underground mine workings as part of potential remediation efforts at the site. Particle tracks were generated to follow the rate and direction of water movement for a simulated period of 100 years. In general, chat emplacement had minimal effect on the direction and rate of movement when compared to baseline (current) flow conditions. Water-level differences between baseline and chat-emplacement scenarios showed declines as much as 2 to 3 feet in areas immediately downgradient from the chat emplacement cells and little or no head change upgradient. Chat emplacements had minimal effect on changes in surfacewater flux with the largest simulated difference in one cell between baseline and chat emplacement scenarios being about 3.5 gallons per minute.

Scientific Investigations Report↗

Validation of a Ground-Water Flow Model of the Mississippi River Valley Alluvial Aquifer Using Water-Level and Water-Use Data for 1998-2005 and Evaluation of Water-Use Scenarios

A ground-water flow model of the Mississippi River Valley alluvial aquifer in eastern Arkansas, developed in 2003 to simulate the period of 1918-98, was validated with the addition of water-level and water-use data that extended the observation period to 2005. The original model (2003) was calibrated using water-level observations from 1972, 1982, 1992, and 1998, and water-use data through 1997. The original model subsequently was used to simulate water levels from 1999 to 2049 and showed that simulation of continued pumping at the 1997 water-use rate could not be sustained indefinitely without causing dry cells in the model. After publication of the original ground-water flow model, a total of 3,616 water-level observations from 698 locations measured during the period of 1998 to 2005 became available. Additionally, water-use data were compiled and used for the same period, totaling 290,005 discrete water-use values from 43,440 wells with as many as 39,169 wells pumping in any one year. Total pumping (which is primarily agricultural) for this 8-year period was about 2.3 trillion cubic feet of water and was distributed over approximately 10,340 square miles within the model area. An updated version of the original ground-water flow model was used to simulate the period of 1998-2005 with the additional water-level and water-use data. Water-level observations for 1998-2005 ranged from 74 to 293 feet above National Geodetic Vertical Datum of 1929 across the model area. The maximum water-level residual (observed minus simulated water-level values) for the 3,616 water-level observations was 52 feet, the minimum water-level residual was 60 feet, the average annual root mean squared error was 8.2 feet, and the annual average absolute residual was 6.0 feet. A correlation coefficient value of 0.96 was calculated for the line of best fit for observed to simulated water levels for the combined 1998-2005 dataset, indicating a good fit to the data and an acceptable validation of the model. After the validation process was completed, additional ground-water model simulations were run to evaluate the response of the aquifer with the 2005 water-use rate applied through 2049 (scenario 1) and the 2005 water-use rate increased 2 percent annually until 2049 (scenario 2). Scenario 1 resulted in 779 dry cells (779 square miles) by 2049 and scenario 2 resulted in 2,910 dry cells (2,910 square miles) by 2049. In both scenarios, the dry cells are concentrated in the Grand Prairie area and Cache River area west of Crowleys Ridge. However, scenario 2 resulted in dry cells to the east of Crowleys Ridge as well. A simulation applying the 1997 water-use rate contained in the original ground-water flow model resulted in 401 dry cells (401 square miles) in the Grand Prairie and Cache River areas.

Scientific Investigations Report↗

Development and application of a groundwater/surface-water flow model using MODFLOW-NWT for the Upper Fox River Basin, southeastern Wisconsin

The Fox River is a 199-mile-long tributary to the Illinois River within the Mississippi River Basin in the states of Wisconsin and Illinois. For the purposes of this study the Upper Fox River Basin is defined as the topographic basin that extends from the upstream boundary of the Fox River Basin to a large wetland complex in south-central Waukesha County called the Vernon Marsh. The objectives for the study are to (1) develop a baseline study of groundwater conditions and groundwater/surface-water interactions in the shallow aquifer system of the Upper Fox River Basin, (2) develop a tool for evaluating possible alternative water-supply options for communities in Waukesha County, and (3) contribute to the methodology of groundwater-flow modeling by applying the recently published U.S. Geological Survey MODFLOW-NWT computer code, (a Newton formulation of MODFLOW-2005 intended for solving difficulties involving drying and rewetting nonlinearities of the unconfined groundwater-flow equation) to overcome computational problems connected with fine-scaled simulation of shallow aquifer systems by means of thin model layers. To simulate groundwater conditions, a MODFLOW grid is constructed with thin layers and small cell dimensions (125 feet per side). This nonlinear unconfined problem incorporates the streamflow/lake (SFR/LAK) packages to represent groundwater/surface-water interactions, which yields an unstable solution sensitive to initial conditions when solved using the Picard-based preconditioned-gradient (PCG2) solver. A particular problem is the presence of many isolated wet water-table cells over dry cells, causing the simulated water table to assume unrealistically high values. Attempts to work around the problem by converting to confined conditions or converting active to inactive cells introduce unacceptable bias. Application of MODFLOW-NWT overcomes numerical problem by smoothing the transition from wet to dry cells and keeps all cells active. The simulation is insensitive to initial conditions and the water-table trend is smooth across layers. The MODFLOW-NWT code permits rigorous calibration and also robust application of the model to transient scenarios. Runtimes on a 64-bit computer are kept reasonably short by use of updated initial conditions and informed choices of solver parameters. The shallow aquifer system consists of unconsolidated material of varying thickness over Silurian dolomite. The unconsolidated material, largely of glacial origin, contains fine-textured and coarse-textured deposits that vary in permeability over short distances. This study at least partly encompasses the inevitable uncertainty in the hydraulic conductivity zones by developing two models&mdash;one favors the continuity of fine-grained deposits and a second favors the continuity of coarse-grained deposits. The separate calibration processes for the fine-favored and coarse-favored models using MODFLOW-NWT and the nonlinear regression algorithms in the parameter estimation (PEST) code produce distinct parameter values for hydraulic conductivity zones, storage parameters, and streambed conductance zones. Both models are applied to a hypothetical scenario involving 27 "riparian" wells completed adjacent to the river channel and open to the shallow aquifer systems along a 10-mile stretch of the Fox River. The results suggest that a riparian well system withdrawing about 9 million gallons per day would induce about one-third to one-half its total discharge from the river, and that this riverbank inducement would appreciably limit drawdown around the hypothetical wells.

Wisconsin↗

Organic wastewater compounds in water and sediment in and near restored wetlands, Great Marsh, Indiana Dunes National Lakeshore, 2009–11

A cooperative investigation between the U.S. Geological Survey and the National Park Service was completed from 2009 through 2011 to understand the occurrence, distribution, and environmental processes affecting concentrations of organic wastewater compounds in water and sediment in and near Great Marsh at the Indiana Dunes National Lakeshore in Beverly Shores, Indiana. Sampling sites were selected to represent hydrologic inputs to the restored wetlands from adjacent upstream residential and less developed areas and to represent discharge points of cascading cells within the restored wetland. A multiphase approach was used for the investigation. Discrete water samples and time-integrated passive samples were analyzed for 69 organic wastewater compounds. Continuous water-level information and periodic streamflow measurements characterized flow conditions at discharge points from restored wetland cells. Wetland sediments were collected and analyzed for sorptive losses of organic wastewater compounds and to evaluate of the potential for wetland sediments to biotransform organic wastewater compounds. A total of 52 organic wastewater compounds were detected in discrete water samples at 1 or more sites. Detections of organic wastewater compounds were widespread, but concentrations were generally low and 95 percent were less than 2.1 micrograms per liter. Six compounds were detected at concentrations greater than 2.1 micrograms per liter—four fecal sterols (beta-sitosterol, cholesterol, beta-stigmastanol, and 2-beta coprostanol), one plasticizer (bis-2-ethylhex ylphthalate), and a non-ionic detergent (4-nonylphenol diethoxylate). Two 1-month deployments of time-integrative passive samplers, called polar organic chemical integrative samplers, detected organic wastewater compounds at lower concentrations than were possible with discrete water samples. Isopropyl benzene (solvent), caffeine (plant alkaloid, stimulant), and hexahydrohexamethyl cyclopentabenzopyran (fragrance) were detected in more than half of the extracts from passive samplers, but they were not detected in any discrete water sample. The Yeast Estrogen Screen assay identified measurable estrogenicity in one passive sampler extract from the most downstream wetland site in both the April and November–December 2011 deployments and in passive sampler extracts from one residential and one upstream site in the November–December 2011 deployment only. Surface-water levels in the restored wetland cells were monitored continuously using submersible pressure transducers in hand-driven well points screened in the surface water. Surface-water levels in the wetland cells responded quickly to precipitation and substantially receded within 2 days following the largest rainfall events. Seasonal patterns in water levels generally showed higher and more variable surface-water levels in the wetland cells during spring and early summer. Water levels in the wetland cells fell below the elevation of the control structures and ceased to flow over the spillways during extended dry periods (primarily late summer and early fall). Daily loads of seven organic wastewater compounds, as indicators of septic system effluent, were estimated for samples collected at wetland outlet spillways when flow measurements could be made. Median daily loads of the indicator organic wastewater compounds increased in downstream order, and the largest median loads were measured at the most downstream site. Median daily loads were higher for samples collected in spring and summer than those collected in fall, as the higher seasonal water levels increased streamflow at the wetland outlet spillways. Wetland sediment samples were analyzed for 84 organic wastewater compounds, polycyclic aromatic hydrocarbons, and semivolatile organic compounds to investigate the fate of contaminants in Great Marsh. The top five detected compounds by total mass in wetland sediment samples were beta-sitosterol, beta-stigmastanol, cholesterol, bis(2-ethylhexyl) phthalate, and phenol. Polycyclic aromatic hydrocarbons also were frequently detected in wetland sediment samples. Source apportionment of polycyclic aromatic hydrocarbon detections indicated atmospheric sources of pyrogenic compounds, rather than residential sources. Comparisons of polycyclic aromatic hydrocarbon concentrations in wetland sediment samples to sediment quality target guidelines indicated the potential for harmful effects on sediment-dwelling organisms at several sites. Biodegradation of select endocrine-disrupting compounds (17α-ethinylestradiol, 4-nonylphenol, triclocarban, and bisphenol A) in shallow wetland sediments was evaluated in laboratory experiments by using carbon-14 radiolabeled model contaminants. Substantial biodegradation of certain organic wastewater compounds were demonstrated, primarily in oxic (oxygen containing) environments. One of four modeled compounds, bisphenol A, was biodegraded in anoxic (oxygen free) environments. Only sediments collected nearest residential areas exhibited degradation of the synthetic birth control pharmaceutical, 17α-ethinylestradiol, possibly owing to adaptation and acclimation of the indigenous microbial community to septic discharge and the resultant selection of a microbial capability for biodegradation of 17α-ethinylestradiol.

Indiana↗

Multi-resource analysis: A proof of concept study of natural resource tradeoffs in the Piceance Basin, Colorado, using the net resources assessment (NetRA) decision support tool

Executive Summary The U.S. Geological Survey (USGS) is developing a multi-resource analysis (MRA) line of products to inform land-use decision makers. Specifically, MRA products will integrate scientific information, include considerations for natural resource interrelations, and quantify the effects of resource management decisions in biophysical, economic, and societal terms. As part of the establishment of the MRA, the USGS, in collaboration with the University of New Mexico, has developed the Net Resources Assessment (NetRA) decision support tool. As a proof of concept analysis, the NetRA was applied to the Piceance basin in Colorado in a hypothetical example to illustrate how resource managers could use the NetRA to consider tradeoffs of natural resources among alternative development plans and land cover patterns within a geographic region. The NetRA is a policy-relevant approach to assess the availability of multiple natural resources. It is an analytical toolset that may be used to examine the spatiotemporal relations between development of energy and mineral resources and delivery of biological natural resources. The NetRA operates at multiple map scales and contains a set of integrated, compatible submodels with specific data requirements for natural resource stocks, engineering economics, biophysical, and ecological data for ecosystem services stocks, market prices, regulations, and nonmarket values. The NetRA includes an explicit process to consider the interdependence between development and conservation, which is a crucial consideration in land-management and land-use decisions. The NetRA is used to estimate an expected net resource value (NRV). The NRV is the expected, present value, economic benefit from the extraction of a resource (for example, natural gas) minus the total cost of production, which is the aggregation of the development, production, and social costs. Social costs include private costs plus any external costs. There can be external social benefits associated with natural gas production, such as increased demand for locally produced goods and increased employment in the local area through backward and forward linkages of natural gas production. The NRV is used to compare development outcomes (scenarios) from a range of exploration and development plans for cumulative energy production. The Piceance basin application of the NetRA uses the NRV to assess the tradeoff between continuous natural gas extraction and the effects to the local populations of Odocoileus hemionus (mule deer) and aquatic species and to consumptive water uses for an area the size and resolution of a USGS energy resource assessment unit. In the proof of concept simulation, the 2.9-square-mile-area of USGS oil and gas assessment unit 50200263 (Piceance basin continuous gas unit of the Mesaverde Total Petroleum System) was gridded into 588 cells. From this area, seven clusters with potential for development and three that cannot be developed were identified; the three clusters that cannot be developed were identified as wilderness study areas, areas of critical environmental concern, and national forests. On the basis of these criteria, there are 118 cells unsuitable for development in the oil and gas assessment unit: 84 are in national forests, 23 are areas of critical environmental concern, and 11 are wilderness study areas. The remaining cells in the oil and gas assessment unit can be developed on both private and public lands. Two scenarios were considered that are distinguished as plan 1 and plan 2. Plan 1 keeps the amount of land disturbance unchanged and limits the number of development locations to 140 grid cells for the production period, which constrains the amount of the energy resources available for development; the plan requires the usage of the Bureau of Land Management (BLM) unsuitability criteria. Plan 2 also limits the number of development locations to 140 grid cells for the production period but provides a constant volume of energy production by increasing the density of well pads within the cells. The effects of plan 2 to the NRV when there are five wells per pad and five pads per square mile happen mostly in the first 5 years of development, even though the effects on the population of mule deer continue in later years. This outcome is the result of the upfront development and investment costs and the initial effect to the ecosystem services.

Colorado↗

Potential effects of out-of-basin groundwater transfers on spring discharge, base flow, and groundwater storage pertaining to the Rush Springs aquifer in and near the Caddo Nation of Oklahoma Tribal jurisdictional area, western Oklahoma

The U.S. Geological Survey (USGS), in cooperation with the Caddo Nation of Oklahoma and Bureau of Indian Affairs, assessed four groundwater-withdrawal scenarios and their potential effects on the Rush Springs aquifer in and near the Caddo Nation of Oklahoma Tribal jurisdictional area in western Oklahoma. Increases in industrial and public water supply needs have led to increased development of water resources within the Rush Springs aquifer. As new areas within the aquifer are developed, increased water withdrawals may result in decreases in available groundwater resources and conflicts among water users. For this study, a previously published numerical groundwater-flow model of the Rush Springs aquifer was modified to simulate the potential effects of four groundwater withdrawal scenarios. For the previously published calibrated model, groundwater flow was simulated from 1979 through 2015. In this study, groundwater flow simulations were extended through 2035. The period from 2016 through 2035 is referred to as the “20-year projection.” Four groundwater withdrawal scenarios starting in 2007 and continuing through 2035 were evaluated. Scenario 1 simulated no groundwater withdrawals; scenario 2 simulated no withdrawals allocated for out-of-basin water-use transfers; scenario 3 simulated withdrawals based on reported withdrawals during the 2007–15 simulation period and compounded annual increases in groundwater use during the subsequent 20-year projection; and scenario 4 simulated maximum permitted withdrawals for allocation to out-of-basin water-use transfers. Out-of-basin water transfers were classified as withdrawals that are not returned back to the aquifer. At the springs of interest, changes in water-level altitudes in response to different groundwater withdrawal scenarios were simulated by comparing the results from different model cells. Between 2007 and 2015, scenarios 2–4 yielded similar simulated water-level altitudes in the model cells containing springs of interest, with water-level altitudes decreasing to below the land surface altitude at 13 of the total 25 springs of interest, whereas under scenario 1 there were only two model cells containing springs of interest where the simulated water-level altitudes of a spring decreased to below land surface altitude. For the 20-year projection, water-level altitudes at springs simulated in model cells in scenarios 2–4 decreased to below land surface altitude for 13 of the total 25 model cells containing springs of interest, whereas under scenario 1 there were only two model cells containing springs of interest where the simulated water-level altitudes of a spring decreased to below land surface altitude. The potential effects of groundwater withdrawals were evaluated by comparing changes in groundwater storage between the four scenarios. The 2007–15 groundwater withdrawal scenarios were used to simulate the potential effects of groundwater withdrawal rates on groundwater storage of the Rush Springs aquifer. The simulated groundwater storage change in the Rush Springs aquifer ranged from an increase of 2.8 percent for scenario 1 to an increase of 1.0 percent for scenario 4. Projected 20-year groundwater withdrawal scenarios were used to simulate the potential effects of selected groundwater withdrawal rates on groundwater storage of the Rush Springs aquifer. Simulated groundwater storage changes ranged from a decrease of 0.5 percent for scenario 1 to a decrease of 0.7 percent for scenario 4.

Oklahoma↗

User Guide and Documentation for Five MODFLOW Ground-Water Modeling Utility Programs

This report documents five utility programs designed for use in conjunction with ground-water flow models developed with the U.S. Geological Survey's MODFLOW ground-water modeling program. One program extracts calculated flow values from one model for use as input to another model. The other four programs extract model input or output arrays from one model and make them available in a form that can be used to generate an ArcGIS raster data set. The resulting raster data sets may be useful for visual display of the data or for further geographic data processing. The utility program GRID2GRIDFLOW reads a MODFLOW binary output file of cell-by-cell flow terms for one (source) model grid and converts the flow values to input flow values for a different (target) model grid. The spatial and temporal discretization of the two models may differ. The four other utilities extract selected 2-dimensional data arrays in MODFLOW input and output files and write them to text files that can be imported into an ArcGIS geographic information system raster format. These four utilities require that the model cells be square and aligned with the projected coordinate system in which the model grid is defined. The four raster-conversion utilities are * CBC2RASTER, which extracts selected stress-package flow data from a MODFLOW binary output file of cell-by-cell flows; * DIS2RASTER, which extracts cell-elevation data from a MODFLOW Discretization file; * MFBIN2RASTER, which extracts array data from a MODFLOW binary output file of head or drawdown; and * MULT2RASTER, which extracts array data from a MODFLOW Multiplier file.

Techniques and Methods↗

MODFLOW–USG version 1: An unstructured grid version of MODFLOW for simulating groundwater flow and tightly coupled processes using a control volume finite-difference formulation

A new version of MODFLOW, called MODFLOW–USG (for UnStructured Grid), was developed to support a wide variety of structured and unstructured grid types, including nested grids and grids based on prismatic triangles, rectangles, hexagons, and other cell shapes. Flexibility in grid design can be used to focus resolution along rivers and around wells, for example, or to subdiscretize individual layers to better represent hydrostratigraphic units. MODFLOW–USG is based on an underlying control volume finite difference (CVFD) formulation in which a cell can be connected to an arbitrary number of adjacent cells. To improve accuracy of the CVFD formulation for irregular grid-cell geometries or nested grids, a generalized Ghost Node Correction (GNC) Package was developed, which uses interpolated heads in the flow calculation between adjacent connected cells. MODFLOW–USG includes a Groundwater Flow (GWF) Process, based on the GWF Process in MODFLOW–2005, as well as a new Connected Linear Network (CLN) Process to simulate the effects of multi-node wells, karst conduits, and tile drains, for example. The CLN Process is tightly coupled with the GWF Process in that the equations from both processes are formulated into one matrix equation and solved simultaneously. This robustness results from using an unstructured grid with unstructured matrix storage and solution schemes. MODFLOW–USG also contains an optional Newton-Raphson formulation, based on the formulation in MODFLOW–NWT, for improving solution convergence and avoiding problems with the drying and rewetting of cells. Because the existing MODFLOW solvers were developed for structured and symmetric matrices, they were replaced with a new Sparse Matrix Solver (SMS) Package developed specifically for MODFLOW–USG. The SMS Package provides several methods for resolving nonlinearities and multiple symmetric and asymmetric linear solution schemes to solve the matrix arising from the flow equations and the Newton-Raphson formulation, respectively.

Techniques and Methods↗

Hydrogeology and leachate plume delineation at a closed municipal landfill, Norman, Oklahoma

The City of Norman operated a solid-waste municipal landfill at two sites on the Canadian River alluvium in Cleveland County, Oklahoma from 1970 to 1985. The sites, referred to as the west and east cells of the landfill, were originally excavations in the unconsolidated alluvial deposits and were not lined. Analysis of ground-water samples indicate that leachate from the west cell is discharging into an adjacent abandoned river channel, referred to as the slough, and is migrating downgradient in ground water toward the Canadian River. The report describes the hydrogeologic features at the landfill, including the topography of the bedrock, water-level changes in the alluvial aquifer, and delineates the leachate plume using specific conductance data. The leading edge of the leachate plume along the 35-80 transect extended over 250 meters downgradient of the west cell. The leading edge of the leachate plume along the 40-SOUTH transect had moved about 60 meters from the west cell in a south-southwesterly direction and had not moved past the slough as of 1997. Specific conductance measurements exceeding 7,000 microsiemens per centimeter at site 40 indicate the most concentrated part of the plume remained in the upper half of the alluvial aquifer adjacent to the west cell. The direction of ground-water flow in the alluvial aquifer surrounding the landfill was generally north-northeast to south-southwest toward the river. However, between the west cell and the slough along the 40-SOUTH transect, head measurements indicate a directional change to the east and southeast toward a channel referred to as the sewage outfall. Near the 35-80 transect, at 0.5 meter below the water table and at the base of the aquifer, the direction of ground-water flow was south-southeast with a gradient of about 30 centimeters per 100 meters. Generally, ground-water levels in the alluvial aquifer were higher during the winter months and lower during summer months, due to a normal decrease in precipitation and increased evapotranspiration in the summer. Hydrographs show temporal water-level changes in ground water and the slough, indicating a hydrologic connection between the alluvial aquifer and the slough.

Oklahoma↗

Ground-water flow simulation and chemical and isotopic mixing equation analysis to determine source contributions to the Missouri River alluvial aquifer in the vicinity of the Independence, Missouri, well field

The city of Independence, Missouri, operates a well field in the Missouri River alluvial aquifer. Steady-state ground-water flow simulation, particle tracking, and the use of chemical and isotopic composition of river water, ground water, and well-field pumpage in a two-component mixing equation were used to determine the source contributions of induced inflow from the Missouri River and recharge to ground water from precipitation in well-field pumpage. Steady-state flow-budget analysis for the simulation-defined zone of contribution to the Independence well field indicates that 86.7 percent of well-field pumpage is from induced inflow from the river, and 6.7 percent is from ground-water recharge from precipitation. The 6.6 percent of flow from outside the simulation-defined zone of contribution is a measure of the uncertainty of the estimation, and occurs because model cells are too large to uniquely define the actual zone of contribution. Flow-budget calculations indicate that the largest source of water to most wells is the Missouri River. Particle-tracking techniques indicate that the Missouri River supplies 82.3 percent of the water to the Independence well field, ground-water recharge from precipitation supplies 9.7 percent, and flow from outside defined zones of contribution supplies 8.0 percent. Particle tracking was used to determine the relative amounts of source water to total well-field pumpage as a function of traveltime from the source. Well-field pumpage that traveled 1 year or less from the source was 8.8 percent, with 0.6 percent from the Missouri River, none from precipitation, and 8.2 percent between starting cells. Well-field pumpage that traveled 2 years or less from the source was 10.3 percent, with 1.8 percent from the Missouri River, 0.2 percent from precipitation, and 8.3 percent between starting cells. Well-field pumpage that traveled 5 years or less from the source was 36.5 percent, with 27.1 percent from the Missouri River, 1.1 percent from precipitation, and 8.3 percent between starting cells. Well-field pumpage that traveled 10 years or less from the source was 42.7 percent, with 32.6 percent from the Missouri River, 1.8 percent from precipitation, and 8.3 percent between starting cells. Well-field pumpage that traveled 25 years or less from the source was 71.9 percent, with 58.9 percent from the Missouri River, 4.7 percent from precipitation, and 8.3 percent between starting cells. Results of chemical (calcium, sodium, iron, and fluoride) and isotopic (oxygen and hydrogen) analyses of water samples collected from the Missouri River, selected monitoring wells around the Independence well field, and combined well-field pumpage were used in a two component mixing equation to estimate the relative amount of Missouri River water in total well-field pumpage. The relative amounts of induced inflow from the Missouri River in well-field pumpage ranged from 49 percent for sodium to 80 percent for calcium, and sensitivities ranged from 0 percent for iron to plus or minus 35 percent for naturally occurring stable isotope ( 18 O). The average of all mixing equation results indicated that 61 percent of well-field pumpage was from induced inflow from the Missouri River. All methods used in the study indicate that more than one-half of the water in well-field pumpage was inflow from the Missouri River. River inflow estimates from ground-water simulation methods are larger and error values are smaller than those using chemical and isotopic data in the mixing equation, although substantial uncertainties exist for both estimation methods. Because of the complex hydrology of the aquifer near the Independence well field, the source estimates using particle tracking probably are the most reliable of the ground-water simulation methods. Mixing equation results are less reliable than those of the ground-water simulation for this study. However, more reliable results can be obtained from the mixing equation by increasing the number of samples and collecting samples for a longer period of time, and during different flow conditions. In the absence of a calibrated ground-water flow simulation, the mixing equation can provide a reasonable estimate of the sources of water to a well field at relatively low cost, if sources of error are clearly understood.

Water-Resources Investigations Report↗

Pore-water extraction from unsaturated tuff by triaxial and one-dimensional compression methods, Nevada Test Site, Nevada

Study of the hydrologic system at Yucca Mountain, Nevada, requires the extraction of pore-water samples from welded and nonwelded, unsaturated tuffs. Two compression methods (triaxial compression and one-dimensional compression) were examined to develop a repeatable extraction technique and to investigate the effects of the extraction method on the original pore-fluid composition. A commercially available triaxial cell was modified to collect pore water expelled from tuff cores. The triaxial cell applied a maximum axial stress of 193 MPa and a maximum confining stress of 68 MPa. Results obtained from triaxial compression testing indicated that pore-water samples could be obtained from nonwelded tuff cores that had initial moisture contents as small as 13 percent (by weight of dry soil). Injection of nitrogen gas while the test core was held at the maximum axial stress caused expulsion of additional pore water and reduced the required initial moisture content from 13 to 11 percent. Experimental calculations, together with experience gained from testing moderately welded tuff cores, indicated that the triaxial cell used in this study could not apply adequate axial or confining stress to expel pore water from cores of densely welded tuffs. This concern led to the design, fabrication, and testing of a one-dimensional compression cell. The one-dimensional compression cell used in this study was constructed from hardened 4340-alloy and nickel-alloy steels and could apply a maximum axial stress of 552 MPa. The major components of the device include a corpus ring and sample sleeve to confine the sample, a piston and base platen to apply axial load, and drainage plates to transmit expelled water from the test core out of the cell. One-dimensional compression extracted pore water from nonwelded tuff cores that had initial moisture contents as small as 7.6 percent; pore water was expelled from densely welded tuff cores that had initial moisture contents as small as 7.7 percent. Injection of nitrogen gas at the maximum axial stress did not produce additional pore water from nonwelded tuff cores, but was critical to recovery of pore water from densely welded tuff cores. Gas injection reduced the required initial moisture content in welded tuff cores from 7.7 to 6.5 percent. Based on the mechanical ability of a pore-water extraction method to remove water from welded and nonwelded tuff cores, one-dimensional compression is a more effective extraction method than triaxial compression. However, because the effects that one-dimensional compression has on pore-water chemistry are not completely understood, additional testing will be needed to verify that this method is suitable for pore-water extraction from Yucca Mountain tuffs.

Water-Resources Investigations Report↗