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USGS2008

Development, Testing, and Sensitivity and Uncertainty Analyses of a Transport and Reaction Simulation Engine (TaRSE) for Spatially Distributed Modeling of Phosphorus in South Florida Peat Marsh Wetlands

Alterations to the predevelopment delivery of water and nutrients into the Everglades of southern Florida have been occurring for nearly a century. Major regional drainage projects, large-scale agricultural development, and changes to the hydrology of the Kissimmee River-Lake Okeechobee watershed have resulted in substantial phosphorus transport increases by surface waters. Excess phosphorus has accumulated in the soils of northern Everglades marshes to levels that have impaired the natural resources of the region. Regulations now limit the amount of phosphorous that enters the Everglades through an extensive network of water-control structures. This study involved the development and application of water-quality modeling components that may be applied to existing hydrologic models of southern Florida to evaluate the effects of different management scenarios. The result of this work is a spatially distributed water-quality model for phosphorus transport and cycling in wetlands. The model solves the advection-dispersion equation on an unstructured triangular mesh and incorporates a wide range of user-selectable mechanisms for phosphorus uptake and release parameters. In general, the phosphorus model contains transfers between stores; examples of stores that can be included are soil, water column (solutes), pore water, macrophytes, suspended solids (plankton), and biofilm. Examples of transfers are growth, senescence, settling, diffusion, and so forth, described with first order, second order, and Monod types of transformations. Local water depths and velocities are determined from an existing two-dimensional, overland-flow hydrologic model. The South Florida Water Management District Regional Simulation Model was used in this study. The model is applied to three case studies: intact cores of wetland soils with water, outdoor mesocosoms, and a large constructed wetland; namely, Cell 4 of Stormwater Treatment Area 1 West (STA-1W Cell 4). Different levels of complexity in the phosphorus cycling mechanisms were simulated in these case studies using different combinations of phosphorus reaction equations. Changes in water column phosphorus concentrations observed under the controlled conditions of laboratory incubations, and mesocosm studies were reproduced with model simulations. Short-term phosphorus flux rates and changes in phosphorus storages were within the range of values reported in the literature, whereas unknown rate constants were used to calibrate the model output. In STA-1W Cell 4, the dominant mechanism for phosphorus flow and transport is overland flow. Over many life cycles of the biological components, however, soils accrue and become enriched in phosphorus. Inflow total phosphorus concentrations and flow rates for the period between 1995 and 2000 were used to simulate Cell 4 phosphorus removal, outflow concentrations, and soil phosphorus enrichment over time. This full-scale application of the model successfully incorporated parameter values derived from the literature and short-term experiments, and reproduced the observed long-term outflow phosphorus concentrations and increased soil phosphorus storage within the system. A global sensitivity and uncertainty analysis of the model was performed using modern techniques such as a qualitative screening tool (Morris method) and the quantitative, variance-based, Fourier Amplitude Sensitivity Test (FAST) method. These techniques allowed an in-depth exploration of the effect of model complexity and flow velocity on model outputs. Three increasingly complex levels of possible application to southern Florida were studied corresponding to a simple soil pore-water and surface-water system (level 1), the addition of plankton (level 2), and of macrophytes (level 3). In the analysis for each complexity level, three surface-water velocities were considered that each correspond to residence times for the selected area (1-kilometer long) of 2, 10, and 20

Scientific Investigations Report↗

USGS2009

Three-dimensional numerical model of ground-water flow in northern Utah Valley, Utah County, Utah

A three-dimensional, finite-difference, numerical model was developed to simulate ground-water flow in northern Utah Valley, Utah. The model includes expanded areal boundaries as compared to a previous ground-water flow model of the valley and incorporates more than 20 years of additional hydrologic data. The model boundary was generally expanded to include the bedrock in the surrounding mountain block as far as the surface-water divide. New wells have been drilled in basin-fill deposits near the consolidated-rock boundary. Simulating the hydrologic conditions within the bedrock allows for improved simulation of the effect of withdrawal from these wells. The inclusion of bedrock also allowed for the use of a recharge model that provided an alternative method for spatially distributing areal recharge over the mountains. The model was calibrated to steady- and transient-state conditions. The steady-state simulation was developed and calibrated by using hydrologic data that represented average conditions for 1947. The transient-state simulation was developed and calibrated by using hydrologic data collected from 1947 to 2004. Areally, the model grid is 79 rows by 70 columns, with variable cell size. Cells throughout most of the model domain represent 0.3 mile on each side. The largest cells are rectangular with dimensions of about 0.3 by 0.6 mile. The largest cells represent the mountain block on the eastern edge of the model domain where the least hydrologic data are available. Vertically, the aquifer system is divided into 4 layers which incorporate 11 hydrogeologic units. The model simulates recharge to the ground-water flow system as (1) infiltration of precipitation over the mountain block, (2) infiltration of precipitation over the valley floor, (3) infiltration of unconsumed irrigation water from fields, lawns, and gardens, (4) seepage from streams and canals, and (5) subsurface inflow from Cedar Valley. Discharge of ground water is simulated by the model to (1) flowing and pumping wells, (2) drains and springs, (3) evapotranspiration, (4) Utah Lake, (5) the Jordan River and mountain streams, and (6) Salt Lake Valley by subsurface outflow through the Jordan Narrows. During steady-state calibration, variables were adjusted within probable ranges to minimize differences between model-computed and measured water levels as well as between model-computed and independently estimated flows that include: recharge by seepage from individual streams and canals, discharge by seepage to individual streams and the Jordan River, discharge to Utah Lake, discharge to drains and springs, discharge by evapotranspiration, and subsurface flows into and out of northern Utah Valley from Cedar Valley and to Salt Lake Valley, respectively. The transient-state simulation was calibrated to measured water levels and water-level changes with consideration given to annual changes in the flows listed above.

Utah↗

USGS2009

Effects of Potential Changes in Groundwater Withdrawals from the Sparta Aquifer on Water-Level Altitudes in Jefferson County, Arkansas

A groundwater-flow model of the Sparta aquifer was used to evaluate changes in water-level altitudes associated with the withdrawal of groundwater at varying rates from a well field near Pine Bluff, Arkansas, in Jefferson County. Water-level altitudes at three different model cell locations from five different scenarios for varying withdrawal rates from the well field were compared for the period 1998 to 2048. The three model cells used for the comparison were located (1) near the center of the well field, (2) near the center of the city of Pine Bluff (about 5 miles west of the center of the well field), and (3) about 15 miles north of the well field. Pumping rates at the well field were varied from 7.2 million gallons per day to 27 million gallons per day for the five scenarios analyzed, and water-level hydrographs were constructed for each scenario for each of the three model cell locations. Water-level altitudes near the center of the well field changed the most of the three model cell locations analyzed. Water-level altitudes were approximately 90 feet higher for the 7.2 million gallon per day scenario in 2048 compared to the baseline scenario of 25.4 million gallons per day. Whereas, water-level altitudes at the same location were 9 feet lower for the 27 million gallon per day scenario in 2048 compared to the baseline scenario.

Scientific Investigations Report↗

USGS2011

Approaches to highly parameterized inversion: Pilot-point theory, guidelines, and research directions

Pilot points have been used in geophysics and hydrogeology for at least 30 years as a means to bridge the gap between estimating a parameter value in every cell of a model and subdividing models into a small number of homogeneous zones. Pilot points serve as surrogate parameters at which values are estimated in the inverse-modeling process, and their values are interpolated onto the modeling domain in such a way that heterogeneity can be represented at a much lower computational cost than trying to estimate parameters in every cell of a model. Although the use of pilot points is increasingly common, there are few works documenting the mathematical implications of their use and even fewer sources of guidelines for their implementation in hydrogeologic modeling studies. This report describes the mathematics of pilot-point use, provides guidelines for their use in the parameter-estimation software suite (PEST), and outlines several research directions. Two key attributes for pilot-point definitions are highlighted. First, the difference between the information contained in the every-cell parameter field and the surrogate parameter field created using pilot points should be in the realm of parameters which are not informed by the observed data (the null space). Second, the interpolation scheme for projecting pilot-point values onto model cells ideally should be orthogonal. These attributes are informed by the mathematics and have important ramifications for both the guidelines and suggestions for future research.

Scientific Investigations Report↗

USGS2024

Hydrology and water quality of a dune-and-swale wetland adjacent to the Grand Calumet River, Indiana, 2019–22

Adverse ecological and water-quality effects associated with industrial land-use changes are common for littoral wetlands connected to river mouth ecosystems in the Grand Calumet River-Indiana Harbor Canal Area of Concern. These effects can be exacerbated by recent high Lake Michigan water levels that are problematic for wetland restoration. Wetlands in the adjacent Clark and Pine Nature Preserve and Pine Station Nature Preserve are intended to mitigate wetland destruction in the area of concern by restoring residual dune-and-swale wetlands and preserving habitat for endangered and threatened plant species. Physical hydrology and water-quality monitoring of restored wetland cells at the preserves were initiated during 2019 to evaluate changes after wetland restoration efforts in 2015 and near record-low water levels in early 2013. Lake Michigan water levels rose steadily between late 2013 and 2018 to record-high water levels in 2019 and 2020. In this report, precipitation, evapotranspiration, and groundwater and surface-water levels are analyzed to better understand wetland inundation controls and flow directions in restored northern dune-and-swale wetland settings relative to the Grand Calumet River. Continuous specific conductance data and discrete water-quality samples were collected and analyzed to provide a synoptic view of water quality for the restored wetlands. High Lake Michigan water levels affected Grand Calumet River stage and shallow groundwater elevations in the study area after the onset of peak lake levels in June 2019, that persisted through summer 2020, before finally receding in September 2020. Grand Calumet River stage peaked soon after lake levels in July 2019, whereas groundwater elevations in the study area peaked in October 2019. Specific conductance values in closed-basin wetland cells in the western and central parts of the nature preserves indicated a dilution trend and contrasted those of interconnected wetland cells along an eastern corridor, where alterations to wetland cells were more pronounced. Monitoring results indicate that varying seasonal wetland inundation trends with low stands in autumn have returned after high water table conditions owing to high water levels on Lake Michigan. Wetland water balance results during the study period indicated that the wetland ecosystem partially moderated flooding during high lake levels through summer evapotranspiration.

Indiana↗

USGS1958

Mineralogical applications of electron diffraction. 1. Theory and techniques

The small wavelengths used in electron-diffraction experiments and the thinness of the crystals necessary for the transmission of the electron beam combine to require a somewhat different diffraction geometry for the interpretation of electron-diffraction patterns than is used in the interpretation of X-ray diffraction patterns. This geometry, based on the reciprocal lattice concept and geometrical construction of Ewald, needed for the interpretation. of transmission electron-diffraction single-crystal patterns is here reviewed. Transmission electron-diffraction single-crystal patterns of two monoclinic substances, colemanite [CaB 3 O 3 (OH) 3 •H 2 O] and potassium chlorate (KC10 3 ), are examined and the .theory necessary for their interpretation is given in detail. The study of these patterns furnishes a basis for the interpretation of single-crystal patterns of materials belonging to any crystal system. It is shown that useful unit-cell data, accurate to a few tenths of a percent, can be obtained from the patterns of colemanite and KClO 3 . A method of evaluating unit-cell data from measurements of such single-crystal patterns is given. The transmission electron-diffraction powder pattern obtained from an oriented aggregate of thin crystals gives the same unit-cell data as are given by the electron-diffraction single-crystal pattern obtained from one crystal of the aggregate., A graphical method is given for precisely evaluating unit-cell constants from measurements of such a powder pattern.

Trace Elements Investigations↗

USGS2011

Computational considerations for collecting and using data in the equidistant cylindrical map projection and the bounds of sampling geographic data at progressively higher resolution

The Equidistant Cylindrical Map projection is popular with digital modelers and others for storing and processing worldwide data sets because of the simple association of latitude and longitude to cell values or pixels in the resulting grid. This projection does not accurately display area, and the diminished geographic area represented by cells at high latitudes is not often carefully considered. A simple mathematical analysis quantifies the discrepancy in area sampled by cells at different latitudes. The presence of this discrepancy indicates that the use of this projection can induce bias in data sets when both sampling and reporting data. It is demonstrated that as the resolution requirements of input data for models increase, the necessity of providing data to accurately describe smaller cells, particularly at high latitude, will be a challenge.

Techniques and Methods↗

USGS2017

Documentation for the “XT3D” option in the Node Property Flow (NPF) Package of MODFLOW 6

This report describes the “XT3D” option in the Node Property Flow (NPF) Package of MODFLOW 6. The XT3D option extends the capabilities of MODFLOW by enabling simulation of fully three-dimensional anisotropy on regular or irregular grids in a way that properly takes into account the full, three-dimensional conductivity tensor. It can also improve the accuracy of groundwater-flow simulations in cases in which the model grid violates certain geometric requirements. Three example problems demonstrate the use of the XT3D option to simulate groundwater flow on irregular grids and through three-dimensional porous media with anisotropic hydraulic conductivity. Conceptually, the XT3D method of estimating flow between two MODFLOW 6 model cells can be viewed in terms of three main mathematical steps: construction of head-gradient estimates by interpolation; construction of fluid-flux estimates by application of the full, three-dimensional form of Darcy’s Law, in which the conductivity tensor can be heterogeneous and anisotropic; and construction of the flow expression by enforcement of continuity of flow across the cell interface. The resulting XT3D flow expression, which relates the flow across the cell interface to the values of heads computed at neighboring nodes, is the sum of terms in which conductance-like coefficients multiply head differences, as in the conductance-based flow expression the NPF Package uses by default. However, the XT3D flow expression contains terms that involve “neighbors of neighbors” of the two cells for which the flow is being calculated. These additional terms have no analog in the conductance-based formulation. When assembled into matrix form, the XT3D formulation results in a larger stencil than the conductance-based formulation; that is, each row of the coefficient matrix generally contains more nonzero elements. The “RHS” suboption can be used to avoid expanding the stencil by placing the additional terms on the right-hand side of the matrix equation and evaluating them at the previous iteration or time step. The XT3D option can be an alternative to the Ghost-Node Correction (GNC) Package. However, the XT3D formulation is typically more computationally intensive than the conductance-based formulation the NPF Package uses by default, either with or without ghost nodes. Before deciding whether to use the GNC Package or XT3D option for production runs, the user should consider whether the conductance-based formulation alone can provide acceptable accuracy for the particular problem being solved.

Techniques and Methods↗

USGS2002

Testing the sensitivity of pumpage to increases in surficial aquifer system heads in the Cypress Creek well-field area, west-central Florida — An optimization technique

Tampa Bay depends on ground water for most of the water supply. Numerous wetlands and lakes in Pasco County have been impacted by the high demand for ground water. Central Pasco County, particularly the area within the Cypress Creek well field, has been greatly affected. Probable causes for the decline in surface-water levels are well-field pumpage and a decade-long drought. Efforts are underway to increase surface-water levels by developing alternative sources of water supply, thus reducing the quantity of well-field pumpage. Numerical ground-water flow simulations coupled with an optimization routine were used in a series of simulations to test the sensitivity of optimal pumpage to desired increases in surficial aquifer system heads in the Cypress Creek well field. The ground-water system was simulated using the central northern Tampa Bay ground-water flow model. Pumping solutions for 1987 equilibrium conditions and for a transient 6-month timeframe were determined for five test cases, each reflecting a range of desired target recovery heads at different head control sites in the surficial aquifer system. Results are presented in the form of curves relating average head recovery to total optimal pumpage. Pumping solutions are sensitive to the location of head control sites formulated in the optimization problem and as expected, total optimal pumpage decreased when desired target head increased. The distribution of optimal pumpage for individual production wells also was significantly affected by the location of head control sites. A pumping advantage was gained for test-case formulations where hydraulic heads were maximized in cells near the production wells, in cells within the steady-state pumping center cone of depression, and in cells within the area of the well field where confining-unit leakance is the highest. More water was pumped and the ratio of head recovery per unit decrease in optimal pumpage was more than double for test cases where hydraulic heads are maximized in cells located at or near the production wells. Additionally, the ratio of head recovery per unit decrease in pumpage was about three times more for the area where confining-unit leakance is the highest than for other leakance zone areas of the well field. For many head control sites, optimal heads corresponding to optimal pumpage deviated from the desired target recovery heads. Overall, pumping solutions were constrained by the limiting recovery values, initial head conditions, and by upper boundary conditions of the ground-water flow model.

Florida↗

USGS1983

Water quality of Lake Arlington on Village Creek, north-central Texas; 1973 to 1981

Water in Lake Arlington on Village Creek in north-central Texas had volume-weighted average concentrations of less than 240 milligrams per liter of dissolved solids, less than 30 milligrams per liter of dissolved chloride, and less than 40 milligrams per liter of dissolved sulfate between January 29, 1973, and August 20, 1981. The water was moderately hard (hardness greater than 60 but less than 120 milligrams per liter as calcium carbonate). The concentrations of each of these constituents were usually greatest during winter, especially during the first few years of the study, but decreased significantly as discharges of municipal wastes were systematically and progressively diverted to treatment facilities downstream from the reservoir. Thermal stratification in Lake Arlington usually begins during March or April and persists until October. Thermal stratification has resulted in significant seasonal and areal variations in the concentration of dissolved oxygen, dissolved iron, dissolved manganese, total inorganic nitrogen, and total phosphorus. Oxygen utilized in the decay of organic matter is not replenished during periods of summer stagnation, and water below depths of 30 to 40 feet usually contains less than 2 milligrams per liter of dissolved oxygen during stagnation. Even though heated effluent from an electrical generating plant is returned to the reservoir at site GC and causes an elevation of water temperature, average dissolved oxygen levels at this site are not significantly different from levels at other sites. During summer stagnation, reducing conditions result in the dissolution of iron and manganese from bottom deposits at deep sites in the reservoir. At site AQ, a deep site near Arlington Dam, dissolved iron concentrations in water near the bottom during summer stagnation ranged from less than 10 to 1,100 micrograms per liter and averaged about 640 micrograms per liter. Dissolved manganese concentrations near the bottom at site AC during summer staynation ranged from 20 to 2,700 micrograms per liter and averaged about 1,500 micrograms per liter. The concentrations of dissolved iron and dissolved manganese in water throughout the reservoir during winter circulation and in water near the reservoir surface during summer stagnation averaged less than 50 micrograms per liter. Seasonal temperature and dissolved oxygen cycles resulted in the recycling of dissolved iron and dissolved manganese between the water and bottom sediments. However, no significant accumulation of these constituents within the reservoir was detected during the study. The concentrations of total inorganic nitrogen and total phosphorus are greatest during summer stagnation in water near the bottom at deep sites. At site AC during the summer, the concentrations of total inorganic nitrogen in the hypolimnion averaged about 0.9 milligram per liter, and the concentration of total phosphorus near the bottom averaged about 0.2 milligram per liter. The concentrations of total inorganic nitrogen in the epilimnion at site AC averaged about 0.1 milligram per liter; the concentrations of total phosphorus averaged less than 0.1 milligram per liter. The densities and composition of algal populations varied seasonally. At site AC, total algae counts ranged from 200 to 240,000 cells per mi Hi liter and averaged about 50,000 cells per milliliter. At site FC, total algae counts ranged from 1,000 to 290,000 cells per milliliter and averaged about 56,000 cells per milliliter. Algal densities were greatest during the summer with blue-green algae being the predominant phyla.

Texas↗

USGS1989

A computer program for converting rectangular coordinates to latitude-longitude coordinates

A computer program was developed for converting the coordinates of any rectangular grid on a map to coordinates on a grid that is parallel to lines of equal latitude and longitude. Using this program in conjunction with groundwater flow models, the user can extract data and results from models with varying grid orientations and place these data into grid structure that is oriented parallel to lines of equal latitude and longitude. All cells in the rectangular grid must have equal dimensions, and all cells in the latitude-longitude grid measure one minute by one minute. This program is applicable if the map used shows lines of equal latitude as arcs and lines of equal longitude as straight lines and assumes that the Earth 's surface can be approximated as a sphere. The program user enters the row number , column number, and latitude and longitude of the midpoint of the cell for three test cells on the rectangular grid. The latitude and longitude of boundaries of the rectangular grid also are entered. By solving sets of simultaneous linear equations, the program calculates coefficients that are used for making the conversion. As an option in the program, the user may build a groundwater model file based on a grid that is parallel to lines of equal latitude and longitude. The program reads a data file based on the rectangular coordinates and automatically forms the new data file. (USGS)

Water-Resources Investigations Report↗

USGS1995

Water-quality conditions at selected landfills in Mecklenburg County, North Carolina, 1986-92

Water-quality conditions at five municipal landfills in Mecklenburg County, North Carolina, were studied during 1986-92. Analytical results of water samples from monitoring wells and streams at and near the landfills were used to evaluate effects of leachate on surface and ground water. Ground-water levels at monitoring wells were used to determine directions of ground-water flow at the landfills. Data from previous studies were used for analysis of temporal trends in selected water-quality properties and chemical constituents. Effects of leachate, such as large biochemical- and chemical-oxygen demands, generally were evident in small streams originating within the landfills, whereas effects of leachate generally were not evident in most of the larger streams. In larger streams, surface-water quality upstream and downstream from most of the landfills was similar. However, the chemical quality of water in Irwin Creek appears to have been affected by the Statesville Road landfill. Concentrations of several constituents indicative of leachate were larger in samples collected from Irwin Creek downstream from the Statesville Road landfill than in samples collected from Irwin Creek upstream from the landfill. The effect of leachate on ground-water quality generally was largest in water from wells adjacent to waste-disposal cells. Concentrations of most constituents considered indicative of leachate generally were smaller with increasing distance from waste-disposal cells. Water samples from offsite wells generally indicated no effect or very small effects of leachate. Action levels designated by the Mecklenburg County Engineering Department and maximum contaminant levels established by the U.S. Environmental Protection Agency were exceeded in some samples from the landfills. Ground-water samples exceeded action levels and maximum contaminant levels more commonly than surface-water samples. Iron and manganese were the constituents that most commonly exceeded action levels in water samples from the landfills. Synthetic organic compounds were detected more commonly and in larger concentrations in ground-water samples than in surface-water samples. Concentrations of synthetic organic compounds detected in water samples from monitoring sites at the landfills generally were much less than maximum contaminant levels. However, concentrations of some chlorinated organic compounds exceeded maximum contaminant levels in samples from several monitoring wells at the Harrisburg Road and York Road landfills. Trend analysis indicated statistically significant temporal changes in concentrations of selected water-quality constituents and properties at some of the monitoring sites. Trends detected for the Holbrooks Road and Statesville Road landfills generally indicated an improvement in water quality and a decrease in effects of leachate at most monitoring sites at these landfills from 1979 to 1992. Water-quality trends detected for monitoring sites at the Harrisburg Road and York Road landfills, the largest landfills in the study, differed in magnitude and direction. Upward trends generally were detected for sites near recently closed waste-disposal cells, whereas downward trends generally were detected for sites near older waste-disposal cells. Temporal trends in water quality generally reflected changes in degradation processes associated with the aging of landfill wastes.

North Carolina↗

USGS1996

Ground-water hydrology, historical water use, and simulated ground-water flow in Cretaceous-age Coastal Plain aquifers near Charleston and Florence, South Carolina

A quasi-three-dimensional, transient, digital, ground-water flow model representing the Coastal Plain aquifers of South Carolina, has been constructed to assist in defining the ground- water-flow system of Cretaceous aquifers near Charleston and Florence, S.C. Both cities are near the centers of large (greater than 150 feet) potentiometric declines in the Middendorf aquifer. In 1989, the diameter of the depressions was approximately 40 miles at Charleston and 15 miles at Florence. The potentiometric decline occurred between predevelopment (1926) and 1982 near Florence, and between predevelopment (1879) and 1989 near Charleston. The city of Charleston does not withdraw water from these aquifers; however, some of the small communities in the area use these aquifers for a potable water supply. The model simulates flow in and between four aquifer systems. The model has a variable-cell-size grid, and spans the Coastal Plain from the Savannah River in the southwest to the Cape Fear Arch in the northeast, and from the Fall Line in the northwest to approximately 30 miles offshore to the southeast. Model-grid cell size is 1 by 1 mile in a 48 by 48 mile area centered in Charleston, and in a 36 by 48 mile area centered in Florence. The model cell size gradually increases to a maximum of 4 by 4 miles outside the two study areas. The entire grid consists of 115 by 127 cells and covers an area of 39,936 square miles. The model was calibrated to historical water-level data. The calibration relied on three techniques: (1) matching simulated and observed potentiometric map surfaces, (2) statistical comparison of observed and simulated heads, and (3) comparison of observed and simulated well hydrographs. Systematic changes in model parameters showed that simulated heads are most sensitive to changes in aquifer transmissivity. Eight predictive ground-water-use scenarios were simulated for the Mount Pleasant area, which presently (1993) uses the Middendorf aquifer as a sole-source of potable water. These simulations use various combinations of spatial distribution, and injection of treated wastewater effluent for existing and future Middendorf aquifer wells.

South Carolina↗

USGS1991

Development of a biotinylated DNA probe for detection of infectious hematopoietic necrosis virus

A nonrad~oact~ve DNA probe assay was developed to detect and ~dent~fy infect~ous hernatopoiet~c necrosls virus (IHNV) uslng a dot blot format The probe a synthet~c DNA oligonucleot~de labeled enzymatlcally w~th biotln hybnd~zed spec~f~cally w~th nucleocaps~d mRNA extracted from Infected cells early In the vlrus repl~cation cycle A rap~d guan~dln~um th~ocyanate based RNA extraction method uslng RNAzol B and rn~crocentrifuge tubes eff~c~ently pioduced h~gh qual~ty RNA from 3 commonly used f~sh cell llnes, CHSE-214, CHH-1, and EPC The probe reacted with 6 d~verse ~solates of IHNV, but d~d not react \nth 2 related rhabdovlruses of fish viral hemorrhagic septlcemla vlrus and H~rame rhabdovlrus The b~ot~nylated probe was sensltlve detect~ng plcogram levels of target mRNA Detect~on and ~dentif~cat~on of IHNV requ~red 2d when cells wele lnoculated at n~ultiplic~t~es of infect~on (MOI) greater than 2 Flve days were necessary to detect and identify IHNV In cells lnoculated at a MO1 of 0 0002

Diseases of Aquatic Organisms↗

USGS1999

Differential expression of the virulence-associated protein p57 and characterization of its duplicated gene rosa in virulent and attenuated strains of Renibacterium salmoninarum

Virulence mechanisms utilized by the salmonid fish pathogen Renibacterium salmoninarum are poorly understood. One potential virulence factor is p57 (also designated MSA for major soluble antigen), an abundant 57 kDa soluble protein that is predominately localized on the bacterial cell surface with significant levels released into the extracellular milieu. Previous studies of an attenuated strain, MT 239, indicated that it differs from virulent strains in the amount of surface-associated p57. In this report, we show overall expression of p57 in R. salmoninarum MT 239 is considerably reduced as compared to a virulent strain, ATCC 33209. The amount of cell-associated p57 is decreased while the level of p57 in the culture supernatant is nearly equivalent between the strains. To determine if lowered amount of cell-associated p57 was due to a sequence defect in p57, a genetic comparison was performed. Two copies of the gene encoding p57 (msa1 and msa2) were found in 33209 and MT 239, as well as in several other virulent isolates. Both copies from 33209 and MT 239 were cloned and sequenced and found to be identical to each other, and identical between the 2 strains. A comparison of msa1 and msa2 within each strain showed that their sequences diverge 40 base pairs 5, to the open reading frame, while sequences 3' to the open reading frame are essentially identical for at least 225 base pairs. Northern blot analysis showed no difference in steady state levels of rosa mRNA between the 2 strains. These data suggest that while cell-surface localization of p57 may be important for R. salmoninarum virulence, the differences in localization, and total p57 expression between 33209 anti MT 239 are not due to differences in rosa sequence or differences in steady state transcript levels.

Diseases of Aquatic Organisms↗

USGS2020

Littoral sediment from rivers: Patterns, rates and processes of river mouth morphodynamics

Rivers provide important sediment inputs to many littoral cells, thereby replenishing sand and gravel of beaches around the world. However, there is limited information about the patterns and processes of littoral-grade sediment transfer from rivers into coastal systems. Here I address these information gaps by examining topographic and bathymetric data of river mouths and constructing sediment budgets to characterize time-dependent patterns of onshore, offshore, and alongshore transport. Two river deltas, which differ in their morphology, were used in this study: the Elwha River, Washington, which builds a mixed sediment Gilbert-style delta, and the Santa Clara River, California, which builds a cross-shore dispersed sand delta from hyperpycnal flows. During and after sediment discharge events, both systems exhibited a similar evolution composed of three phases: (i) submarine delta growth during offshore transport of river sediment, (ii) onshore-dominated transport from the submarine delta to a subaerial river mouth berm, and (iii) longshore-dominated transport away from the river mouth following subaerial berm development. Although stage (ii) occurred within days to weeks for the systems studied and was associated with the greatest rates of net erosion and deposition, onshore transport of sediment from submarine deposit to the beach persisted for years following the river discharge event. These morphodynamics were similar to simple equilibrium profile concepts that were modified with an onshore-dominated cross-shore transport rule. Additionally, both study sites revealed that littoral-grade sediment was initially exported to depths beyond the active littoral cell (i.e., below the depth of closure) during the stage (i). Following several years of reworking by coastal processes, bathymetric surveys suggested that 14 and 46% of the original volume of littoral-grade sediment discharged by the Santa Clara and Elwha Rivers, respectively, continued to be below the depth of closure. Combined, this suggests that integration of river sediment into a littoral cell can be a multi-year process and that the full volume of littoral-grade sediment discharged by small rivers may not be integrated into littoral cells because of sand and gravel “losses” to the continental shelf.

California, Washington↗

USGS2025

Testicular neoplasms and other abnormalities in common carp Cyprinus carpio from the Lower Colorado River, United States

Abnormalities were observed in the testes of common carp Cyprinus carpio collected from Willow Beach, Arizona, USA, a site on the lower Colorado River, downstream of Lake Mead and Hoover Dam. Testicular tissue collected from this site in 2003 exhibited numerous large, pigmented macrophage aggregates (MAs) and a novel, previously undescribed hypertrophy and proliferation of putative Sertoli cells. In testes samples collected in 2007, numerous testicular MA, testicular oocytes, and proliferations of Sertoli cells were observed. Three carp collected in 2007 also had raised nodules within the testes, and, microscopically, seminoma, spermatogenic seminoma, and mixed stromal cell–germ cell neoplasms were diagnosed. Several risk factors for these adverse effects were identified. Carp collected at this site in 2003 ranged in age from 35 to 54 years and had the oldest mean age of the thirteen sites sampled within the Colorado River basin. This site also has an unusual thermal regime when compared to other sites studied in Lake Mead and upstream sites, in that temperatures varied little over the seasons (amplitude around 1.5 °C) and barely reached 15 °C. Additionally, carp from this site had the highest total polychlorinated biphenyl (PCB) body burden. Hence, advanced age, low water temperature, and exposure to PCBs and other environmental contaminants may contribute to the observed abnormalities, highlighting the complex environmental factors initiating pre-neoplastic and neoplastic changes in wild carp.

Arizona↗

USGS2003

Big Soda Lake (Nevada). 1. Pelagic bacterial heterotrophy and biomass

Bacterial activities and abundance were measured seasonally in the water column of meromictic Big Soda Lake which is divided into three chemically distinct zones: aerobic mixolimnion, anaerobic mixolimnion, and anaerobic monimolimnion. Bacterial abundance ranged between 5 and 52 x 10 6 cells ml −1 , with highest biomass at the interfaces between these zones: 2–4 mg C liter −1 in the photosynthetic bacterial layer (oxycline) and 0.8–2.0 mg C liter −1 in the chemocline. Bacterial cell size and morphology also varied with depth: small coccoid cells were dominant in the aerobic mixolimnion, whereas the monimolimnion had a more diverse population that included cocci, rods, and large filaments. Heterotrophic activity was measured by [methyl- 3 H]thymidine incorporation and [ 14 C]glutamate uptake. Highest uptake rates were at or just below the photosynthetic bacterial layer and were attributable to small (<1 µ m) heterotrophs rather than the larger photosynthetic bacteria. These high rates of heterotrophic uptake were apparently linked with fermentation; rates of other mineralization processes (e.g. sulfate reduction, methanogenesis, denitrification) in the anoxic mixolimnion were insignificant. Heterotrophic activity in the highly reduced monimolimnion was generally much lower than elsewhere in the water column. Therefore, although the monimolimnion contained most of the bacterial abundance and biomass (&sim;60%), most of the cells there were inactive.

Nevada↗