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At least 973 records · Page 54Linked to original sources
USGS1997

Digital simulation of ground-water flow in the Warwick Aquifer, Fort Totten Indian Reservation, North Dakota

The demand for water from the Warwick aquifer, which underlies the Fort Totten Indian Reservation in northeastern North Dakota, has been increasing during recent years. Therefore, the Spirit Lake Sioux Nation is interested in resolving questions about the quantity and quality of water in the aquifer and in developing a water-management plan for future water use. A study was conducted to evaluate the surface-water and ground-water resources of the Fort Totten Indian Reservation and, in particular, the ground-water resources in the area of the Warwick aquifer. A major component of the study, addressed by this report, was to define the ground-water flow system of the aquifer. The Warwick aquifer consists of outwash deposits of the Warwick outwash plain that are as much as 30 feet thick and buried-valley deposits beneath the outwash plain that are as much as 200 feet thick. The aquifer is bounded on the north and west by end-moraine deposits and Devils Lake, on the south by the Sheyenne River Valley, and on the east by outwash deposits and ravines. The aquifer is underlain by Pierre Shale or by glacial till, clay, or silt. Ground-water gradients generally are small and rarely are more than 3 or 4 feet per mile. From 1982 to 1993, withdrawals from the Devils Lake well field averaged 1.5 cubic feet per second, and withdrawals from irrigation wells averaged 1.29 cubic feet per second. The combined discharge from springs may be about 3 cubic feet per second. During the early 1990s, the Warwick aquifer probably was in a steady-state condition with regard to storage change in the aquifer. A finite-difference, three-dimensional, ground-water flow model provided a reasonable simulation of ground-water flow in the Warwick aquifer. The aquifer was divided vertically into two layers and horizontally into a grid of 83 by 109 cells, each measuring 656 feet (200 meters) per side. The steady-state simulation was conducted using 1992 pumpage rates and October 1992 water levels. The mean absolute difference between simulated and derived water-level altitudes during final calibration of the model was 1.52 feet. The two transient simulations were conducted for 20 time intervals of 1 year each using both the small and large storage estimates, doubled 1992 pumpage from the Devils Lake well field, 1992 irrigation pumpage, and initial water-level altitudes simulated by the October 1992 steady-state simulation. In the simulation using the small storage estimate and doubled pumpage, model cells in the area of the well field went dry after 13 years. Assumptions made in the design of the model generally are supported by the digital simulation. Except in the area of Warwick Springs and smaller springs, lateral and basal boundaries of the aquifer are impermeable. The flow system is dominated by recharge and evapotranspiration. Recharge rates obtained during the calibration process were lower in topographically high areas than in topographically low areas. Hydraulic conductivity in the area of the Devils Lake well field was larger than that in the rest of the aquifer.

Water-Resources Investigations Report↗
USGS1997

Mesocosm experiments to assess factors affecting phosphorus retention and release in an extended Wisconsin wetland

Phosphorus retention by wetland sediments and vegetation was investigated in Jackson Creek wetland, an extension of an existing prairie marsh in southeastern Wisconsin. The extended wetland construction was undertaken in 1992-93 to help reduce the phosphorus loading to a downstream eutrophic lake. Two approaches were used to study potential and actual phosphorus retention in the system. Mesocosm experiments of 20-40 days duration indicated that retention of total and dissolved reactive phosphorus in mesocosm cells containing macrophytes and/or sediments was reduced by factors of 2-20 relative to cells containing only water or a copper algicide to suppress metabolic activity. In contrast to the nutrient trapping function, these results show a potential for net phosphorus release that can be associated with increased biological richness. Measurements of water flow and nutrient loads at the wetland's inflow and outflow points demonstrated 9-39% net uptake of phosphorus on an annual scale but frequent occurrences of net phosphorus release over shorter (one-month) time scales. These episodes of release are most likely during the summer months. Thus, the wetland role in phosphorus cycling is not one of a true source or sink, although the annual budget data alone suggest substantial net retention. Effective management of the wetland for its nutrient trapping potential can be hindered by this oversimplification. The system is instead subject to relatively short-term alternation between net import and export. The periodic phosphorus export, although representing a small fraction of net annual import, could be critical for growth of macrophyte and algal communities downstream.

Wisconsin↗
USGS1998

Hydrogeology and simulation of ground-water flow in the Paluxy aquifer in the vicinity of Landfills 1 and 3, U.S. Air Force Plant 4, Fort Worth, Texas

Ground-water contamination of the surficial terrace alluvial aquifer has occurred at U.S. Air Force Plant 4, a government-owned, contractor-operated facility, northwest of Fort Worth, Texas. A poorly constructed monitoring well, P–22M, open to the underlying middle zone of the Paluxy aquifer was installed at landfill 3, October 1987, allowing leakage of contaminated ground water to reach the Paluxy aquifer. This well was plugged and abandoned in November 1995. Additionally, volatile organic compounds have been detected in fractures in the Goodland-Walnut confining unit, the hydrogeologic unit separating the terrace alluvial aquifer from the underlying Paluxy aquifer, beneath the western part of landfill 1. Volatile organic compounds in concentrations near the analytical detection limit were detected in the upper Paluxy prior to the drilling of well P–22M. The ground-water-flow simulation model described in this report was developed to examine the best logistically feasible location to install recovery wells to capture the low concentration (less than 100 micrograms per liter) trichloroethylene plume beneath landfills 1 and 3 (west Paluxy plume). Once the recovery wells were installed (1996), the simulation model was recalibrated with new data. This report documents the capture area of the installed recovery wells. Four geologic units are pertinent to this site-specific model. From oldest to youngest, these are the Glen Rose Formation, Paluxy Formation, Walnut Formation, and Goodland Limestone. The Glen Rose Formation is relatively impermeable in the study area and forms the confining unit underlying the Paluxy Formation. The Paluxy Formation forms the Paluxy aquifer, which is a public drinking water supply for the City of White Settlement. The Walnut Formation and Goodland Limestone form the Goodland-Walnut confining unit overlying the Paluxy aquifer. Near landfill 3, gamma-ray logs indicate three distinct zones of the Paluxy Formation; upper, middle, and lower. The formation is about 170-feet thick near landfill 3, and each zone is about 57-feet thick. Two steady-state simulations using the computer program MODFLOW were analyzed using the particle-tracking computer program, MODPATH. One simulation is the calibration simulation using Paluxy aquifer water-level data for May 1993. The second simulation includes the installed recovery wells. A variably spaced grid was designed for the model. The smallest grid cells, 25 by 25 feet, are in the vicinity of landfills 1 and 3. The largest cells, 4,864.5 by 1,441.5 feet, are at the northwestern corner of the model grid near the Parker-Tarrant County line. The modeling was accomplished with three layers representing the upper, middle, and lower zones of the Paluxy aquifer. Particles, which represent contaminant molecules moving in solution with the ground water, were tracked from well P–22M and an area below landfill 1, at the top of the upper zone of the Paluxy aquifer, for 9 years (forward tracking). The forward tracking estimates where contaminants might move by advection from 1987 to 1996. Analysis of backward tracking from the new recovery wells indicates that the simulated contributing area to the recovery wells intercepts the contaminant plume, minimizing off-site migration of the west Paluxy plume. To determine the effectiveness of the recovery wells, monitoring wells southeast of Building 14 have been installed (1996–97) for sampling.

Texas↗
USGS2000

Methods of rating unsaturated zone and watershed characteristics of public water supplies in North Carolina

Overlay and index methods were derived for rating the unsaturated zone and watershed characteristics for use by the State of North Carolina in assessing more than 11,000 public water-supply wells and approximately 245 public surface-water intakes. The rating of the unsaturated zone and watershed characteristics represents a practical and effective means of assessing part of the inherent vulnerability of water supplies to potential contamination. Factors that influence the inherent vulnerability of the drinking water supply to potential contamination were selected and assigned ratings (on a scale of 1 to 10) to cover the possible range of values in North Carolina. These factors were assigned weights of 1, 2, or 3 to reflect their relative influence on the inherent vulnerability of the drinking water supply. The factor values were obtained from Geographic Information System data layers, and were transformed into grids having 60-meter by 60-meter cells, with each cell being assigned a value. Identification of factors, the development of ratings for each, and assignment of weights were based on (1) a literature search, which included examination of potential factors and their effects on the drinking water; and (2) consultation with experts in the science and engineering of hydrology, geology, forestry, agriculture, and water management. Factors selected for rating the inherent vulnerability of the unsaturated zone are vertical hydraulic conductance, land-surface slope, land cover, and land use. Vertical hydraulic conductance is a measure of the capacity of unsaturated material to transmit water. Land-surface slope influences whether precipitation runs off land surfaces or infiltrates into the subsurface. Land cover, the physical overlay of the land surface, influences the amount of precipitation that becomes overland flow or infiltrates into the subsurface. Land use describes activities that occur on the land surface and influence the potential generation of nonpoint-source contamination. Factors selected for rating the watershed characteristics upstream from surface-water intakes are average annual precipitation, land-surface slope, land cover, land use, and ground-water contribution. The average annual precipitation represents the mass of water that becomes available for transport in a watershed. Land-surface slope, land cover, and land use have similar influences in watersheds as those identified for the unsaturated zone. Ground-water contribution represents the part of streamflow that is derived from ground-water discharge.

North Carolina↗
USGS1969

Factors initiating phytoplankton blooms and resulting effects on dissolved oxygen in Duwamish River estuary, Seattle, Washington

Phytoplankton productivity, standing stock, and related environmental factors were studied during 1964-66 in the Duwamish River estuary, at Seattle, Wash., to ascertain the factors that affect phytoplankton growth in the estuary; a knowledge of these factors in turn permits the detection and evaluation of the influence that effluent nutrients have on phytoplankton production. The factors that control the concentration of dissolved oxygen were also evaluated because of the importance of dissolved oxygen to the salmonid populations that migrate through the estuary. Phytoplankton blooms, primarily of diatoms, occurred in the lower estuary during August 1965 and 1966. No bloom occurred during 1964, but the presence of oxygen-supersaturated surface water in August 1963 indicates that a bloom did occur then. Nutrients probably were not the primary factor controlling the timing of phytoplankton blooms. Ammonia ,and phosphate concentrations increased significantly downstream from the Municipality of Metropolitan Seattle's Renton Treatment Plant outfall after the plant began operation in June 1965, and concentrations of nitrogen and phosphorus were relatively high before operation of the Renton Treatment Plant and during nonbloom periods. The consistent coincidence of blooms with minimum fresh-water discharge and tidal exchange during August throughout the study period indicates that bloom timing probably was controlled mostly by hydrographic factors that determine retention time and stability of the surface-water layer. This control was demonstrated in part by a highly significant correlation of gross productivity with retention time (as indicated by fresh-water discharge) and vertical stability (as indicated by the difference between mean surface and mean bottom temperatures). The failure of a bloom to develop in 1964 is related to a minimum fresh-water discharge that was much greater than normal during that summer. Hydrographic factors are apparently important because, as shown by studies of other estuarine environments by other workers, phytoplankton production increases when the zone of vertical turbulent mixing is not markedly deeper than the compensation depth. Phytoplankton cells produced in the surface waters sink, thereby contributing oxidizable organic matter to the bottom saline-water wedge. The maximum BOD (biochemical oxygen demand) in this bottom wedge occurs in the same section of the estuary and ,at the same time as the maximum phytoplankton biomass (as indicated by chlorophyll a) and minimum DO (dissolved oxygen). Other sources of BOD occur in the estuary, and conditions of minimum discharge and tidal exchange assist in reducing DO. Nonetheless, the highly significant correlation of chlorophyll a with BOD throughout the summer indicates that respiration and decomposition of phytoplankton cells is dearly an important contributor of BOD. Increases in the biomass and resultant B0D of blooms because of increased effluent nutrients presumably would further decrease the concentration of DO. This possible effect of effluent nutrients was evaluated by laboratory .bioassays and by a comparison of mean annual biomasses in the estuary. A green algal population in vitro did increase in response to added effluent nutrients; however, the available field data suggest that a 46-percent increase in effluent discharge between 1965 and 1966 did not increase the estuary's phytoplankton biomass significantly.

Water Supply Paper↗
USGS1979

Magnitudes, nature, and effects of point and nonpoint discharges in the Chattahoochee River Basin, Atlanta to West Point Dam, Georgia

During the period April 1975 to June 1978, the U.S. Geological Survey conducted a river-quality assessment of the Upper Chattahoochee River basin in Georgia. One objective of the study was to assess the magnitudes, nature, and effects of point and non-point discharges in the Chattahoochee River basin from Atlanta to the West Point Dam. On an average annual basis and during the storm period of March 1215, 1976, non-point-source loads for most constituents analyzed were larger than point-source loads at the Whitesburg station, located on the Chattahoochee River about 40 river miles downstream of Atlanta. Most of the non-point-source constituent loads in the Atlanta-to-Whitesburg reach were from urban areas. Average annual point-source discharges accounted for about 50 percent of the dissolved nitrogen, total nitrogen, and total phosphorus loads, and about 70 percent of the dissolved phosphorus loads at Whitesburg. During weekends, power generation at the upstream Buford Dam hydroelectric facility is minimal. Streamflow at the Atlanta station during dry-weather weekends is estimated to be about 1,200 ft3/s (cubic feet per second). Average daily dissolved-oxygen concentrations of less than 5.0 mg/L (milligrams per liter) occurred often in the river, about 20 river miles downstream from Atlanta during these periods from May to November. During a low-flow period, June 1-2, 1977, five municipal point sources contributed 63 percent of the ultimate biochemical oxygen demand, 97 percent of the ammonium nitrogen, 78 percent of the total nitrogen, and 90 percent of the total phosphorus loads at the Franklin station, at the upstream end of West Point Lake. Average daily concentrations of 13 mg/L of ultimate biochemical oxygen demand and 1.8 mg/L of ammonium nitrogen were observed about 2 river miles downstream from two of the municipal point sources. Carbonaceous and nitrogenous oxygen demands caused dissolved-oxygen concentrations between 4.1 and 5.0 mg/L to occur in a 22-mile reach of the river downstream from Atlanta. Nitrogenous oxygen demands were greater than carbonaceous oxygen demands in the reach from river mile 303 to 271, and carbonaceous demands were greater from river mile 271 to 235. The heat load from the Atkinson-McDonough thermoelectric power-plants caused a decrease in the dissolved-oxygen concentrations of about 0.2 mg/L. During a critical low-flow period, a streamflow at Atlanta of about 1,800 ft3/s, with present (1977) point-source flows of 185 ft3/s containing concentrations of 45 mg/L of ultimate biochemical oxygen demand and 15 mg/L of ammonium nitrogen, results in a computed minimum dissolved-oxygen concentration of 4.7 mg/L in the river downstream from Atlanta. In the year 2000, a streamflow at Atlanta of about 1,800 ft3/s with point-source flows of 373 ft3/s containing concentrations of 45 mg/L of ultimate biochemical oxygen demand and 5.0 mg/L of ammonium nitrogen, will result in a computed minimum dissolved-oxygen concentration of 5.0 mg/L. A streamflow of about 1,050 ft3/s at Atlanta in the year 2000 will result in a dissolved-oxygen concentration of 5.0 mg/L if point-source flows contain concentrations of 15 mg/L of ultimate biochemical oxygen demand and 5.0 mg/L of ammonium nitrogen. Phytoplankton concentrations in West Point Lake, about 70 river miles downstream from Atlanta, could exceed 3 million cells per milliliter during extended low-flow periods in the summer with present point- and non-point-source nitrogen and phosphorus loads. In the year 2000, phytoplankton concentrations in West Point Lake are not likely to exceed 700,000 cells per milliliter during extended low-flow periods in the summer, if phosphorus concentrations do not exceed 1.0 mg/L in point-source discharges.

Georgia↗
USGS1997

Hydrogeology and simulation of ground-water flow in the thick regolith-fractured crystalline rock aquifer system of Indian Creek basin, North Carolina

The Indian Creek Basin in the southwestern Piedmont of North Carolina is one of five type areas studied as part of the Appalachian Valleys-Piedmont Regional Aquifer-System analysis. Detailed studies of selected type areas were used to quantify ground-water flow characteristics in various conceptual hydrogeologic terranes. The conceptual hydrogeologic terranes are considered representative of ground-water conditions beneath large areas of the three physiographic provinces--Valley and Ridge, Blue Ridge, and Piedmont--that compose the Appalachian Valleys-Piedmont Regional Aquifer-System Analysis area. The Appalachian Valleys-Piedmont Regional Aquifer-System Analysis study area extends over approximately 142,000 square miles in 11 states and the District of Columbia in the Appalachian highlands of the Eastern United States. The Indian Creek type area is typical of ground-water conditions in a single hydrogeologic terrane that underlies perhaps as much as 40 percent of the Piedmont physiographic province. The hydrogeologic terrane of the Indian Creek model area is one of massive and foliated crystalline rocks mantled by thick regolith. The area lies almost entirely within the Inner Piedmont geologic belt. Five hydrogeologic units occupy major portions of the model area, but statistical tests on well yields, specific capacities, and other hydrologic characteristics show that the five hydrogeologic units can be treated as one unit for purposes of modeling ground-water flow. The 146-square-mile Indian Creek model area includes the Indian Creek Basin, which has a surface drainage area of about 69 square miles. The Indian Creek Basin lies in parts of Catawba, Lincoln, and Gaston Counties, North Carolina. The larger model area is based on boundary conditions established for digital simulation of ground-water flow within the smaller Indian Creek Basin. The ground-water flow model of the Indian Creek Basin is based on the U.S. Geological Survey?s modular finite-difference ground-water flow model. The model area is divided into a uniformly spaced grid having 196 rows and 140 columns. The grid spacing is 500 feet. The model grid is oriented to coincide with fabric elements such that rows are oriented parallel to fractures (N. 72° E.) and columns are oriented parallel to foliation (N. 18° W.). The model is discretized vertically into 11 layers; the top layer represents the soil and saprolite of the regolith, and the lower 10 layers represent bedrock. The base of the model is 850 feet below land surface. The top bedrock layer, which is only 25 feet thick, represents the transition zone between saprolite and unweathered bedrock. The assignment of different values of transmissivity to the bedrock according to the topographic setting of model cells and depth results in inherent lateral and vertical anisotropy in the model with zones of high transmissivity in bedrock coinciding with valleys and draws, and zones of low transmissivity in bedrock coinciding with hills and ridges. Lateral anisotropy tends to be most pronounced in the north-northwest to south-southeast direction. Transmissivities decrease nonlineraly with depth. At 850 feet, depending on topographic setting, transmissivities have decreased to about 1 to 4 percent of the value of transmissivity immediately below the regolith-bedrock interface. The model boundaries are, for the most part, specified-flux boundaries that coincide with streams that surround the Indian Creek Basin. The area of active model nodes within the boundaries is about 146 square miles and has about 17,400 active cells. The numerical model is designed not as a predictive tool, but as an interpretive one. The model is designed to help gain insight into flow-system dynamics. Predictive capabilities of the numerical model are limited by the constraints placed on the flow system by specified fluxes and recharge distribution.

North Carolina↗
USGS1996

Simulation of ground-water flow in the Saginaw Aquifer, Clinton, Eaton, and Ingham counties, Michigan

A numerical model was developed to simulate ground-water flow in the Tri-County region, which consists of Clinton, Eaton, and Ingham Counties, Michigan. This region includes a nine-township area surrounding Lansing, Michigan. The model simulates the regional response of the Saginaw aquifer to major groundwater withdrawals associated with public-supply wells. The Saginaw aquifer, which is in the Grand River and Saginaw Formations of Pennsylvanian age, is the primary source of ground water for Tri-County residents. The Saginaw aquifer is overlain by glacial deposits, which also are important ground-water sources in some locations. Flow in the Saginaw aquifer and the glacial deposits is simulated by discretizing the flow system into model cells arranged in two layers. Each cell, which corresponds to a land area of 0.0625 square mile, represents the locally averaged properties of the system. The spatial variation of hydraulic properties controlling ground-water flow was estimated by geostatistical analysis of 4,947 well logs. Parameter estimation, a form of nonlinear regression, was used to calibrate the flow model. Results of steady-state ground-water-flow simulations show close agreement between water flowing into and out of the model area for 1992 pumping conditions; standard error of the difference between simulated and measured heads is 14.7 feet. Simulation results for three alternative pumping scenarios for the year 2020 show that the glacial aquifer could be dewatered in places if hypothetical increases in pumping are not distributed throughout the Tri-County region. Contributing areas to public-supply wells in the nine-township area were delineated by a particle-tracking analysis. These areas cover about 121 square miles. Contributing areas for particles having travel times of 40 years or less cover about 42 square miles. Results of tritium sampling support results of model simulations to delineate contributing areas.

Michigan↗
USGS1991

Comparison of genome size and synthesis of structural proteins of Hirame Rhabdovirus, infectious hematopoietic necrosis virus, and viral hemorrhagic Septicemia virus

Genomic RNA was extracted from purified virions of hirame rhabdovirus (HRV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The full-length RNA was analyzed using formaldehyde agarose gel electrophoresis followed by ethidium bromide staining. Compared with an internal RNA size standard, all three viral genomic RNAs appeared to have identical relative mobilities and were estimated to be approximately 10.7 kilobases in length or about 3.7 megadaltons in molecular mass. Structural protein synthesis of HRV, IHNV, and VHSV was studied using cell cultures treated with actinomycin D. At 2 h intervals, proteins were labeled with 35 S-methionine, extracted, and analyzed by SDS-polyacrylamide gel electrophoresis and autoradiography. The five structural proteins of each of the three viruses appeared in the following order : nucleoprotein (N), matrix protein 1 (M1), matrix protein 2 (M2), glycoprotein (G), and polymerase (L) reflecting both the approximate relative abundance of each protein within infected cells and the gene order within the viral genome.

Fish Pathology↗
USGS1993

Isolates of viral hemorrhagic septicemia virus from North America and Europe can be detected and distinguished by DNA probes

Biotinylated DNA probes were constructed to hybndize with speclfic sequences within the messenger RNA (mRNA) of the nucleoprotein (N) gene of vlral hemorrhagic septicemia virus (VHSV) reference strains from Europe (07-71) and North Arnenca (Makah) Probes were synthesized that were complementary to (1) a 29-nucleotide sequence near the center of the N gene conlmon to both the 07-71 and Makah reference strains of the virus (2) a unique 28- nucleotide sequence that followed the open readng frame of the Makah N gene mRNA most of which was absent In the 07-71 strain, and (3) a 22-nucleobde sequence wthin the 07-71 N gene that had 6 nllsmatches \nth the Makah straln Sixteen dlverse isolates of VHSV from North Amenca and Europe were tested by dot blot hybridization The first probe reacted with all isolates of the virus the second probe reacted with only the North Amencan isolates (includng those from Pacific cod), and the third probe reacted with only the European isolates, Including those from rainbow trout brown trout and Atlantic cod The probes did not react with mRNA extracted from uninfected cells or from cells infected with infectious hematopoletic necrosls vlrus (IHNV) a related fish rhabdovlrus The results showed that VHSV isolates from North Amenca and Europe formed 2 genetically distlnct strains of the virus in which isolates from different years or species of flsh on each continent were more related to each other than to isolates from the other continent The results of this and other studies indicate that the North Amencan straln of VHSV is enzootic in the North Pacific Ocean and IS not a result of a recent importation of fish from Europe When used In conlunchon with a biotinylated probe that recognizes all isolates of IHNV, these reagents promse to slrnphfy the detechon of salmonid rhabdoviruses

Diseases of Aquatic Organisms↗
USGS1994

Involvement of rainbow trout leucocytes in the pathogenesis of infectious hematopoietic necrosis

Rainbow trout Oncorhynchus myluss leucocytes were tested for their ability to support replication of infectious hematopoietic necrosis virus (IHNV). Viral replication occurred in vitro uslng leucocytes cultured from peripheral blood, kidney, and thymus where viral titers peaked at 2 to 4 d post-inoculation. Leucocytes collected from trout following waterborne challenge with IHNV were cocultured on EPC cell monolayers. These assays detected IHNV in leucocytes infected in vivo as early as 6 h post-exposure before the challenge virus had undergone replication. These data showed that leucocyte populations could serve as target cells in the initial phase of IHNV infection.

Diseases of Aquatic Organisms↗
USGS2013

Universal reverse-transcriptase real-time PCR for infectious hematopoietic necrosis virus (IHNV)

Infectious hematopoietic necrosis virus (IHNV) is an acute pathogen of salmonid fishes in North America, Europe and Asia and is reportable to the World Organization for Animal Health (OIE). Phylogenetic analysis has identified 5 major virus genogroups of IHNV worldwide, designated U, M, L, E and J; multiple subtypes also exist within those genogroups. Here, we report the development and validation of a universal IHNV reverse-transcriptase real-time PCR (RT-rPCR) assay targeting the IHNV nucleocapsid (N) gene. Properties of diagnostic sensitivity (DSe) and specificity (DSp) were defined using laboratory-challenged steelhead trout Oncorhynchus mykiss, and the new assay was compared to the OIE-accepted conventional PCR test and virus isolation in cell culture. The IHNV N gene RT-rPCR had 100% DSp and DSe and a higher estimated diagnostic odds ratio (DOR) than virus culture or conventional PCR. The RT-rPCR assay was highly repeatable within a laboratory and highly reproducible between laboratories. Field testing of the assay was conducted on a random sample of juvenile steelhead collected from a hatchery raceway experiencing an IHN epizootic. The RT-rPCR detected a greater number of positive samples than cell culture and there was 40% agreement between the 2 tests. Overall, the RT-rPCR assay was highly sensitive, specific, repeatable and reproducible and is suitable for use in a diagnostic setting.

Diseases of Aquatic Organisms↗
USGS2002

Spring viremia of carp

pring viremia of carp (SVC) is an important disease affecting cyprinids, mainly common carp Cyprinus carpio . The disease is widespread in European carp culture, where it causes significant morbidity and mortality. Designated a notifiable disease by the Office International des Epizooties, SVC is caused by a rhabdovirus, spring viremia of carp virus (SVCV). Affected fish show destruction of tissues in the kidney, spleen and liver, leading to hemorrhage, loss of water-salt balance and impairment of immune response. High mortality occurs at water temperatures of 10 to 17°C, typically in spring. At higher temperatures, infected carp develop humoral antibodies that can neutralize the spread of virus and such carp are protected against re-infection by solid immunity. The virus is shed mostly with the feces and urine of clinically infected fish and by carriers. Waterborne transmission is believed to be the primary route of infection, but bloodsucking parasites like leeches and the carp louse may serve as mechanical vectors of SVCV. The genome of SVCV is composed of a single molecule of linear, negative-sense, single-stranded RNA containing 5 genes in the order 3¹-NPMGL-5¹ coding for the viral nucleoprotein, phosphoprotein, matrix protein, glycoprotein, and polymerase, respectively. Polyacrylamide gel electrophoresis of the viral proteins, and sequence homologies between the genes and gene junctions of SVCV and vesicular stomatitis viruses, have led to the placement of the virus as a tentative member of the genus Vesiculovirus in the family Rhabdoviridae . These methods also revealed that SVCV is not related to fish rhabdoviruses of the genus Novirhabdovirus . In vitro replication of SVCV takes place in the cytoplasm of cultured cells of fish, bird and mammalian origin at temperatures of 4 to 31°C, with an optimum of about 20°C. Spring viremia of carp can be diagnosed by clinical signs, isolation of virus in cell culture and molecular methods. Antibodies directed against SVCV react with the homologous virus in serum neutralization, immunofluorescence, immunoperoxidase, or enzyme-linked immunosorbent assays, but they cross-react to various degrees with the pike fry rhabdovirus (PFR), suggesting the 2 viruses are closely related. However, SVCV and PFR can be distinguished by certain serological tests and molecular methods such as the ribonuclease protection assay.

Diseases of Aquatic Organisms↗
USGS2004

Molecular characterization of birnaviruses isolated from wild marine fishes at the Flemish Cap (Newfoundland)

Several isolates of aquatic birnaviruses were recovered from different species of wild fish caught in the Flemish Cap, a Newfoundland fishery close to the Atlantic coast of Canada. The nucleotide sequence of a region of the NS gene was identical among the isolates and was most similar to the Dry Mills and West Buxton reference strains of infectious pancreatic necrosis virus (IPNV). Phylogenetic analysis of the sequence of a region of the VP2 gene demonstrated that the isolates were most closely aligned with the American strains of IPNV serotype Al. Electron microscopy of virus structures clarified and concentrated from cultures of infected chinook salmon embryo (CHSE-214) cells revealed a majority of typical IPNV-like icosahedral particles, as well as a low proportion of type I tubules having a diameter of approximately 55 nm and a variable length of up to 2 µm . The tubules could be propagated in cell cultures, but always in the presence of low proportions of icosahedral particles. Cloning of selected isolates by serial dilution yielded preparations with a high proportion of the tubular structures with a density in CsCl gradients of approximately 1.30 g cm -3 . Polyacrylamide gel electrophoresis revealed the material in the band was composed of the IPNV pVP2 and VP2 proteins.

Flemish Cap↗
USGS2007

Detection of viral hemorrhagic septicemia in round gobies in New York State (USA) waters of Lake Ontario and the St. Lawrence River

In May 2006 a large mortality of several thousand round gobies Neogobius melanostomus (Pallas, 1814) occurred in New York waters of the St. Lawrence River and Lake Ontario. Necropsies of sampled fish from these areas showed pallor of the liver and gills, and hemorrhagic areas in many organs. Histopathologic examination of affected tissues revealed areas of necrosis and hemorrhage. Inoculations of fathead minnow Pimephales promelas (Rafinesque, 1820) cell cultures with dilutions of tissue samples from the necropsied gobies produced a cytopathic effect within 5 d post-inoculation. Samples of cell culture supernatant were tested using RT-PCR and confirmed the presence of viral hemorrhagic septicemia virus (VHSV). Sequence analysis of the VHSV isolate resulted in its assignment to the type-IVb subgroup. The detection of VHSV in a relatively recent invasive fish species in the Great Lakes and the potential impact of VHSV on the ecology and economy of the area will require further investigation and careful management considerations. Inter-Research 2007.

New York↗
USGS2007

Poplar Island Environmental Restoration Project: Challenges in waterbird restoration on an island in Chesapeake Bay

At 460 hectares, the Paul Sarbanes Environmental Restoration Project at Poplar Island, Talbot County, Maryland, represents the largest 'beneficial use' dredged material project of the U. S. Army Corps of Engineers (a cooperative project with Maryland Port Administration). Begun in 1998, the 15-year restoration project will ultimately consist of roughly 220 ha of uplands and 220 ha of tidal wetland habitats, with limited areas of dike roads, perimeter riprap, and unvegetated mudflats. Wetland restoration began in one small section (or 'cell') in 2002, but not all cells will be filled with dredged material until at least 2013. As a major objective of the restoration, six species of waterbirds were identified as 'priority species' for Chesapeake Bay: American black duck ( Anas rubripes ), snowy egret ( Egretta thula ), cattle egret ( Bubulcus ibis ), osprey ( Pandion haliaetus ), common tern ( Sterna hirundo ), and least tern ( S. antillarum ). Monitoring of nesting activities of these species from 2002 to 2005 indicated that all species except black ducks colonized the site rapidly. More than 800 pairs of common terns nested in 2003 to 2004. Because of predation by red fox ( Vulpes vulpes ) and great horned owl ( Bubo virginianus ), reproductive success was very low for the terns. Trapping was effective in removing the foxes, and other controls have been applied to opportunistic nesting species including herring gulls ( Larus argentatus ) and Canada geese ( Branta canadensis ). An effective public education program on the island has helped address concerns about animal control.

Maryland↗
USGS2023

Unprecedented distribution data for Joshua trees (Yucca brevifolia and Y. jaegeriana) reveal contemporary climate associations of a Mojave Desert icon

Introduction: Forecasting range shifts in response to climate change requires accurate species distribution models (SDMs), particularly at the margins of species' ranges. However, most studies producing SDMs rely on sparse species occurrence datasets from herbarium records and public databases, along with random pseudoabsences. While environmental covariates used to fit SDMS are increasingly precise due to satellite data, the availability of species occurrence records is still a large source of bias in model predictions. We developed distribution models for hybridizing sister species of western and eastern Joshua trees ( Yucca brevifolia and Y. jaegeriana , respectively), iconic Mojave Desert species that are threatened by climate change and habitat loss. Methods: We conducted an intensive visual grid search of online satellite imagery for 672,043 0.25 km 2 grid cells to identify the two species' presences and absences on the landscape with exceptional resolution, and field validated 29,050 cells in 15,001 km of driving. We used the resulting presence/absence data to train SDMs for each Joshua tree species, revealing the contemporary environmental gradients (during the past 40 years) with greatest influence on the current distribution of adult trees. Results: While the environments occupied by Y. brevifolia and Y. jaegeriana were similar in total aridity, they differed with respect to seasonal precipitation and temperature ranges, suggesting the two species may have differing responses to climate change. Moreover, the species showed differing potential to occupy each other's geographic ranges: modeled potential habitat for Y. jaegeriana extends throughout the range of Y. brevifolia , while potential habitat for Y. brevifolia is not well represented within the range of Y. jaegeriana . Discussion: By reproducing the current range of the Joshua trees with high fidelity, our dataset can serve as a baseline for future research, monitoring, and management of this species, including an increased understanding of dynamics at the trailing and leading margins of the species' ranges and potential for climate refugia.

Frontiers Ecology and Evolution↗
USGS2019

Standardized IMGT nomenclature of salmonidae IGH genes, the paradigm of Atlantic salmon and rainbow trout: From genomics to repertoires

In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.

Frontiers in Immunology↗