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USGS2014

Long Term Resource Monitoring Program procedures: fish monitoring

This manual constitutes the second revision of the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration-Environmental Management Program (UMRR-EMP) Long Term Resource Monitoring Program (LTRMP) element Fish Procedures Manual. The original (1988) manual merged and expanded on ideas and recommendations related to Upper Mississippi River fish sampling presented in several early documents. The first revision to the manual was made in 1995 reflecting important protocol changes, such as the adoption of a stratified random sampling design. The 1995 procedures manual has been an important document through the years and has been cited in many reports and scientific manuscripts. The resulting data collected by the LTRMP fish component represent the largest dataset on fish within the Upper Mississippi River System (UMRS) with more than 44,000 collections of approximately 5.7 million fish. The goal of this revision of the procedures manual is to document changes in LTRMP fish sampling procedures since 1995. Refinements to sampling methods become necessary as monitoring programs mature. Possible refinements are identified through field experiences (e.g., sampling techniques and safety protocols), data analysis (e.g., planned and studied gear efficiencies and reallocations of effort), and technological advances (e.g., electronic data entry). Other changes may be required because of financial necessity (i.e., unplanned effort reductions). This version of the LTRMP fish monitoring manual describes the most current (2014) procedures of the LTRMP fish component.

Illinois;Iowa;Minnesota;Montana;Wisconsin↗

USGS2013

Evidence for deposition of 10 million tonnes of impact spherules across four continents 12,800 y ago

Airbursts/impacts by a fragmented comet or asteroid have been proposed at the Younger Dryas onset (12.80 ± 0.15 ka) based on identification of an assemblage of impact-related proxies, including microspherules, nanodiamonds, and iridium. Distributed across four continents at the Younger Dryas boundary (YDB), spherule peaks have been independently confirmed in eight studies, but unconfirmed in two others, resulting in continued dispute about their occurrence, distribution, and origin. To further address this dispute and better identify YDB spherules, we present results from one of the largest spherule investigations ever undertaken regarding spherule geochemistry, morphologies, origins, and processes of formation. We investigated 18 sites across North America, Europe, and the Middle East, performing nearly 700 analyses on spherules using energy dispersive X-ray spectroscopy for geochemical analyses and scanning electron microscopy for surface microstructural characterization. Twelve locations rank among the world’s premier end-Pleistocene archaeological sites, where the YDB marks a hiatus in human occupation or major changes in site use. Our results are consistent with melting of sediments to temperatures >2,200 °C by the thermal radiation and air shocks produced by passage of an extraterrestrial object through the atmosphere; they are inconsistent with volcanic, cosmic, anthropogenic, lightning, or authigenic sources. We also produced spherules from wood in the laboratory at >1,730 °C, indicating that impact-related incineration of biomass may have contributed to spherule production. At 12.8 ka, an estimated 10 million tonnes of spherules were distributed across ∼50 million square kilometers, similar to well-known impact strewnfields and consistent with a major cosmic impact event.

Proceedings of the National Academy of Sciences of↗

USGS2013

Usefulness of hemocytometer as a counting chamber in a computer assisted sperm analyzer (CASA)

Several methods are used to determine sperm cell concentration, such as the haemocytometer, spectrophotometer, electronic cell counter and computer-assisted semen analysers (CASA). The utility of CASA systems has been limited due to the lack of characterization of individual systems and the absence of standardization among laboratories. The aims of this study were to: 1) validate and establish setup conditions for the CASA system utilizing the haemocytometer as a counting chamber, and 2) compare the different methods used for the determination of sperm cell concentration in bull semen. Two ejaculates were collected and the sperm cell concentration was determined using spectrophotometer and haemocytometer. For the Hamilton-Thorn method, the haemocytometer was used as a counting chamber. Sperm concentration was determined three times per ejaculate samples. A difference (P < 0.05) was found between all methods of measuring sperm cell concentration. However, no difference was found between the haemocytometer and CASA system when the haemocytometer was used as a counting chamber (P > 0.05) or between the haemocytometer count and the spectrophotometer. Based on the results of this study, we concluded that the haemocytometer can be used in computerized semen analysis systems as a substitute for the commercially available disposable counting chambers, therefore avoiding disadvantageous high costs and slower procedures.

Animal Reproduction↗

USGS2014

Viral erythrocytic necrosis

Viral erythrocytic necrosis (VEN), originally termed piscine erythrocytic necrosis, is a condition that has been reported to affect the red blood cells (RBCs) of many species of marine and anadromous fishes in both the Atlantic and Pacific Oceans (Nicholson and Reno 1981; Smail 1982; Wolf 1988; Dannevig and Thorud 1999). Fish with VEN may develop a severe anemia that can reduce their stamina, predispose them to other infections or increase the impact of other stressors (MacMillan et al. 1980; Nicholson and Reno 1981; Meyers et al. 1986; Haney et al. 1992) resulting in population-scale impacts in susceptible species (Hershberger et al. 2009). In spite of extensive efforts, the etiological agent of VEN has not been propagated in fish cell lines making its characterization difficult. However, transmission electron microscopy (TEM) of red blood cells from diseased fish convincingly demonstrates the presence of iridovirus-like particles that have been given the name erythrocytic necrosis virus (ENV). While the ENV virions in red blood cells of various species of fish from differing geographic locations may appear morphologically distinct (Smail 1982; Wolf 1988), at least one strain of ENV has now been partially sequenced, confirming it to be a member of the family Iridoviridae (Emmenegger et al. in press). However, the genetic relatedness of ENV from various fish hosts has not yet been investigated.

Book chapter↗

USGS2014

U.S. Geological Survey external quality-assurance project report for the National Atmospheric Deposition Program / National Trends Network and Mercury Deposition Network, 2011-2012

The U.S. Geological Survey operated six distinct programs to provide external quality-assurance monitoring for the National Atmospheric Deposition Program (NADP) / National Trends Network (NTN) and Mercury Deposition Network (MDN) during 2011–2012. The field-audit program assessed the effects of onsite exposure, sample handling, and shipping on the chemistry of NTN samples; a system-blank program assessed the same effects for MDN. Two interlaboratory-comparison programs assessed the bias and variability of the chemical analysis data from the Central Analytical Laboratory and Mercury Analytical Laboratory (HAL). A blind-audit program was implemented for the MDN during 2011 to evaluate analytical bias in HAL total mercury concentration data. The co-located–sampler program was used to identify and quantify potential shifts in NADP data resulting from the replacement of original network instrumentation with new electronic recording rain gages and precipitation collectors that use optical precipitation sensors. The results indicate that NADP data continue to be of sufficient quality for the analysis of spatial distributions and time trends of chemical constituents in wet deposition across the United States. Co-located rain gage results indicate -3.7 to +6.5 percent bias in NADP precipitation-depth measurements. Co-located collector results suggest that the retrofit of the NADP networks with the new precipitation collectors could cause +10 to +36 percent shifts in NADP annual deposition values for ammonium, nitrate, and sulfate; -7.5 to +41 percent shifts for hydrogen-ion deposition; and larger shifts (-51 to +52 percent) for calcium, magnesium, sodium, potassium, and chloride. The prototype N-CON Systems bucket collector typically catches more precipitation than the NADP-approved Aerochem Metrics Model 301 collector.

Report↗

USGS2015

The importance of particulate texture to the flow strength of ice + dust

Preliminary experimental surveys of the flow of dilute mixtures of ice plus hard particulates under planetary conditions indicate a strengthening effect with respect to pure ice, but with dependencies on environmental conditions (temperature, stress, grain size) that vary widely from study to study [1-4]. With the expectation that the textural character of the particulate fraction (size, shape, spatial distribution of particulates; relationship of particulates to ice grain boundaries, etc.) also influences rheological behavior, we have begun a more systematic investigation of the effect of particulates on strength. We rely extensively on cryogenic scanning electron microscopy (CSEM) and to maximize planetary relevance we focus on behavior at low stress and small grain size.

Conference Paper↗

USGS2015

Uranium Sequestration During Biostimulated Reduction and In Response to the Return of Oxic Conditions In Shallow Aquifers

A proposed approach for groundwater remediation of uranium contamination is to generate reducing conditions by stimulating the growth of microbial populations through injection of electron donor compounds into the subsurface. Sufficiently reducing conditions will result in reduction of soluble hexavalent uranium, U(VI), and precipitation of the less soluble +4 oxidation state uranium, U(IV). This process is termed biostimulated reduction. A key issue in the remediation of uranium (U) contamination in aquifers by biostimulated reduction is the long term stability of the sequestered uranium. Three flow-through column experiments using aquifer sediment were used to evaluate the remobilization of bioreduced U sequestered under conditions in which biostimulation extended well into sulfate reduction to enhance precipitation of reduced sulfur phases such as iron sulfides. One column received added ferrous iron, Fe(II), increasing production of iron sulfides, to test their effect on remobilization of the sequestered uranium, either by serving as a redox buffer by competing for dissolved oxygen, or by armoring the reduced uranium. During biostimulation of the ambient microbial population with acetate, dissolved uranium was lowered by a factor of 2.5 or more with continued removal for over 110 days of biostimulation, well after the onset of sulfate reduction at ~30 days. Sequestered uranium was essentially all U(IV) resulting from the formation of nano-particulate uraninite that coated sediment grains to a thickness of a few 10’s of microns, sometimes in association with S and Fe. A multicomponent biogeochemical reactive transport model simulation of column effluents during biostimulation was generally able to describe the acetate oxidation, iron, sulfate, and uranium reduction for all three columns using parameters derived from simulations of field scale biostimulation experiments. Columns were eluted with artificial groundwater at equilibrium with atmospheric oxygen to simulate the upper limit of dissolved oxygen in recharge water. Overall about 9% of total uranium removed from solution during biostimulation was remobilized. Release of U during oxic elution was a continuous process over 140 days with dissolved uranium concentrations about 0.2 and 0.8 aM for columns with and without ferrous iron addition, respectively. Uranium remaining on the sediment was in the reduced form. The prolonged period of biostimulation and concomitant sulfate reduction appears to limit the rate of U(IV) oxidative remobilization in contrast to a large release observed for columns in previous studies that did not undergo sulfate reduction. Although continued sulfate reduction may cause decreased permeability from precipitation of iron sulfide, the greater apparent stability of the sequestered U(IV) provided by the sustained biostimulation should be considered in design of field scale remediation efforts. Remobilization of uranium following biostimulated reduction should be tested further at the field scale.

Report↗

USGS1974

Origin of spongy cherts

The spongy-textured surface in some cherts, visible on electron micrographs, is inherited from authigenic cristobalite. Spongy bedded cherts were originally bedded porcelanites similar to the porcelanite in the Miocene Monterey Formation of California.

Journal of Research of the U.S. Geological Survey↗

USGS1975

Diagenesis of Miocene siliceous shales, Temblor Range, California

Siliceous Monterey Shale and related shales of the Temblor Range, Calif., are subdivided into three depth-controlled zones characterized by different forms of silica. These are, in descending stratigraphic order: (1) Biogenic opal zone, with remains of diatoms and other siliceous organisms, (2) diagenetic cristobalite zone, and (3) diagenetic quartz zone. Using the top of the youngest marine unit, the overlying Etchegoin Formation, as datum, the transition from biogenic opal to disordered cristobalite occurs within the Monterey Shale of Chico Martinez Creek at -730 m, and the ordered cristobalite-to-microquartz transition at about -2,030 m. Temperatures that prevailed at these transition depths while the sedimentary pile lay at the bottom of the sea are estimated at about 50° and 110°C, respectively. Diagenetic cristobalite manifests, downward through a 1,300-m interval of section, a progressive decrease in its d (101) spacing because of a gradual ordering of its internal structure through adjustments in the solid state. Diagenetic microquartz forms only from well-ordered cristobalite that provides the most appropriate concentration of dissolved silica for precipitation of microquartz. Scanning electron micrographs of the silica mineral in pores of rocks made up of disordered cristobalite show aggregates of well-formed bladed crystals, like those described from deep-sea cherts. The pore silica minerals in rocks made up of ordered cristobalite occur as dendritic growths of poorly formed stubby crystals, and the change in crystal habit could be an external expression of the internal ordering process.

California↗

USGS1976

Bulk chemical analyses of petrographic thin sections of rocks of the Samli area, western Turkey

Petrographic thin sections have been analyzed for their major-element composition using a fusion-dilution technique and measuring the intensity of X-rays by means of the electron microprobe. The balsam-mounted thin sections were removed from the glass slides by soaking them in methylene chloride. The freed sections were mixed with twice their weight of Li 2 B 4 O 7 , and fused at 1100° C. A fragment of the resulting glasslike bead was mounted for probe analysis. Both wavelength and energy-dispersive detector systems were used for quantitative determinations of elements sodium through iron. Because the samples and standards are diluted and fused, powdered rock standards may be used as reference materials. The calibration curves obtained by plotting X-ray intensity versus concentration of the analyte are linear over the concentration ranges used in this work and have an overall range of error of 2 to 8 percent. Although some of the analytical values show excessive scatter for petrographically similar rocks, in general the analyses are acceptable given the sample size and analytical uncertainties. Bulk chemical analyses were made of 18 thin sections, including altered diabase, amphibolite, and calc-silicate hornfels produced by progressive contact metamorphism and associated with metasomatic magnetite deposits in the Samli area, western Turkey. Normative plots indicate that (1) diabase and amphibolite are compositionally related and are similar to average compositions of basalts and orthoamphibolites, and (2) calc-silicate hornfels appears to have been derived in part from amphibolite and in part from crystalline limestone that underlies much of the region.

Journal of Research of the U.S. Geological Survey↗

USGS2015

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

Micropaleontology↗

USGS2011

Re-establishing marshes can return carbon sink functions to a current carbon source in the Sacramento-San Joaquin Delta of California, USA

The Sacramento-San Joaquin Delta in California was an historic, vast inland freshwater wetland, where organic soils almost 20 meters deep formed over the last several millennia as the land surface elevation of marshes kept pace with sea level rise. A system of levees and pumps were installed in the late 1800s and early 1900s to drain the land for agricultural use. Since then, land surface has subsided more than 7 meters below sea level in some areas as organic soils have been lost to aerobic decomposition. As land surface elevations decrease, costs for levee maintenance and repair increase, as do the risks of flooding. Wetland restoration can be a way to mitigate subsidence by re-creating the environment in which the organic soils developed. A preliminary study of the effect of hydrologic regime on carbon cycling conducted on Twitchell Island during the mid-1990s showed that continuous, shallow flooding allowing for the growth of emergent marsh vegetation re-created a wetland environment where carbon preservation occurred. Under these conditions annual plant biomass carbon inputs were high, and microbial decomposition was reduced. Based on this preliminary study, the U.S. Geological Survey re-established permanently flooded wetlands in fall 1997, with shallow water depths of 25 and 55 centimeters, to investigate the potential to reverse subsidence of delta islands by preserving and accumulating organic substrates over time. Ten years after flooding, elevation gains from organic matter accumulation in areas of emergent marsh vegetation ranged from almost 30 to 60 centimeters, with average annual carbon storage rates approximating 1 kg/m2, while areas without emergent vegetation cover showed no significant change in elevation. Differences in accretion rates within areas of emergent marsh vegetation appeared to result from temporal and spatial variability in hydrologic factors and decomposition rates in the wetlands rather than variability in primary production. Decomposition rates were related to differences in hydrologic conditions, including water temperature, pH, dissolved oxygen concentration, and availability of alternate electron acceptors. The study showed that marsh re-establishment with permanent, low energy, shallow flooding can limit oxidation of organic soils, thus, effectively turning subsiding land from atmospheric carbon sources to carbon sinks, and at the same time reducing flood vulnerability.

California↗

USGS2015

Mining for metals in society's waste

Metals are crucial to society and enable our modern standard of living. Look around and you can't help but see products made of metals. For instance, a typical gasoline-powered automobile contains over a ton of iron and steel, 240 pounds of aluminum, 42 pounds of copper, 41 pounds of silicon, 22 pounds of zinc and more than 30 other mineral commodities including titanium, platinum and gold. Metals and minerals are natural resources that human beings have been mining for thousands of years. Contemporary metal mining is dominated by iron ore, copper and gold, with 2 billion tons of iron ore, nearly 20 million tons of copper and 2,000 tons of gold produced every year. Tens to hundreds of tons of other metals that are essential components for electronics, green energy production, and high-technology products are produced annually.

The Conversation↗

USGS1973

Microprobe analysis of biotites - A method of correlating tuff beds in the Green River Formation, Colorado and Utah

Quantitative electron microprobe analyses of biotite grains for iron, magnesium, and titanium from tuff beds in the lacustrine Green River Formation (Eocene) of Colorado and Utah provide a tentative method of identification and a permissive stratigraphic correlation of tuffs. Tuff beds that have been identified and correlated by stratigraphic means were sampled at five localities in Colorado and Utah to determine if microprobe analyses of biotite could be used as a method of correlation. Although most of the original phenocrysts and glass shards of these pyroclastic beds have undergone extensive postdepositional alteration, biotite seems to have been unaffected. The iron, magnesium, and titanium contents of the biotite do not uniquely characterize individual tuff beds, but when the proportions of these elements are compared in a continuous stratigraphic sequence of beds, correlation of individual tuffs or groups of tuffs is possible over areas exceeding several hundred square miles. The method may be used for detailed correlation of pyroclastic beds where stratigraphic, faunal, and radiometric methods have been unsatisfactory.

Colorado, Utah↗

USGS1973

New data on cuprobismutite

Cuprobismutite from Tunnel Extension Number Two mine, Ohio mining district, Utah, was chemically analyzed using the electron microprobe. Its empirical formula was determined to be Cu 20.8 Ag 0.97 Pb 0.35 Mn 0.22 Bi 26.7 Sb 0.06 Te 0.05 Se 0.55 S 50.4. The tentative conclusion is that unsubstituted cuprobismutite has the chemical formula 6Cu 2 S*6Bi 2 S 3 rather than the previously ascribed formula 6Cu 2 S*6Bi 2 S 3 and that cuprobismutite is therefore not dimorphous with emplectite.

Utah↗

USGS1973

A study of the distribution of the polychlorinated biphenyls in the aquatic environment

Data gathered from monitoring activities and project studies indicate the ubiquitous occurrence and distribution of polychlorinated biphenyls in the aquatic environment. Residues have been detected in samples from 19 States, representing nearly every region of the country. Concentrations ranged from 0.1 to 4.0 ug/l in unfiltered water samples and 5.0 to 3,200 ug/kg in bottom sediments. PCB residues were also found in fish and aquatic plants. Samples were prepared by the same techniques used for general chlorinated insecticide detection, with special attention to cleanup and separation of PCB's from other compounds. Basic identification and quantification were made by dual-column electron-capture gas chromatography and confirmed by gas chromatography mass spectrometry whenever possible. The sampling program is expected to be broadened geographically in 1973 and increased in successive years in order to more adequately define the distribution of PCB residues in the major drainage basins of the United States.

Journal of Research of the U.S. Geological Survey↗

USGS1989

Persistent infections of fish cell lines by paramyxovirus isolates from Chinook salmon ( Oncorhynchus tschawytscha )

We have reported the isolation of a paramyxovirus from stocks of adult chinook salmon ( Oncorhynchus tshawytscha ) returning to coastal rivers of Oregon, USA (Winton et al 1985). The isolates were obtained from kidney and spleen tissues using the chinook salmon embryo cell line, CHSE-214. Initial cytopathic effect (CPE) was slow to develop, requiring 28 days incubation at 18°C. The virus replicated in CHSE-214, chum heart (CHH-1), kokanee ovary (K0-6), coho salmon embryo (CSE-119), and fathead minnow (FHM) cell lines where it produced a lytic type of CPE. The virus was stable at pH 3-11 and iodo-deoxyuridine did not inhibit wiral replication. Infectivity was lost after treatment with chloroform indicating the presence of essential lipids. The density of virions in CsCl was 1.2 g/ml. The virus hemagglutinated cells of 11 of 14 species of birds, mammals, and fish tested. Electron microscopy of infected cells revealed enveloped particles 125-250 nm in dia. containing coiled nucleocapsids and examination of freon-treated virions showed the nucleocapsid was a helix approximately 18 nm in dia. and > 1000 nm in length (Winton et al 1985). In addition to causing hemagglutination, members of the Paramyxoviridae are known for the ability to establish persistent infections of cell lines (Choppin and Compans 1975). The purpose of this study was to determine if the paramyxovirus isolates from salmon were able to establish persistent infections in fish cell lines and to study the nature of the infection.

Book chapter↗

USGS1989

Picornaviruses and reoviruses of fishes

The number of fish viruses isolated in cell culture or observed by electron microscopy continues to increase rapidly. Until recently, most viruses that were isolated from finfish and characterized were found to be members of the Rhabdoviridae, Iridoviridae, or Herpesviridae (Wolf and Mann 1980). In a comprehensive review of fish viruses published in 1984, there were no picornaviruses and only two reoviruses listed (Wolf 1984). The expansion of aquaculture into the rearing of new species at high density in different geographic areas, and the use of improved methods of detection that include newly developed cell lines and increased sampling effort, have led to the discovery of fish viruses representing nearly all families of animal viruses. Among the newest additions, are a member of the family Picornaviridae and several new viruses that belong within the Reoviridae.

Book chapter↗