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USGS2022

Indicator mineral analyses of stream-sediment samples using automated mineralogy and mineral chemistry: Applicability to exploration in covered terranes in eastern Alaska, USA

In the past two decades, significant research efforts have been devoted to porphyry copper indicator mineral (PCIM) identification and mineral chemistry to assist exploration. Such studies are important in the Yukon-Tanana upland region of eastern Alaska because well-established geochemical exploration techniques, such as the geochemistry of stream-sediment samples, are less effective in the search for mineral resources owing to cover materials that subdue geochemical signatures. The unglaciated Yukon-Tanana upland region is well-endowed with mineral resources, including porphyry Cu-Mo-Au deposits at Taurus, Bluff, Dennison, and Oreo. Using automated scanning electron microscope (SEM) techniques, numerous PCIMs have been identified in rocks and stream-sediment samples that would likely not have been observed using visual binocular microscope methods. Sulfide minerals such as chalcopyrite, chalcocite, covellite, bornite, molybdenite, and pyrrhotite were identified in rock samples, and more than half of the stream-sediment samples from drainages containing known porphyry mineral occurrences contain chalcopyrite with or without bornite. Many drainages without known occurrences also contain these minerals, which suggests potential for additional occurrences. Svanbergite, an aluminum phosphate sulfate (APS) mineral [SrAl 3 (PO 4 )(SO 4 )(OH) 6 ], was identified in some of the altered or mineralized rock samples from Taurus, and in stream drainages containing porphyry occurrences and may represent the best indicator mineral for Taurus-like porphyry deposits. Apatite chemistry has great potential as a tool for assessing the presence of porphyry mineralization. Grains from rock and stream-sediment samples that contain high Cl (>∼0.4 wt%), Fe (>0.4 wt%), and Mn (>2000 ppm) clearly distinguish apatite from other sources (metamorphic, unmineralized igneous rocks). This study is one of the first to document new streamlined indicator mineral sample collection and processing methods and to combine automated SEM techniques and chemistry of minerals derived from both bedrock and surficial (stream) sediments as they apply to porphyry exploration.

Alaska↗

USGS2017

Organic petrology and micro-spectroscopy of Tasmanites microfossils: Applications to kerogen transformations in the early oil window

The transformation of kerogen to hydrocarbons in the early stages of oil generation is critical for understanding the resource potential of liquid-rich shale plays. Organic petrology commonly is used for visual evaluation of type, quality, and thermal maturity of organic matter, but the relationship of visual petrographic changes to chemical transformations is not well characterized. To improve understanding of these processes, organic-walled microfossils of the unicellular green alga Tasmanites (composed of algaenan) in Upper Devonian Ohio Shale (Huron Member, Appalachian Basin) were analyzed by micro-spectroscopy techniques including micro-Fourier transform infrared (micro-FTIR), X-ray photoelectron (XPS), electron probe microanalysis (EPMA), and fluorescence. Immature to mid-oil window maturation sequences of core and outcrop samples with solid bitumen reflectance (BR) and vitrinite reflectance (VR) values ranging from 0.45 to 0.80 %Ro were used. Hydrous pyrolysis was applied to low-maturity (BR: 0.25–0.39 %Ro) Huron and time-correlative New Albany shale samples to create similar artificial maturation sequences for comparison. Micro-FTIR spectroscopy revealed a decrease in the CH 2 /CH 3 ratio with increasing maturity, indicating Tasmanites aliphatic chains become shorter and more branched. Oxygenated functional groups decreased relative to aliphatic stretching bands and increased aromaticity was noted at the highest maturities. In samples that were pyrolyzed for 72 h at temperatures of 300–320 °C (BR: 0.56–0.68 %Ro), Tasmanites showed similar trends, whereas at pyrolysis temperatures of 340 °C and higher (BR > 1.0 %Ro), Tasmanites was pseudomorphed by accumulations of solid bitumen, carbonate and sulfide. Replacement of Tasmanites by these phases in hydrous pyrolysis experiments ≥340 °C and its absence at higher maturities (peak oil, VR and BR ≥ 0.9 %Ro) in naturally matured samples, as documented in a previous study, implies that a large fraction of the algaenan component of original organic carbon is converted to petroleum during thermal maturation. XPS analysis indicated the molar proportion of aliphatic carbon increases with increasing thermal maturity, accompanied by decreases in oxygenated functional groups and olefinic carbon. EPMA of Tasmanites showed highest concentrations of S, with concentrations of redox-sensitive trace elements U, Mo, Ni and V generally at or below detection limits. Decrease in organic S with increasing thermal maturity may be related to cleavage of Tasmanites at C S linkages; however, this relationship was inconsistent and presence of adjacent or entrained nanoscale silicate or sulfide phases may impact measured trace element concentrations. Fluorescence microscopy and spectroscopy showed a red shift in spectral maxima and decreased emission intensities with increasing maturity, interpreted as due to non-radiative energy loss possibly because of increased aromaticity. Collectively, these results provide new insights into the in situ chemical transformations that accompany petrographic changes as oil-prone kerogen converts to petroleum with thermal advance from immature conditions into the mid-oil window.

Organic Geochemistry↗

USGS2026

Evidence for a biological origin of uranium-rich carbon masses within the Ediacaran Salt Range Formation of Pakistan

Thucholites are unique organic structures found in igneous and sedimentary rocks composed of a U-C-rich interior enclosed by an organic outer shell. Their formation and occurrence have perplexed scientists for over 100 years. Typically, thucholites are sparse in sedimentary rocks but where found in abundance, they may be the result of rapid paleoecological disruptions, e.g., volcanic ashfall. Here, we evaluated thucholites from the Ediacaran Salt Range Formation of the Indus Basin in Pakistan using field emission scanning electron microscopy (FESEM) and nanoscale secondary ion mass spectroscopy (NanoSIMS) to propose a two-stage mechanism for thucholite development. NanoSIMS results suggest organic matter in thucholite cores formed by biological fractionation (represented by the presence of lighter 13 C/ 12 C and 34 S/ 32 S) while the outer organic mantle formed via radiolysis-induced polymerization. FESEM elemental analysis confirms compositional differences between the two thucholite components (core and mantle), further implying their contrasting origins. Dimensional comparison of thucholite cores and their U-bearing mineral morphologies to ancient and modern U-biomineralized microbes suggests that the thucholite cores formed from metal-biological interactions. The presence of volcanogenic biotite, alkali feldspar, and clay spherules (interpreted as devitrified volcanic glass) with thucholite suggests that the thucholite cores in the Salt Range Formation are biological responses to rapid paleoenvironmental change from volcanic eruption which preserved the fossilized morphologies of Proterozoic microorganisms.

Salt Range↗

USGS2010

Separation, characterization and initial reaction studies of magnetite particles from Hanford sediments

Magnetic and density separation methods have been applied to composite sediment samples from the Hanford formation from sediment recovered during drilling of an uncontaminated borehole located near the 200 West Area of the Hanford Site in southeastern Washington State. This paper describes the results of using those separation methods and from the characterization and initial reactivity measurements on a highly magnetic fraction isolated from that sediment. X-ray diffraction (XRD) analysis of the highly magnetic sediment fraction indicates that this material contains predominantly magnetite (Fe 3 O 4 ). Particle morphology observed by scanning electron microscopy (SEM) and compositions determined energy dispersive spectroscopy (EDS) are consistent with this identification. Analyses by X-ray photoelectron spectroscopy (XPS) indicates that there is a thin coating on the particles that are likely a type of aluminosilicate. This highly magnetic fraction of material is not reactive with indigo carmine, an organic redox probe molecule that was shown to readily react with synthetic magnetite. Because of the limited amounts of material readily available, initial tests have been conducted that demonstrate the ability to complete U(VI) sorption on individual particles (nominally ∼100 μm in size) of the isolated sediment and to remove and mount these individual particles for analysis of the concentration and chemical state of the sorbed U species using small area XPS.

Washington↗

USGS2007

The Sonju Lake layered intrusion, northeast Minnesota: Internal structure and emplacement history inferred from magnetic fabrics

The Sonju Lake intrusion (SLI), in northeastern Minnesota, is a layered mafic complex of Keweenawan age (1096.1 ?? 0.8 Ma) related to the Midcontinent rift. The cumulate paragenesis of the intrusion is recognized as broadly similar to the Skaergaard intrusion, a classic example of closed-system differentiation of a tholeiitic mafic magma. The SLI represents nearly closed-system differentiation through bottom-up fractional crystallization. Geochemical studies have identified the presence of a stratabound, 50-100 m thick zone anomalously enriched in Au + PGE. Similar to the PGE reefs of the Skaergaard intrusion, this PGE-enriched zone is hosted within oxide gabbro cumulates, about two-third of the way up from the base of the intrusion. We present a petrofabric study using the anisotropy of magnetic susceptibility (AMS) to investigate the emplacement and flow patterns within the Sonju Lake intrusion. Petrographic and electron microprobe studies, combined with AMS and hysteresis measurements indicate the primary source of the magnetic signal is pseudo-single domain (PSD) magnetite or titanomagnetite. Low field AMS was measured at 32 sites within the Sonju Lake intrusion, which provided information about primary igneous fabrics. The magnetic fabrics in the layered series of the Sonju Lake intrusion are consistent with sub-horizontal to inclined emplacement of the intrusion and show evidence that the cumulate layers were deposited in a dynamic environment. Well-aligned magnetic lineations, consistently plunging shallowly toward the southwest, indicate the source of the magma is a vertical sill-like feeder, presumably located beneath the Finland granite. The Finland granite acted as a density trap for the Sonju Lake magmas, forcing lateral flow of magma to the northeast. The strongly oblate magnetic shape fabrics indicate the shallowly dipping planar fabrics were enhanced by compaction of the crystal mush. ?? 2007 Elsevier B.V. All rights reserved.

Precambrian Research↗

USGS2011

Neoarchean paleoweathering of tonalite and metabasalt: Implications for reconstructions of 2.69Ga early terrestrial ecosystems and paleoatmospheric chemistry

Field and laboratory investigations of a 2690.83 Ma ( 207 Pb/ 206 Pb age of Saganaga Tonalite) unconformity exposed in outcrop in northeastern Minnesota, USA, reveal evidence for development of a deep paleoweathering profile with geochemical biosignatures consistent with the presence of microbial communities and weakly oxygenated conditions. Weathering profiles are characterized by a 5–50 m thick regolith that consists of saprolitized Saganaga Tonalite and Paulson Lake succession basaltic metavolcanic rocks retaining rock structure, which is cross-cut by a major unconformity surface marking development of a successor basin infilled with alluvial deposits. The regolith and unconformity are overlain by thick conglomerate deposits that contain both intrabasinal (saprock) as well as extrabasinal detritus. Thin-section microscopy and electron microprobe analyses reveal extensive hydrolysis and sericitization of feldspars, exfoliation and chloritization of biotite, and weathering of Fe-Mg silicates and Cu-Fe sulfides; weathering of Fe-Ti oxides was relatively less intense than for other minerals and evidence was found for precipitation of Fe oxides. Geochemical analyses of the tonalite, assuming immobile TiO 2 during weathering ( τ Ti, j ), show depletion of SiO 2 , Al 2 O 3 , Na 2 O, CaO, MgO, and MnO, and to a lesser degree of K 2 O, relative to least-weathered parent materials. Significant Fe was lost from the tonalite. A paleoatmospheric pCO 2 of 10–50 times PAL is estimated based on geochemical mass-balance of the tonalite profile and assuming a formation time of 50–500 Kyr. Interpretations of metabasalt paleoweathering are complicated by additions of sediment to the profile and extensive diagenetic carbonate (dolomite) overprinting. Patterns of release of P and Fe and retention of Y and Cu in tonalite are consistent with recent laboratory experiments of granite weathering, and with the presence of acidic conditions in the presence of organic ligands (produced, for example, by a primitive microbial community) during weathering. Cu metal in the profile may document lower pO 2 than present day at the surface. Comparison with previous studies of weathered tonalite and basalt (Denison, 2.45–2.22 Ga) in Ontario, Canada, reveal general similarities in paleoweathering with our study, as well as important differences related to lower paleoatmospheric pO 2 and terrestrial biosignature for the older Minnesota profile. A falling water table in the Alpine Lake locality is presumed to have promoted formation of this gossan-like deep-weathering system that extends to 50-m depth.

Minnesota↗

USGS2007

230Th-U dating of surficial deposits using the ion microprobe (SHRIMP-RG): A microstratigraphic perspective

We used the sensitive high-resolution ion microprobe reverse-geometry (SHRIMP-RG) to date pedogenic opal using the 230 Th–U system. Due to the high-spatial resolution of an ion microprobe (typically 30 μm), regions of pure opal within a sample can be targeted and detrital material can be avoided. In addition, because the technique is non-destructive, the sample can be preserved for other types of analyses including electron microprobe or other stable isotope or trace element ion microprobe measurements. The technique is limited to material with U concentrations greater than ∼50 ppm. However, the high spatial resolution, small sample requirements, and the ability to avoid detrital material make this technique a suitable technique for dating many Pleistocene deposits formed in semi-arid environments. To determine the versatility of the method, samples from several different deposits were analyzed, including silica-rich pebble coatings from pedogenic carbonate horizons, a siliceous sinter deposit, and opaline silica deposited as a spring mound. U concentrations for 30-μm-diameter spots ranged from 50 to 1000 ppm in these types of materials. The 230 Th/ 232 Th activity ratios also ranged from ∼100 to 10 6 , eliminating the need for detrital Th corrections that reduce the precision of traditional U-Th ages for many milligram- and larger-sized samples. In pedogenic material, layers of high-U opal (ca. 500 ppm) are commonly juxtaposed next to layers of calcite with much lower U concentrations (1–2 ppm). If these types of samples are not analyzed using a technique with the appropriate spatial resolution, the ages may be strongly biased towards the age of the opal. Comparison with standard TIMS (Thermal Ionization Mass Spectrometry) measurements from separate microdrilled samples suggests that although the analytical precision of the ion microprobe (SHRIMP-RG) measurements is less than TIMS, the high spatial resolution results in better accuracy in the age determination for finely layered or complex deposits. The ion microprobe approach also may be useful for pre-screening samples to determine the age and degree of post-depositional alteration, analyzing finely layered samples or samples with complex growth histories, and obtaining simultaneous measurements of trace elements.

Quaternary International↗

USGS2022

The effect of diagenesis and acetolysis on the preservation of morphology and ultrastructural features of pollen

Pollen morphology on its own and in conjunction with other characteristics has elucidated the origin and evolution of various plant groups. Previous studies of fossil pollen rarely discuss the effects of diagenesis and sample preparation on pollen characteristics, i.e., variability in staining, pollen morphology, and pollen wall ultrastructural characteristics. This paper examines the effect of acetolysis on reflectance and spectral epi-fluorescence measurements. Based on empirical studies, different species under similar experimental conditions display different reflectance values, indicating individual species respond differently to similar post-depositional thermal events. The quantitative pollen fluorescence spectra showed significant variability, but there is an overall increase in the mean wavelength of maximum emission with acetolysis. Increases in these spectral parameters are used to infer thermal maturation and diagenetic pathways in fossil pollen. The paper also discusses observations made on fossil pollen of a known thermal maturity using Pearson's Pollen/Spore Color Standard. Assessment of pollen thermal maturity using this color standard can be an indicator of the quality of morphological and ultrastructural information that can be extracted from fossil pollen. Increasing thermal maturity of pollen may have an effect on staining variability. Based on observations, staining for brightfield or electron microscopy in fossil pollen, although useful for improving contrast in the specimen, must be used with caution when interpreting pollen wall structure. Although single fossil pollen investigations are useful, replication of these studies on similar or the same specimens from the same locality or various localities will collectively provide more information for elucidation of the morphology and ultrastructure of the once living pollen, and is helpful in sorting out characteristics that may be artifacts from post-depositional diagenesis.

Review of Palaeobotany and Palynology↗

USGS2013

Pre-flight calibration and initial data processing for the ChemCam laser-induced breakdown spectroscopy instrument on the Mars Science Laboratory rover

The ChemCam instrument package on the Mars Science Laboratory rover, Curiosity, is the first planetary science instrument to employ laser-induced breakdown spectroscopy (LIBS) to determine the compositions of geological samples on another planet. Pre-processing of the spectra involves subtracting the ambient light background, removing noise, removing the electron continuum, calibrating for the wavelength, correcting for the variable distance to the target, and applying a wavelength-dependent correction for the instrument response. Further processing of the data uses multivariate and univariate comparisons with a LIBS spectral library developed prior to launch as well as comparisons with several on-board standards post-landing. The level-2 data products include semi-quantitative abundances derived from partial least squares regression. A LIBS spectral library was developed using 69 rock standards in the form of pressed powder disks, glasses, and ceramics to minimize heterogeneity on the scale of the observation (350–550 μm dia.). The standards covered typical compositional ranges of igneous materials and also included sulfates, carbonates, and phyllosilicates. The provenance and elemental and mineralogical compositions of these standards are described. Spectral characteristics of this data set are presented, including the size distribution and integrated irradiances of the plasmas, and a proxy for plasma temperature as a function of distance from the instrument. Two laboratory-based clones of ChemCam reside in Los Alamos and Toulouse for the purpose of adding new spectra to the database as the need arises. Sensitivity to differences in wavelength correlation to spectral channels and spectral resolution has been investigated, indicating that spectral registration needs to be within half a pixel and resolution needs to match within 1.5 to 2.6 pixels. Absolute errors are tabulated for derived compositions of each major element in each standard using PLS regression. Sources of errors are investigated and discussed, and methods for improving the analytical accuracy of compositions derived from ChemCam spectra are discussed.

Spectrochimica Acta Part B: Atomic Spectroscopy↗

USGS2004

Historical trends in occurrence and atmospheric inputs of halogenated volatile organic compounds in untreated ground water used as a source of drinking water

Analyses of samples of untreated ground water from 413 community-, non-community- (such as restaurants), and domestic-supply wells throughout the US were used to determine the frequency of detection of halogenated volatile organic compounds (VOCs) in drinking-water sources. The VOC data were compiled from archived chromatograms of samples analyzed originally for chlorofluorocarbons (CFCs) by purge-and-trap gas chromatography with an electron-capture detector (GC-ECD). Concentrations of the VOCs could not be ascertained because standards were not routinely analyzed for VOCs other than trichloromonofluoromethane (CFC-11), dichlorodifluoromethane (CFC-12) and 1,1,2-trichloro-1,2,2-trifluoroethane (CFC-113). Nevertheless, the peak areas associated with the elution times of other VOCs on the chromatograms can be classified qualitatively to assess concentrations at a detection limit on the order of parts per quadrillion. Three or more VOCs were detected in 100% (percent) of the chromatograms, and 77.2% of the samples contained 10 or more VOCs. The maximum number of VOCs detected in any sample was 24. Modeled ground-water residence times, determined from concentrations of CFC-12, were used to assess historical trends in the cumulative occurrence of all VOCs detected in this analysis, as well as the occurrence of individual VOCs, such as CFC-11, carbon tetrachloride (CCl 4 ), chloroform and tetrachloroethene (PCE). The detection frequency for all of the VOCs detected has remained relatively constant from approximately 1940 to 2000; however, the magnitude of the peak areas on the chromatograms for the VOCs in the water samples has increased from 1940 to 2000. For CFC-11, CCl 4 , chloroform and PCE, small peaks decrease from 1940 to 2000, and large peaks increase from 1940 to 2000. The increase in peak areas on the chromatograms from analyses of more recently recharged water is consistent with reported increases in atmospheric concentrations of the VOCs. Approximately 44% and 6.7% of the CCl 4 and PCE detections, respectively, in pre-1940 water, and 68% and 62% of the CCl 4 and PCE detections, respectively, in water recharged in 2000 exceed solubility equilibrium with average atmospheric concentrations. These exceedences can be attributed to local atmospheric enrichment or direct contaminant input to ground-water flow systems. The detection of VOCs at concentrations indicative of atmospheric sources in 100% of the samples indicates that untreated drinking water from ground-water sources in the US recharged within the past 60 years has been affected by anthropogenic activity. Additional inputs from a variety of sources such as spills, underground injections and leaking landfills or storage tanks increasingly are providing additional sources of contamination to ground water used as drinking-water sources.

Science of the Total Environment↗

USGS2014

Methylmercury production in sediment from agricultural and non-agricultural wetlands in the Yolo Bypass, California, USA

As part of a larger study of mercury (Hg) biogeochemistry and bioaccumulation in agricultural (rice growing) and non-agricultural wetlands in California's Central Valley, USA, seasonal and spatial controls on methylmercury (MeHg) production were examined in surface sediment. Three types of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow fields) and two types of managed (non-agricultural) wetlands (permanently and seasonally flooded) were sampled monthly-to-seasonally. Dynamic seasonal changes in readily reducible ‘reactive’ mercury (Hg(II) R ), Hg(II)-methylation rate constants (k meth ), and concentrations of electron acceptors (sulfate and ferric iron) and donors (acetate), were all observed in response to field management hydrology, whereas seasonal changes in these parameters were more muted in non-agricultural managed wetlands. Agricultural wetlands exhibited higher sediment MeHg concentrations than did non-agricultural wetlands, particularly during the fall through late-winter (post-harvest) period. Both sulfate- and iron-reducing bacteria have been implicated in MeHg production, and both were demonstrably active in all wetlands studied. Stoichiometric calculations suggest that iron-reducing bacteria dominated carbon flow in agricultural wetlands during the growing season. Sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands during the growing season, suggesting that labile organic matter, rather than sulfate, limited their activity in these wetlands. Along the continuum of sediment geochemical conditions observed, values of k meth increased approximately 10,000-fold, whereas Hg(II) R decreased 100-fold. This suggests that, with respect to the often opposing trends of Hg(II)-methylating microbial activity and Hg(II) availability for methylation, microbial activity dominated the Hg(II)-methylation process, and that along this biogeochemical continuum, conditions that favored microbial sulfate reduction resulted in the highest calculated MeHg production potential rates. Rice straw management options aimed at limiting labile carbon supplies to surface sediment during the post-harvest fall–winter period may be effective in limiting MeHg production within agricultural wetlands.

California↗

USGS2017

The precipitation of indium at elevated pH in a stream influenced by acid mine drainage

Indium is an increasingly important metal in semiconductors and electronics and has uses in important energy technologies such as photovoltaic cells and light-emitting diodes (LEDs). One significant flux of indium to the environment is from lead, zinc, copper, and tin mining and smelting, but little is known about its aqueous behavior after it is mobilized. In this study, we use Mineral Creek, a headwater stream in southwestern Colorado severely affected by heavy metal contamination as a result of acid mine drainage, as a natural laboratory to study the aqueous behavior of indium. At the existing pH of ~ 3, indium concentrations are 6–29 μg/L (10,000 × those found in natural rivers), and are completely filterable through a 0.45 μm filter. During a pH modification experiment, the pH of the system was raised to > 8, and > 99% of the indium became associated with the suspended solid phase (i.e. does not pass through a 0.45 μm filter). To determine the mechanism of removal of indium from the filterable and likely primarily dissolved phase, we conducted laboratory experiments to determine an upper bound for a sorption constant to iron oxides, and used this, along with other published thermodynamic constants, to model the partitioning of indium in Mineral Creek. Modeling results suggest that the removal of indium from the filterable phase is consistent with precipitation of indium hydroxide from a dissolved phase. This work demonstrates that nonferrous mining processes can be a significant source of indium to the environment, and provides critical information about the aqueous behavior of indium.

Colorado↗

USGS2020

The assessment and remediation of mercury contaminated sites: A review of current approaches

Remediation of mercury (Hg) contaminated sites has long relied on traditional approaches, such as removal and containment/capping. Here we review contemporary practices in the assessment and remediation of industrial-scale Hg contaminated sites and discuss recent advances. Significant improvements have been made in site assessment, including the use of XRF to rapidly identify the spatial extent of contamination, Hg stable isotope fractionation to identify sources and transformation processes, and solid-phase characterization (XAFS) to evaluate Hg forms. The understanding of Hg bioavailability for methylation has been improved by methods such as sequential chemical extractions and porewater measurements, including the use of diffuse gradient in thin-film (DGT) samplers. These approaches have shown varying success in identifying bioavailable Hg fractions and further study and field applications are needed. The downstream accumulation of methylmercury (MeHg) in biota is a concern at many contaminated sites. Identifying the variables limiting/controlling MeHg production—such as bioavailable inorganic Hg, organic carbon, and/or terminal electron acceptors (e.g. sulfate, iron) is critical. Mercury can be released from contaminated sites to the air and water, both of which are influenced by meteorological and hydrological conditions. Mercury mobilized from contaminated sites is predominantly bound to particles, highly correlated with total sediment solids (TSS), and elevated during stormflow. Remediation techniques to address Hg contamination can include the removal or containment of Hg contaminated materials, the application of amendments to reduce mobility and bioavailability, landscape/waterbody manipulations to reduce MeHg production, and food web manipulations through stocking or extirpation to reduce MeHg accumulated in desired species. These approaches often rely on knowledge of the Hg forms/speciation at the site, and utilize physical, chemical, thermal and biological methods to achieve remediation goals. Overall, the complexity of Hg cycling allows many different opportunities to reduce/mitigate impacts, which creates flexibility in determining suitable and logistically feasible remedies.

Science of the Total Environment↗

USGS2021

Influence of redox gradients on nitrate transport from the landscape to groundwater and streams

Increases in nitrogen applications to the land surface since the 1950s have led to a cascade of negative environmental impacts, including degradation of drinking water supplies, nutrient enrichment of aquatic ecosystems and contributions to global climate change. In this study, groundwater, streambed porewater, and stream sampling were used to establish trends in nitrate concentrations and how redox gradients influence nitrate transport across diverse glacial terranes. Decadal sampling has found that elevated nitrate concentrations in shallow groundwater beneath cropland have been sustained for decades. Redox gradients established in the saturated zone using dissolved O 2 , iron, nitrate and excess N 2 from denitrification suggest that nitrate-bearing zones are thin in glacial terranes dominated by fine materials. These thin nitrate-bearing zones lead to suboxic, low nitrate streambed porewater and limit the contributions of nitrate to streams from slow-flow groundwater. In contrast, thick oxic zones in more coarse-grained glacial terranes allow nitrate to reach deeper groundwater, resulting in streambed porewater with elevated nitrate concentrations and causing a large portion of stream nitrate to be derived from slow-flow groundwater. Groundwater age tracer data indicate that denitrification occurs more quickly in the terrane dominated by fine material than in the more coarse-grained terrane. The quicker depletion of nitrate in the more fine-grained terrane suggests that the thinner oxic zone in this terrane is due, in part, to the greater availability and reactivity of electron donors in this terrane than in the more coarse-grained terrane. Groundwater age tracer data and hydrograph separation analysis suggest that saturated zone lag times between when changes in land use practices occur and when changes in stream water are fully observed may vary widely across hydrogeologic settings.

Illinois, Indiana, Iowa, Michigan, Minnesota, Wisc↗

USGS2023

Per- and polyfluorinated alkyl substances (PFAS) in Pennsylvania surface waters: A statewide assessment, associated sources, and land-use relations

The objectives of this study are to identify per- and polyfluoroalkyl substances (PFAS) in Pennsylvania surface waters, corresponding associations with potential sources of PFAS contamination (PSOC) and other parameters, and compare raw surface water concentrations to human and ecological benchmarks. Surface water samples from 161 streams were collected in September 2019 and were analyzed for 33 target PFAS and water chemistry. Land use and physical attributes in upstream catchments and geospatial counts of PSOC in local catchments are summarized. The hydrologic yield of the sum of 33 PFAS (∑PFAS) for each stream was computed by normalizing each site's load by the drainage area of the upstream catchment. Utilizing conditional inference tree analysis, the percentage of development (>7.58 %) was identified as a primary driver of the ∑PFAS hydrologic yields. When percentage of development was removed from analysis, ∑PFAS yields were closely related to surface water chemistry associated with landscape alteration (e.g., development or agricultural cropland), such as concentrations of total nitrogen, chloride, and ammonia, but also to count of water pollution control facilities (agricultural, industrial, stormwater, and/or municipal waste pollution abatement facilities). In oil and gas development regions, ∑PFAS yields were associated with combined sewage outfalls. Sites surrounded by ≥2 electronic manufacturing facilities had elevated ∑PFAS yields (median = 241 ng/s/km 2 ). Study results are critical to guide future research, regulatory policy, best practices that will mitigate PFAS contamination, and the communication of human health and ecological risks associated with PFAS exposure from surface waters.

Pennsylvania↗

USGS2014

Mycoplasmosis and upper respiratory tract disease of tortoises: a review and update

Tortoise mycoplasmosis is one of the most extensively characterized infectious diseases of chelonians. A 1989 outbreak of upper respiratory tract disease (URTD) in free-ranging Agassiz's desert tortoises ( Gopherus agassizii ) brought together an investigative team of researchers, diagnosticians, pathologists, immunologists and clinicians from multiple institutions and agencies. Electron microscopic studies of affected tortoises revealed a microorganism in close association with the nasal mucosa that subsequently was identified as a new species, Mycoplasma agassizii . Over the next 24 years, a second causative agent, Mycoplasma testudineum , was discovered, the geographic distribution and host range of tortoise mycoplasmosis were expanded, diagnostic tests were developed and refined for antibody and pathogen detection, transmission studies confirmed the pathogenicity of the original M. agassizii isolate, clinical (and subclinical) disease and laboratory abnormalities were characterized, many extrinsic and predisposing factors were found to play a role in morbidity and mortality associated with mycoplasmal infection, and social behavior was implicated in disease transmission. The translation of scientific research into management decisions has sometimes led to undesirable outcomes, such as euthanasia of clinically healthy tortoises. In this article, we review and assess current research on tortoise mycoplasmosis, arguably the most important chronic infectious disease of wild and captive North American and European tortoises, and update the implications for management and conservation of tortoises in the wild.

The Veterinary Journal↗

USGS2012

Viral tropism and pathology associated with viral hemorrhagic septicemia in larval and juvenile Pacific herring

Viral hemorrhagic septicemia virus (VHSV) genotype IVa causes mass mortality in wild Pacific herring, a species of economic value, in the Northeast Pacific Ocean. Young of the year herring are particularly susceptible and can be carriers of the virus. To understand its pathogenesis, tissue and cellular tropisms of VHSV in larval and juvenile Pacific herring were investigated with immunohistochemistry, transmission electron microscopy, and viral tissue titer. In larval herring, early viral tropism for epithelial tissues (6d post-exposure) was indicated by foci of epidermal thickening that contained heavy concentrations of virus. This was followed by a cellular tropism for fibroblasts within the fin bases and the dermis, but expanded to cells of the kidney, liver, pancreas, gastrointestinal tract and meninges in the brain. Among wild juvenile herring that underwent a VHS epizootic in the laboratory, the disease was characterized by acute and chronic phases of death. Fish that died during the acute phase had systemic infections in tissues including the submucosa of the gastrointestinal tract, spleen, kidney, liver, and meninges. The disease then transitioned into a chronic phase that was characterized by the appearance of neurological signs including erratic and corkscrew swimming and darkening of the dorsal skin. During the chronic phase viral persistence occurred in nervous tissues including meninges and brain parenchymal cells and in one case in peripheral nerves, while virus was mostly cleared from the other tissues. The results demonstrate the varying VHSV tropisms dependent on the timing of infection and the importance of neural tissues for the persistence and perpetuation of chronic infections in Pacific herring.

Veterinary Microbiology↗

USGS2014

Molecular identification of erythrocytic necrosis virus (ENV) from the blood of Pacific herring ( Clupea pallasii )

Viral erythrocytic necrosis (VEN) is a condition affecting the red blood cells of more than 20 species of marine and anadromous fishes in the North Atlantic and North Pacific Oceans. Among populations of Pacific herring ( Clupea pallasii ) on the west coast of North America the disease causes anemia and elevated mortality in periodic epizootics. Presently, VEN is diagnosed by observation of typical cytoplasmic inclusion bodies in stained blood smears from infected fish. The causative agent, erythrocytic necrosis virus (ENV), is unculturable and a presumed iridovirus by electron microscopy. In vivo amplification of the virus in pathogen-free laboratory stocks of Pacific herring with subsequent virus concentration, purification, DNA extraction, and high-throughput sequencing were used to obtain genomic ENV sequences. Fragments with the highest sequence identity to the family Iridoviridae were used to design four sets of ENV-specific polymerase chain reaction (PCR) primers. Testing of blood and tissue samples from experimentally and wild infected Pacific herring as well as DNA extracted from other amphibian and piscine iridoviruses verified the assays were specific to ENV with a limit of detection of 0.0003 ng. Preliminary phylogenetic analyses of a 1448 bp fragment of the putative DNA polymerase gene supported inclusion of ENV in a proposed sixth genus of the family Iridoviridae that contains other erythrocytic viruses from ectothermic hosts. This study provides the first molecular evidence of ENV's inclusion within the Iridoviridae family and offers conventional PCR assays as a means of rapidly surveying the ENV-status of wild and propagated Pacific herring stocks.

Veterinary Microbiology↗