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Dissimilatory arsenate reduction with sulfide as the electron donor--Experiments with Mono Lake water and isolation of strain MLMS-1, a chemoautotrophic arsenate-respirer

Anoxic bottom water from Mono Lake, California, can biologically reduce added arsenate without any addition of electron donors. Of the possible in situ inorganic electron donors present, only sulfide was sufficiently abundant to drive this reaction. We tested the ability of sulfide to serve as an electron donor for arsenate reduction in experiments with lake water. Reduction of arsenate to arsenite occurred simultaneously with the removal of sulfide. No loss of sulfide occurred in controls without arsenate or in sterilized samples containing both arsenate and sulfide. The rate of arsenate reduction in lake water was dependent on the amount of available arsenate. We enriched for a bacterium that could achieve growth with sulfide and arsenate in a defined, mineral medium and purified it by serial dilution. The isolate, strain MLMS-1, is a gram-negative, motile curved rod that grows by oxidizing sulfide to sulfate while reducing arsenate to arsenite. Chemoautotrophy was confirmed by the incorporation of H 14 CO 3 − into dark-incubated cells, but preliminary gene probing tests with primers for ribulose-1,5-biphosphate carboxylase/oxygenase did not yield PCR-amplified products. Alignment of 16S rRNA sequences indicated that strain MLMS-1 was in the δ- Proteobacteria , located near sulfate reducers like Desulfobulbus sp. (88 to 90% similarity) but more closely related (97%) to unidentified sequences amplified previously from Mono Lake. However, strain MLMS-1 does not grow with sulfate as its electron acceptor.

California

Thin-section electron microscopy of mature Myxosoma cerebralis (Myxosporidea) spores

The morphology of purified, mature Myxosoma cerebralis spores was examined by thin-section electron microscopy. Surface architecture corresponded closely to that described in an earlier scanning electron microscopy study of this organism (Lom and Hoffman, 1971). A uniformly thick spore wall is composed of finely granular, electron-lucent material. Intrawall "valvoplasm" at the sutural border region contains small, light spheroidal profiles with dense centers situated in a background matrix; such structures are absent in the intermediate wall areas. Ovoid polar capsules contain complex filamentous profiles within the peripheral matrix region. Individual filaments appear twisted into S-shaped configurations and contain moderately electron-opaque material within their lumina.

Journal of Parasitology

Electron donor concentrations in sediments and sediment properties at the agricultural chemicals team research site near New Providence, Iowa, 2006-07

The concentrations of electron donors in aquifer sediments are important to the understanding of the fate and transport of redox-sensitive constituents in groundwater, such as nitrate. For a study by the U.S. Geological Survey National Water-Quality Assessment Program, 50 sediment samples were collected from below the water table from 11 boreholes at the U.S. Geological Survey Agricultural Chemicals Team research site near New Providence, Iowa, during 2006-07. All samples were analyzed for gravel, sand (coarse, medium, and fine), silt, clay, Munsell soil color, inorganic carbon content, and for the following electron donors: organic carbon, ferrous iron, and inorganic sulfide. A subset of 14 sediment samples also was analyzed for organic sulfur, but all of these samples had concentrations less than the method detection limit; therefore, the presence of this potential electron donor was not considered further. X-ray diffraction analyses provided important semi-quantitative information of well-crystallized dominant minerals within the sediments that might be contributing electron donors.

Iowa

Identification and measurement of chlorinated organic pesticides in water by electron-capture gas chromatography

Pesticides, in minute quantities, may affect the regimen of streams, and because they may concentrate in sediments, aquatic organisms, and edible aquatic foods, their detection and their measurement in the parts-per-trillion range are considered essential. In 1964 the U.S. Geological Survey at Menlo Park, Calif., began research on methods for monitoring pesticides in water. Two systems were selected--electron-capture gas chromatography and microcoulometric-titration gas chromatography. Studies on these systems are now in progress. This report provides current information on the development and application of an electron-capture gas chromatographic procedure. This method is a convenient and extremely sensitive procedure for the detection and measurement of organic pesticides having high electron affinities, notably the chlorinated organic pesticides. The electron-affinity detector is extremely sensitive to these substances but it is not as sensitive to many other compounds. By this method, the chlorinated organic pesticide may be determined on a sample of convenient size in concentrations as low as the parts-per-trillion range. To insure greater accuracy in the identifications, the pesticides reported were separated and identified by their retention times on two different types of gas chromatographic columns.

Water Supply Paper

Applications of correlative light and electron microscopy (CLEM) to organic matter in the North American shale petroleum systems

Scanning electron microscopy (SEM) has revolutionized our understanding of shale petroleum systems through microstructural characterization of dispersed organic matter (OM). However, due to the low atomic weight of carbon, all OM appears black in SEM (BSE image) regardless of differences in thermal maturity or OM type (kerogen types or solid bitumen). Traditional petrographic identification of OM uses optical microscopy, where reflectance (%Ro), form, relief and fluorescence can be used to discern OM types and thermal maturation stage. Unfortunately, most SEM studies of shale OM do not employ correlative optical techniques, leading to misidentifications or to the conclusion that all OM (i.e., kerogen and solid bitumen) is the same. To improve the accuracy of SEM identifications of dispersed OM in shale, this study used correlative light and electron microscopy (CLEM) to create optical and SEM images of OM in the same fields of view (500x magnification) under white light, blue light, secondary electron, and backscatter electron conditions. Samples (n=8) of varying thermal maturities and typical of the North American shale petroleum systems were used, including the Green River Mahogany Zone, Bakken Formation, Ohio Shale, Eagle Ford Formation, Barnett Formation, Haynesville Formation and Woodford Shale. The CLEM image sets demonstrate the importance of correlative microscopy by showing how easily OM can be misidentified when viewed by SEM alone. Without CLEM techniques, petrographic data from SEM such as observations of organic nano-porosity may be misinterpreted, resulting in false or ambiguous results and impairing an improved understanding of organic diagenesis and catagenesis.

Book chapter

A spherical electron-channelling pattern map for use in quartz petrofabric analysis

Electron channelling patterns (ECP's) are formed in the scanning electron microscope (SEM) by the interaction between the incident electrons and the lattice of crystalline specimens. The patterns are unique for a particular crystallographic orientation and are therefore of considerable potential in petrofabric studies provided they can be accurately indexed. Indexing requires an ECP-map of the crystallographic stereogram or unit triangle covering all possible orientations and hence ECP patterns. Due to the presence of long-range distortions in planar ECP-maps, it is more convenient to construct the maps over a spherical surface. This also facilitates the indexing of individual ECP's. A spherical ECP-map for quartz is presented together with an example of its use in petrofabric analysis.

Journal of Structural Geology

Middle UV to near-IR spectrum of electron-excited SO 2

We investigated the electron impact–induced fluorescence spectrum of SO 2 to provide excitation cross sections for modeling Io's emission spectrum and analyzing Cassini Imaging Science Subsystem observations. The electron-excited middle-ultraviolet visible optical near-infrared (VOIR) emission spectrum of SO 2 gas was generated in the laboratory and studied from 2000 to 11,000 Å at a resolution of Δ λ ∼ 2.5 Å full width at half maximum (FWHM). The VOIR laboratory spectrum longward of 6000 Å consists entirely of S I, II and O I, II multiplets for electron impact energies above ∼15 eV. Between 2000 and 6000 Å, we find previously identified molecular bands from both SO and SO 2 . This work represents a significant improvement in spectral resolution over our earlier work done at 18 Å FWHM. From a measurement of the medium-resolution spectrum, we provide detailed 25- and 100-eV emission cross sections for spectral features from 2000 to 11,000 Å. On the basis of these data, we suggest future ground-based and satellite telescopic observations in the VOIR that are of promise for understanding Io's atmosphere.

Journal of Geophysical Research E: Planets

First observation of the ground-state electron-capture of 40K

Potassium-40 is a widespread, naturally occurring isotope whose radioactivity impacts estimated geological ages spanning billions of years, nuclear structure theory, and subatomic rare-event searches—including those for dark matter and neutrinoless double-beta decay. The decays of this long-lived isotope must be precisely known for its use as a geochronometer, and to account for its presence in low-background experiments. There are several known decay modes for potassium-40, but a predicted electron-capture decay directly to the ground state of argon-40 has never been observed. The existence of this decay mode impacts several fields, while theoretical predictions span an order of magnitude. Here we report on the first, successful observation of this rare decay mode, obtained by the KDK (potassium decay) Collaboration using a novel combination of a low-threshold x-ray detector surrounded by a tonne-scale, high-efficiency γ -ray tagger at Oak Ridge National Laboratory. A blinded analysis reveals a distinctly nonzero ratio of intensities of ground-state electron-captures ( I EC 0 ) over excited-state ones ( I EC ∗ ) of I EC 0 / I EC ∗ = 0.0095 stat ± 0.0022 sys ± 0.0010 (68% CL), with the null hypothesis rejected at 4 σ [Stukel et al. , Phys. Rev. Lett. 131 , 052503 (2023) ]. In terms of branching ratio, this unambiguous signal yields I EC 0 = 0.098 % stat ± 0.023 % sys ± 0.010 % , roughly half of the commonly used prediction. This first observation of a third-forbidden unique electron capture improves our understanding of low-energy backgrounds in dark-matter searches and has implications for nuclear-structure calculations. For example, a shell-model based theoretical estimate for the neutrinoless double-beta decay half-life of calcium-48 is increased by a factor of 7 + 3 − 2 . Our nonzero measurement shifts geochronological ages by up to a percent; implications are illustrated for Earth and solar system chronologies.

Physical Review C

Utilization of integrated correlative light and electron microscopy (iCLEM) for imaging sedimentary organic matter

We report here a new microscopic technique for imaging and identifying sedimentary organic matter in geologic materials that combines inverted fluorescence microscopy with scanning electron microscopy and allows for sequential imaging of the same region of interest without transferring the sample between instruments. This integrated correlative light and electron microscopy technique is demonstrated with observations from an immature lacustrine oil shale from the Eocene Green River Mahogany Zone and mid‐oil window paralic shale from the Upper Cretaceous Tuscaloosa Group. This technique has the potential to allow for identification and characterization of organic matter in shale hydrocarbon reservoirs that is not possible using either light or electron microscopy alone, and may be applied to understanding the organic matter type and thermal regime in which organic nanoporosity forms, thereby reducing uncertainty in the estimation of undiscovered hydrocarbon resources.

Journal of Microscopy

Growth of strain SES-3 with arsenate and other diverse electron acceptors

The selenate-respiring bacterial strain SES-3 was able to use a variety of inorganic electron acceptors to sustain growth. SES-3 grew with the reduction of arsenate to arsenite, Fe(III) to Fe(II), or thiosulfate to sulfide. It also grew in medium in which elemental sulfur, Mn(IV), nitrite, trimethylamine N -oxide, or fumarate was provided as an electron acceptor. Growth on oxygen was microaerophilic. There was no growth with arsenite or chromate. Washed suspensions of cells grown on selenate or nitrate had a constitutive ability to reduce arsenate but were unable to reduce arsenite. These results suggest that strain SES-3 may occupy a niche as an environmental opportunist by being able to take advantage of a diversity of electron acceptors.

Applied and Environmental Microbiology

Comparative morphology of zebra ( Dreissena polymorpha ) and quagga ( Dreissena bugensis ) mussel sperm: Light and electron microscopy

Adult zebra ( Dreissena polymorpha ) and quagga ( Dreissena bugensis ) mussels were induced to release large quantities of live spermatozoa by the administration of 5-hydroxytryptamine (serotonin). Sperm were photographed alive using phase-contrast microscopy and were fixed subsequently with glutaraldehyde followed by osmium tetroxide for eventual examination by transmission or scanning electron microscopy. The sperm of both genera are of the ect-aquasperm type. Their overall dimensions and shape allow for easy discrimination at the light and scanning electron microscopy level. Transmission electron microscopy of the cells reveals a barrel-shaped nucleus in zebra mussel sperm and an elongated nucleus in quagga mussel sperm. In both species, an acrosome is cradled in a nuclear fossa. The ultrastructure of the acrosome and axial body, however, is distinctive for each species. The structures of the midpiece are shown, including a unique mitochondrial "skirt" that includes densely packed parallel cristae and extends in a narrow sheet from the mitochondria.

Canadian Journal of Zoology

Tracking animals in freshwater with electronic tags: past, present and future

Considerable technical developments over the past half century have enabled widespread application of electronic tags to the study of animals in the wild, including in freshwater environments. We review the constraints associated with freshwater telemetry and biologging and the technical developments relevant to their use. Technical constraints for tracking animals are often influenced by the characteristics of the animals being studied and the environment they inhabit. Collectively, they influence which and how technologies can be used and their relative effectiveness. Although radio telemetry has historically been the most commonly used technology in freshwater, passive integrated transponder (PIT) technology, acoustic telemetry and biologgers are becoming more popular. Most telemetry studies have focused on fish, although an increasing number have focused on other taxa, such as turtles, crustaceans and molluscs. Key technical developments for freshwater systems include: miniaturization of tags for tracking small-size life stages and species, fixed stations and coded tags for tracking large samples of animals over long distances and large temporal scales, inexpensive PIT systems that enable mass tagging to yield population- and community-level relevant sample sizes, incorporation of sensors into electronic tags, validation of tag attachment procedures with a focus on maintaining animal welfare, incorporation of different techniques (for example, genetics, stable isotopes) and peripheral technologies (for example, geographic information systems, hydroacoustics), development of novel analytical techniques, and extensive international collaboration. Innovations are still needed in tag miniaturization, data analysis and visualization, and in tracking animals over larger spatial scales (for example, pelagic areas of lakes) and in challenging environments (for example, large dynamic floodplain systems, under ice). There seems to be a particular need for adapting various global positioning system and satellite tagging approaches to freshwater. Electronic tagging provides a mechanism to collect detailed information from imperilled animals and species that have no direct economic value. Current and future advances will continue to improve our knowledge of the natural history of aquatic animals and ecological processes in freshwater ecosystems while facilitating evidence-based resource management and conservation.

Animal Biotelemetry

Arsenite as an electron donor for anoxygenic photosynthesis: Description of three strains of Ectothiorhodospria from Mono Lake, California, and Big Soda Lake, Nevada

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243 T , and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243 T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion.

Life Sciences

Use of electronic microprocessor-based instrumentation by the U.S. geological survey for hydrologic data collection

The U.S. Geological Survey is acquiring a new generation of field computers and communications software to support hydrologic data-collection at field locations. The new computer hardware and software mark the beginning of the Survey's transition from the use of electromechanical devices and paper tapes to electronic microprocessor-based instrumentation. Software is being developed for these microprocessors to facilitate the collection, conversion, and entry of data into the Survey's National Water Information System. The new automated data-collection process features several microprocessor-controlled sensors connected to a serial digital multidrop line operated by an electronic data recorder. Data are acquired from the sensors in response to instructions programmed into the data recorder by the user through small portable lap-top or hand-held computers. The portable computers, called personal field computers, also are used to extract data from the electronic recorders for transport by courier to the office computers. The Survey's alternative to manual or courier retrieval is the use of microprocessor-based remote telemetry stations. Plans have been developed to enhance the Survey's use of the Geostationary Operational Environmental Satellite telemetry by replacing the present network of direct-readout ground stations with less expensive units. Plans also provide for computer software that will support other forms of telemetry such as telephone or land-based radio.

Conference Paper

Collecting, shipping, storing, and imaging snow crystals and ice grains with low-temperature scanning electron microscopy

Methods to collect, transport, and store samples of snow and ice have been developed that enable detailed observations of these samples with a technique known as low-temperature scanning electron microscopy (LTSEM). This technique increases the resolution and ease with which samples of snow and ice can be observed, studied, and photographed. Samples are easily collected in the field and have been shipped to the electron microscopy laboratory by common air carrier from distances as far as 5,000 miles. Delicate specimens of snow crystals and ice grains survive the shipment procedures and have been stored for as long as 3 years without undergoing any structural changes. The samples are not subjected to the melting or sublimation artifacts. LTSEM allows individual crystals to be observed for several hours with no detectable changes. Furthermore, the instrument permits recording of photographs containing the parallax information necessary for three-dimensional imaging of the true shapes of snowflakes, snow crystals, snow clusters, ice grains, and interspersed air spaces. This study presents detailed descriptions of the procedures that have been used successfully in the field and the laboratory to collect, ship, store, and image snow crystals and ice grains. Published 2003 Wiley-Liss, Inc.

Microscopy Research and Technique

Cluster molecular orbital description of the electronic structures of mixed-valence iron oxides and silicates

A molecular orbital description, based on spin-unrestricted X α-scattered wave calculations, is given for the electronic structures of mixed valence iron oxides and silicates. The cluster calculations show that electron hopping and optical intervalence charge-transger result from weak FeFe bonding across shared edges of FeO 6 coordination polyhedra. In agreement with Zener's double exchange model, FeFe bonding is found to stabilize ferromagnetic coupling between Fe 2+ and Fe 3+ cations.

Solid State Communications

Analytical electron microscopy in mineralogy; exsolved phases in pyroxenes

Analytical scanning transmission electron microscopy has been successfully used to characterize the structure and composition of lamellar exsolution products in pyroxenes. At operating voltages of 100 and 200 keV, microanalytical techniques of x-ray energy analysis, convergent-beam electron diffraction, and lattice imaging have been used to chemically and structurally characterize exsolution lamellae only a few unit cells wide. Quantitative X-ray energy analysis using ratios of peak intensities has been adopted for the U.S. Geological Survey AEM in order to study the compositions of exsolved phases and changes in compositional profiles as a function of time and temperature. The quantitative analysis procedure involves 1) removal of instrument-induced background, 2) reduction of contamination, and 3) measurement of correction factors obtained from a wide range of standard compositions. The peak-ratio technique requires that the specimen thickness at the point of analysis be thin enough to make absorption corrections unnecessary (i.e., to satisfy the “thin-foil criteria”). In pyroxenes, the calculated “maximum thicknesses” range from 130 to 1400 nm for the ratios Mg/Si, Fe/Si, and Ca/Si; these “maximum thicknesses” have been contoured in pyroxene composition space as a guide during analysis. Analytical spatial resolutions of 50–100 nm have been achieved in AEM at 200 keV from the composition-profile studies, and analytical reproducibility in AEM from homogeneous pyroxene standards is ± 1.5 mol% endmember.

Ultramicroscopy

Application of electron microscopy TEM and SEM for analysis of coals, organic-rich shales and carbonaceous matter

This paper provides a brief summary of the history, development and variety of applications of electron microscopy techniques to analyze coals, organic-rich shales, and carbonaceous materials. General construction and principles of operation of transmitted (TEM) and scanning electron microscope (SEM) are outlined, along with guidance on specimen preparation, and a brief overview of published TEM and SEM applications related to coal, shales, and carbonaceous materials. This work was accepted as the chapter 18.2 of International Committee for Coal and Organic Petrology Methods Handbook at the ICCP Plenary Session on September 27, 2018 in Brisbane (Australia).

International Journal of Coal Geology