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Fungal diversity and function in metagenomes sequenced from extreme environments

Fungi are increasingly recognized as key players in various extreme environments. Here we present an analysis of publicly-sourced metagenomes from global extreme environments, focusing on fungal taxonomy and function. The majority of 855 selected metagenomes contained scaffolds assigned to fungi. Relative abundance of fungi was as high as 10% of protein-coding genes with taxonomic annotation, with up to 289 fungal genera per sample. Despite taxonomic clustering by environment, fungal communities were more dissimilar than archaeal and bacterial communities, both for within- and between-environment comparisons. Relatively abundant fungal classes in extreme environments included Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Saccharomycetes, and Sordariomycetes. Broad generalists and prolific aerial spore formers were the most relatively abundant fungal genera detected in most of the extreme environments, bringing up the question of whether they are actively growing in those environments or just surviving as spores. More specialized fungi were common in some environments, such as zoosporic taxa in cryosphere water and hot springs. Relative abundances of genes involved in adaptation to general, thermal, oxidative, and osmotic stress were greatest in soda lake, acid mine drainage, and cryosphere water samples.

60 APPLIED LIFE SCIENCES↗

Far-infrared emission lines of CO and OH in the Orion-KL molecular shock

Observations of far infrared rotational emission lines which arise in the shocked gas associated with Orion-Kl are presented, including detections of the CO J = 34 yields 33, J = 31 yields 30, J = 26 yields 25, and OH sup 2 PI sub (3/2) J sup P = 7/2(-) yields 5/2(+) emission lines, as well as improved measurements of the CO J = 22 yields 21 and OH sup 2 PI sub (3/2) J = 5/2 yields 3/2 lines. These lines are observed to have velocity widths of Del V approx. 20 to 30 km/sec, somewhat less than either the 2 micro H sub 2 lines or the high velocity plateau component of the millimeter wave CO lines seen in this object. An H sub 2 column density of approx. 3 x 10 to the 21st power, a total mass of approx. 1 solar mass and characteristic temperature and density T approx. 750 K and approx. 2 x 10 to the 6th power per cu cm can be derived from the CO intensities. The density is too low by at least an order of magnitude for the observed infrared H sub 2 and far infrared CO emission to be accounted for by a purely hydrodynamic shock, and support is lent to hydromagnetic shock models. From the present measurements, the relative abundance of CO is estimated to be CO H sub 2 = 1.2 x .0001, corresponding to 20% of the cosmic abundance of C existing in the form of CO. The average relative abundance of OH in the shocked gas is O/H sub 2 or = 5 x 10 to the -7th power. An upper limit to the intensity of the HD J = 1 yields 0 line is used to derive an upper limit of tau or = 3 for the D/H relative abundance in the Orion cloud core.

Watson, D. M.↗

Far-infrared emission lines of CO and OH in the Orion-KL molecular shock

Observations of far infrared rotational emission lines which arise in the shocked gas associted with Orion-Kl are presented, including detections of the CO J = 34 yields 33, J = 31 yields 30, J = 26 yields 25, and OH sup 2 PI sub (3/2) J sup P = 7/2(-) yields 5/2(+) emission lines, as well as improved measurements of the CO J = 22 yields 21 and OH sup 2 PI sub (3/2) J = 5/2 yields 3/2 lines. These lines are observed to have velocity widths of Del V approx. 20 to 30 km/sec, somewhat less than either the 2 micro H sub 2 lines or the high velocity plateau component of the millimeter wave CO lines seen in this object. An H sub 2 column density of aprox. 3 x 10 to the 21st power, a total mass of approx. 1 solar mass and characteristic temperature and density T approx. 750 K and approx. 2 x 10 to the 6th power per cu cm can be derived from the CO intensities. The density is too low by at least an order of magnitude for the observed infrared H sub 2 and far infrared CO emission to be accounted for by a purely hydrodynamic shock, and support is lent to hydromagnetic shock models. From the present measurements, the relative abundance of CO is estimated to be CO H sub 2 = 1.2 x .0001, corresponding to 20 percent of the cosmic abundance of C existing in the form of CO. The average relative abundance of OH in the shocked gas is O/H sub 2 or = 5 x 10 to the -7th power. An upper limit to the intensity of the HD J - 1 yields 0 line is used to derive an upper limit of tau or = 3 for the D/H relative abundance in the Orion cloud core.

Watson, D. M.↗

Homogeneous condensation of gaseous mixtures of Si, Fe, O, N, and C in relative cosmic abundance and implications for astronomical condensation

The pressure versus temperature curves for homogeneous nucleation and condensation of two gaseous mixtures with nearly relative solar abundance of Si, Fe, O, N, and C in an excess of H were determined experimentally. Mixtures of CO, Fe(CO)5, H2, SiH4, and N2O in Ar were heated behind reflected shocks in a shock tube. The nucleation and condensation, which took place in the subsequent gas-dynamic expansion (cooling phase), was monitored by light scattering and turbidity. Grain morphologies and crystalline phases present in the condensates were determined by electron microscopy. These data cast doubt on the validity of both equilibrium and classical nucleation theoretical approaches to predict homogeneous condensation in a solar nebula or stellar atmosphere.

Stephens, J. R.↗

Spectrophotometric results from the Copernicus satellite. III - Ionization and composition of the intercloud medium.

Interstellar lines have been studied in the unreddened stars lambda Sco, upsilon Sco, alpha Leo, and alpha Eri, which are located between 20 and 150 pc from the sun. The lines are on the linear and saturated Doppler portions of the curve of growth. Preliminary analysis shows that processes producing large amounts of highly ionized species are not dominant. Doubly ionized C, N, Si, and S have been detected, but are all quite weak relative to the singly ionized species. Abundances relative to nitrogen are in the cosmic ratios or slightly lower, with some indication of general depletion of the heavier elements. Hydrogen number densities range from a measured value of 0.22 per cu cm for lambda Sco to a derived value of 0.02 per cu cm for alpha Leo assuming nitrogen to have its solar abundance relative to hydrogen.

Rogerson, J. B.↗

Test Would Quantify Combustion Oxygen From Different Sources

Proposed isotope-enrichment scheme enables determination of contributions of dual sources of oxygen for combustion. Liquid oxygen or other artificial stream enriched with O(18) to about 1 percent by weight. Combustion products analyzed by mass spectrometer to measure relative abundances of H2O(18) and H2O(16). From relative abundances of water products measured, one computes relative contribution of oxygen extracted from stream compared to other source of oxygen in combustion process. Used to determine contributions of natural oxygen in air and liquid oxygen supplied in separate stream mixed with air or sent directly into combustion chamber.

Tapphorn, Ralph M.↗

The (32)S/(33)S abundance as a function of galactocentric radius in the Milky Way

Astration of heavy elements by the stars of the Milky Way forms a fossil record which may preserve spacial distribution of the mass function for the stars in the galaxy. Sulfur is among the last common element for which the relative abundance of its various isotopes have yet to be completely measured within our galaxy. Explosive oxygen burning in massive stars is thought to be the process which dominates sulfur production within stars. There models predict that the various isotopes (S-32, S-33, S-34) are formed in relative abundance which depend strongly upon the mass of the parent star. This relative abundance is thought to be unaffected by subsequent stellar procesing since all important sinks of sulfur destroy it without regard for isotopic form. Hence the spacial variation of the mass function (MF) can be studied by measuring the abundance variation of sulfur isotopes in the galaxy provided that the product yields for these isotopes are known accurately as a function of stellar mass.

Greenhouse, M. A.↗

Comparing Spatial Distributions of Solar Prominence Mass Derived from Coronal Absorption

In the present work we extend the use of this mass-inference technique to a sample of prominences observed in at least two coronal lines. This approach, in theory, allows a direct calculation of prominence mass and helium abundance and how these properties vary spatially and temporally. Our motivation is two-fold: to obtain a He(exp 0)/H(exp 0) abundance ratio, and to determine how the relative spatial distribution of the two species varies in prominences. The first of these relies on the theoretical expectation that the amount of absorption at each EUV wavelength is well-characterized. However, in this work we show that due to a saturation of the continuum absorption in the 625 A and 368 A lines (which have much higher opacity compared to 195 A-) the uncertainties in obtaining the relative abundances are too high to give meaningful estimates. This is an important finding because of its impact on future studies in this area. The comparison of the spatial distribution of helium and hydrogen presented here augments previous observational work indicating that cross-field diffusion of neutrals is an important mechanism for mass loss. Significantly different loss timescales for neutral He and H (helium drains much more rapidly than hydrogen) can impact prominence structure, and both the present and past studies suggest this mechanism is playing a role in structure and possibly dynamics. Section 2 of this paper contains a description of the observations and Section 3 summarizes the method used to infer mass along with the criteria imposed in choosing prominences appropriate for this study. Section 3 also contains a discussion of the problems due to limitations of the available data and the implications for determining relative abundances. We present our results in Section 4, including plots of radial-like scans of prominence mass in different lines to show the spatial distribution of the different species. The last section contains a discussion summarizing the importance of the qualitative results found in this work. The Appendix provides a detailed derivation of how to obtain prominence mass and helium abundance (A 1) and includes the data for all prominences studied (A2).

Gilbert, Holly↗

Abundances of energy spectra of individual iron-secondary elements

Relative abundances of individual Iron-secondary elements have been measured using a balloon-borne 6.6 m ster ionization/Cerenkov detector system. The unusually large geometry factor and single-charge resolution yield empirical atmospheric attenuation curves for individual elements which combine with high statistics at float altitude to yield individual element abundances, extrapolated to the top of the atmosphere, with high precision. Results are presented for top-of-the-atmosphere abundances (relative to iron) of individual elements in the Z range 13-30.

Israel, M. H.↗

Effects of solar wind composition, anisotropy, and streaming on ordinary mode electromagnetic instability

The stability of the low-frequency waves propagating transverse to the magnetic field of a plasma composed of electrons, protons, and alpha particles with anisotropic electron and ion temperatures is explored. The threshold for the ordinary mode instability and the growth rates have a very strong dependence on the electron temperature anisotropy but have a comparatively weaker dependence on the ion temperature anisotropy, on the relative abundance of helium to hydrogen, and on the relative streaming of two ion species. The threshold for the instability of these low-frequency waves is (m sub e/m sub p) to the 1/2 power times smaller than the one corresponding to high-frequency waves; however, for a relative abundance of helium to hydrogen up to 20% for the relevant known magnetic fields, particle densities, temperatures, and drifts, the solar wind remains below the threshold for this instability.

Buti, B.↗

Composition, Growth, Succession, and Function in the Cladophora Microbiome: Insights From Quantitative Stable Isotope Probing and NanoSIMS Imaging

The branching green macroalga Cladophora glomerata and its epiphytic microbiome dominate summer biomass in the Eel River, a Northern California river under Mediterranean (summer drought, winter rain) seasonality. Green Cladophora streamers proliferate in early summer, then change to yellow and then red-brown as epiphyte loads increase. Here, we characterised successional changes in epiphytic bacteria on Cladophora, examining both community composition and growth rates, using quantitative Stable Isotope Probing (qSIP) and 16S rRNA gene amplicon sequencing. The number of bacterial taxa increased with succession while growth rates peaked in the middle stage. NanoSIMS imaging confirmed high sulphur (S) concentrations in Cladophora cell walls relative to surrounding biomass, coinciding with a bloom of sulphur bacteria (bacteria that reduce or oxidise sulphur/sulphates). In general, relative abundances and growth rates were independent, indicating that either metric alone is insufficient for understanding how taxonomy and functional groups affect ecosystem processes. For instance, the relative abundance of nitrogen fixers peaked in the late summer when their relative growth rates were slowest. Such patterns may be driven by space competition limiting growth. Together, changes in abundance and relative growth rates suggest different limiting factors for different functional groups in the Cladophora microbiome at multiple successional stages.

Biological and medical sciences↗

Calibrating Laser Gas Measurements by Use of Natural CO2

An improved method of calibration has been devised for instruments that utilize tunable lasers to measure the absorption spectra of atmospheric gases in order to determine the relative abundances of the gases. In this method, CO2 in the atmosphere is used as a natural calibration standard. Unlike in one prior calibration method, it is not necessary to perform calibration measurements in advance of use of the instrument and to risk deterioration of accuracy with time during use. Unlike in another prior calibration method, it is not necessary to include a calibration gas standard (and the attendant additional hardware) in the instrument and to interrupt the acquisition of atmospheric data to perform calibration measurements. In the operation of an instrument of this type, the beam from a tunable diode laser or a tunable quantum-cascade laser is directed along a path through the atmosphere, the laser is made to scan in wavelength over an infrared spectral region that contains one or two absorption spectral lines of a gas of interest, and the transmission (and, thereby, the absorption) of the beam is measured. The concentration of the gas of interest can then be calculated from the observed depth of the absorption line(s), given the temperature, pressure, and path length. CO2 is nearly ideal as a natural calibration gas for the following reasons: CO2 has numerous rotation/vibration infrared spectral lines, many of which are near absorption lines of other gases. The concentration of CO2 relative to the concentrations of the major constituents of the atmosphere is well known and varies slowly and by a small enough amount to be considered constant for calibration in the present context. Hence, absorption-spectral measurements of the concentrations of gases of interest can be normalized to the concentrations of CO2. Because at least one CO2 calibration line is present in every spectral scan of the laser during absorption measurements, the atmospheric CO2 serves continuously as a calibration standard for every measurement point. Figure 1 depicts simulated spectral transmission measurements in a wavenumber range that contains two absorption lines of N2O and one of CO2. The simulations were performed for two different upper-atmospheric pressures for an airborne instrument that has a path length of 80 m. The relative abundance of CO2 in air was assumed to be 360 parts per million by volume (approximately its natural level in terrestrial air). In applying the present method to measurements like these, one could average the signals from the two N2O absorption lines and normalize their magnitudes to that of the CO2 absorption line. Other gases with which this calibration method can be used include H2O, CH4, CO, NO, NO2, HOCl, C2H2, NH3, O3, and HCN. One can also take advantage of this method to eliminate an atmospheric-pressure gauge and thereby reduce the mass of the instrument: The atmospheric pressure can be calculated from the temperature, the known relative abundance of CO2, and the concentration of CO2 as measured by spectral absorption. Natural CO2 levels on Mars provide an ideal calibration standard. Figure 2 shows a second example of the application of this method to Mars atmospheric gas measurements. For sticky gases like H2O, the method is particularly powerful, since water is notoriously difficult to handle at low concentrations in pre-flight calibration procedures.

Webster, Chris↗

The Compositional Evolution of C/2012 S1 (ISON) from Ground-Based High-Resolution Infrared Spectroscopy as Part of a Worldwide Observing Campaign

Volatile production rates, relative abundances, rotational temperatures, and spatial distributions in the coma were measured in C/2012 S1 (ISON) using long-slit high-dispersion (lambda/delta lambda approximately 2.5 times 10 (sup 4)) infrared spectroscopy as part of a worldwide observing campaign. Spectra were obtained on Universal Time 2013 October 26 and 28 with NIRSPEC (Near Infrared Spectrometer) at the W.M. Keck Observatory, and Universal Time 2013 November 19 and 20 with CSHELL (Cryogenic Echelle Spectrograph) at the NASA IRTF (Infrared Telescope Facility). H2O was detected on all dates, with production rates increasing markedly from (8.7 plus or minus 1.5) times 10 (sup 27) molecules per second on October 26 (Heliocentric Distance = 1.12 Astronomical Units) to (3.7 plus or minus 0.4) times 10 (sup 29) molecules per second on November 20 (Heliocentric Distance = 0.43 Astronomical Units). Short-term variability of H2O production is also seen as observations on November 19 show an increase in H2O production rate of nearly a factor of two over a period of about 6 hours. C2H6, CH3OH and CH4 abundances in ISON (International Scientific Optical Network) are slightly depleted relative to H2O when compared to mean values for comets measured at infrared wavelengths. On the November dates, C2H2, HCN and OCS abundances relative to H2O appear to be within the range of mean values, whereas H2CO and NH3 were significantly enhanced. There is evidence that the abundances with respect to H2O increased for some species but not others between October 28 (Heliocentric Distance = 1.07 Astronomical Units) and November 19 (Heliocentric Distance = 0.46 Astronomical Units). The high mixing ratios of H2CO to CH3OH and C2H2 to C2H6 on November 19, and changes in the mixing ratios of some species with respect to H2O between October 28 to November 19, indicates compositional changes that may be the result of a transition from sampling radiation-processed outer layers in this dynamically new comet to sampling more pristine natal material as the outer processed layer was increasingly eroded and the thermal wave propagated into the nucleus as the comet approached perihelion for the first time. On November 19 and 20, the spatial distribution for dust appears asymmetric and enhanced in the antisolar direction, whereas spatial distributions for volatiles (excepting CN) appear symmetric with their peaks slightly offset in the sunward direction compared to the dust. Spatial distributions for H2O, HCN, C2H6, C2H2, and H2CO on November 19 show no definitive evidence for significant contributions from extended sources; however, broader spatial distributions for NH3 and OCS may be consistent with extended sources for these species. Abundances of HCN and C2H2 on November 19 and 20 are insufficient to account for reported abundances of CN and C2 in ISON near this time. Differences in HCN and CN spatial distributions are also consistent with HCN as only a minor source of CN in ISON on November 19 as the spatial distribution of CN in the coma suggests a dominant distributed source that is correlated with dust and not volatile release. The spatial distributions for NH3 and NH2 are similar, suggesting that NH3 is the primary source of NH2 with no evidence of a significant dust source of NH2; however, the higher production rates derived for NH3 compared to NH2 on November 19 and 20 remain unexplained. This suggests a more complete analysis that treats NH2 as a distributed source and accounts for its emission mechanism is needed for future work.

Russo, N. Dello↗

Cosmic-ray elemental abundances from 1 to 10 GeV per amu for boron through nickel

The relative abundances of cosmic-ray nuclei in the charge range boron through nickel over the energy range 1-10 GeV per amu were measured with a balloon-borne detector. The instrument consists of a scintillation and Cerenkov counter telescope with a multiwire proportional chamber hodoscope and has been flown in four high-altitude balloon flights. Good charge resolution (sigma = 0.2 charge units at iron) and high statistical accuracy have been achieved. These data are used to derive the energy dependence of the leakage path length using the leaky box model of propagation and confinement in the galaxy. This energy dependence is found to be best fit by lambda = E(tot) exp -n, where n = 0.49 + or - 0.06 over 1-10 GeV per amu. Relative abundances at the source are consistent with an energy-independent composition.

Dwyer, Robert↗

Abundance ratios of oxygen, neon, and magnesium in solar active regions and flares: The FIP effect

Relative abundances of oxygen, neon, and magnesium have been derived for a sample of nine solar active regions, flares, and an erupting prominance by combining plots of the ion differential emission measures. The observations were photographed in the 300-600 A range by the Naval Research Laboratory (NRL) spectroheliograph on Skylab. Methods for deriving the Mg/Ne abundance ratio-which measures the separation between the low- first ionization potential (FIP) and high-FIP abundnace plateaus-have been described in previous papers. In this paper we describe the spectroscopic methods for deriving the O/Ne abundance ratio, which gives the ratio between two high-FIP elements. The plot of the O/Ne ratio versus the Mg/Ne ratio in the sample of nine Skylab events is shown. The variation in the Mg/Ne ratio by a factor of 6 is associated with a much smaller range in the O/Ne ratio. This is broadly consistent with the presence of the standard FIP pattern of abundances in the outer atmosphere of the Sun. However, a real change in the relative abundances of oxygen and neon by a factor of 1.5 cannot be excluded.

Widing, K. G.↗

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗

Digital Equivalent Data System for XRF Labeling of Objects

A digital equivalent data system (DEDS) is a system for identifying objects by means of the x-ray fluorescence (XRF) spectra of labeling elements that are encased in or deposited on the objects. As such, a DEDS is a revolutionary new major subsystem of an XRF system. A DEDS embodies the means for converting the spectral data output of an XRF scanner to an ASCII alphanumeric or barcode label that can be used to identify (or verify the assumed or apparent identity of) an XRF-scanned object. A typical XRF spectrum of interest contains peaks at photon energies associated with specific elements on the Periodic Table (see figure). The height of each spectral peak above the local background spectral intensity is proportional to the relative abundance of the corresponding element. Alphanumeric values are assigned to the relative abundances of the elements. Hence, if an object contained labeling elements in suitably chosen proportions, an alphanumeric representation of the object could be extracted from its XRF spectrum. The mixture of labeling elements and for reading the XRF spectrum would be compatible with one of the labeling conventions now used for bar codes and binary matrix patterns (essentially, two-dimensional bar codes that resemble checkerboards). A further benefit of such compatibility is that it would enable the conversion of the XRF spectral output to a bar or matrix-coded label, if needed. In short, a process previously used only for material composition analysis has been reapplied to the world of identification. This new level of verification is now being used for "authentication."

Schramm, Harry F.↗

Cosmic-ray energy spectra between 10 and several hundred GeV per atomic mass unit for elements from Ar-18 to Ni-28 - Results from HEAO 3

Results from the Heavy Nuclei experiment on HEAO 3 are used to determine the primary abundances of Ni and Fe. Ni and Fe are found to have nearly constant relative abundances over the interval of 10 to about 500 GeV per amu. Individual secondary elements derived principally from interactions of primary Fe nuclei are shown to display a power-law decrease in relative abundance up to about 150 GeV per amu. Ar/Fe and Ca/Fe ratios of 2.6 + or - 0.7 percent and 8.8 + or - 0.7 percent, respectively, are found, confirming a fractionation of source abundances in which elements with high values of the first ionization potential are depleted relative to those with low first ionization potential.

Binns, W. R.↗