Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Surface freshwater storage variations in the Orinoco floodplains using multi-satellite observations

Variations in surface water extent and storage are poorly characterized from regional to global scales. In this study, a multi-satellite approach is proposed to estimate the water stored in the floodplains of the Orinoco Basin at a monthly time-scale using remotely-sensed observations of surface water from the Global Inundation Extent Multi-Satellite (GIEMS) and stages from Envisat radar altimetry. Surface water storage variations over 2003-2007 exhibit large interannual variability and a strong seasonal signal, peaking during summer, and associated with the flood pulse. The volume of surface water storage in the Orinoco Basin was highly correlated with the river discharge at Ciudad Bolivar (R = 0.95), the closest station to the mouth where discharge was estimated, although discharge lagged one month behind storage. The correlation remained high (R = 0.73) after removing seasonal effects. Mean annual variations in surface water volume represented similar to 170 km(3), contributing to similar to 45% of the Gravity Recovery and Climate Experiment (GRACE)-derived total water storage variations and representing similar to 13% of the total volume of water that flowed out of the Orinoco Basin to the Atlantic Ocean

Analyzing power in nucleon-deuteron scattering and three-nucleon forces

Three-nucleon forces have been considered to be one possibility to resolve the well known discrepancy between experimental values and theoretical calculations of the nucleon analyzing power in low energy nucleon-deuteron scattering. In this paper, we investigate possible effects of two-pion exchange three-nucleon forces on the analyzing power and the differential cross section. We found that the reason for different effects on the analyzing power by different three-nucleon forces found in previous calculations is related to the existence of the contact term. Effects of some variations of two-pion exchange three-nucleon forces are investigated. Also, an expression for the measure of the nucleon analyzing power with quartet P-wave phase shifts is presented.Comment: 11 pages including 2 eps figures, use epsfig.sty, to appear in Phys. Rev.

Polarization observables in p-d scattering below 30 MeV

Differential and total breakup cross sections as well as vector and tensor analyzing powers for p-d scattering are studied for energies above the deuteron breakup threshold up to E(lab)=28 MeV. The p-d scattering wave function is expanded in terms of the correlated hyperspherical harmonic basis and the elastic S-matrix is obtained using the Kohn variational principle in its complex form. The effects of the Coulomb interaction, which are expected to be important in this energy range, have been rigorously taken into account. The Argonne AV18 interaction and the Urbana URIX three-nucleon potential have been used to perform a comparison to the available experimental data.Comment: 31 pages, 8 figure

Expression of inhibitor of apoptosis protein Livin in renal cell carcinoma and non-tumorous adult kidney

The antiapoptotic Livin/ML-IAP gene has recently gained much attention as a potential new target for cancer therapy. Reports indicating that livin is expressed almost exclusively in tumours, but not in the corresponding normal tissue, suggested that the targeted inhibition of livin may present a novel tumour-specific therapeutic strategy. Here, we compared the expression of livin in renal cell carcinoma and in non-tumorous adult kidney tissue by quantitative real-time reverse transcription-PCR, immunoblotting, and immunohistochemistry. We found that livin expression was significantly increased in tumours (P=0.0077), but was also clearly detectable in non-tumorous adult kidney. Transcripts encoding Livin isoforms α and β were found in both renal cell carcinoma and normal tissue, without obvious qualitative differences. Livin protein in renal cell carcinoma samples exhibited cytoplasmic and/or nuclear staining. In non-tumorous kidney tissue, Livin protein expression was only detectable in specific cell types and restricted to the cytoplasm. Thus, whereas the relative overexpression of livin in renal cell carcinoma indicates that it may still represent a therapeutic target to increase the apoptotic sensitivity of kidney cancer cells, this strategy is likely to be not tumour-specific

Characterization of the second- and third-harmonic optical susceptibilities of atomically thin tungsten diselenide

Supplementary information accompanies this paper at https://doi.org/10.1038/s41598-018-28374-1We report the first detailed characterization of the sheet third-harmonic optical susceptibility, χ(3)s, of tungsten diselenide (WSe2). With a home-built multiphoton microscope setup developed to study harmonics generation, we map the second and third-harmonic intensities as a function of position in the sample, pump power and polarization angle, for single- and few-layers flakes of WSe2. We register a value of |χ(3)s| ≈ 0.9 × 10-28 m3 V-2 at a fundamental excitation frequency of ℏω = 0.8 eV, which is comparable in magnitude to the third-harmonic susceptibility of other group-VI transition metal dichalcogenides. The simultaneously recorded sheet second-harmonic susceptibility is found to be |χ(2)s| ≈ 0.7 × 10-19 m2 V-1 in very good agreement on the order of magnitude with recent reports for WSe2, which asserts the robustness of our values for |χ(3)s|.Y.W.H. acknowledges scholarship support from NGS. G.E. acknowledges financial support from National Research Foundation of Singapore (NRF Research Fellowship NRF-NRFF2011-02 and medium-sized centre programme) and Ministry of Education of Singapore (AcRF Tier 2 MOE2015-T2-2-123). V. M. P. acknowledges fnancial support from Ministry of Education of Singapore (FRC AcRF Tier 1 R-144-000-386-114). J.C.V.G. acknowledges fnancial support from CA2DM through National Research Foundation of Singapore (NRF-CRP Grant No. R-144-000-295-281)

A Large Area Detector proposed for the Large Observatory for X-ray Timing (LOFT)

The Large Observatory for X-ray Timing (LOFT) is one of the four candidate ESA M3 missions considered for launch in the 2022 time-frame. It is specifically designed to perform fast X-ray timing and probe the status of the matter near black holes and neutron stars. The LOFT scientific payload is composed of a Large Area Detector (LAD) and a Wide Field Monitor (WFM). The LAD is a 10 m2-class pointed instrument with 20 times the collecting area of the best past timing missions (such as RXTE) over the 2-30 keV range, which holds the capability to revolutionize studies of X-ray variability down to the millisecond time scales. Its ground-breaking characteristic is a low mass per unit surface, enabling an effective area of ~10 m^2 (@10 keV) at a reasonable weight. The development of such large but light experiment, with low mass and power per unit area, is now made possible by the recent advancements in the field of large-area silicon detectors - able to time tag an X-ray photon with an accuracy <10 {\mu}s and an energy resolution of ~260 eV at 6 keV - and capillary-plate X-ray collimators. In this paper, we will summarize the characteristics of the LAD instrument and give an overview of its capabilities.Comment: Proceedings of SPIE, Vo. 8443, Paper No. 8443-8

Dynamics and distribution of bacterial and archaeal communities in oil-contaminated temperate coastal mudflat mesocosms

Mudflats are ecologically important habitats that are susceptible to oil pollution, but intervention is difficult in these fine-grained sediments, and so clean-up usually relies on natural attenuation. Therefore, we investigated the impact of crude oil on the bacterial, diatom and archaeal communities within the upper parts of the diatom-dominated sediment and the biofilm that detached from the surface at high tide. Biodegradation of petroleum hydrocarbons was rapid, with a 50 % decrease in concentration in the 0–2-mm section of sediment by 3 days, indicating the presence of a primed hydrocarbon-degrading community. The biggest oil-induced change was in the biofilm that detached from the sediment, with increased relative abundance of several types of diatom and of the obligately hydrocarbonoclastic Oleibacter sp., which constituted 5 % of the pyrosequences in the oiled floating biofilm on day 3 compared to 0.6 % in the non-oiled biofilm. Differences in bacterial community composition between oiled and non-oiled samples from the 0–2-mm section of sediment were only significant at days 12 to 28, and the 2–4-mm-sediment bacterial communities were not significantly affected by oil. However, specific members of the Chromatiales were detected (1 % of sequences in the 2–4-mm section) only in the oiled sediment, supporting other work that implicates them in anaerobic hydrocarbon degradation. Unlike the Bacteria, the archaeal communities were not significantly affected by oil. In fact, changes in community composition over time, perhaps caused by decreased nutrient concentration and changes in grazing pressure, overshadowed the effect of oil for both Bacteria and Archaea. Many obligate hydrocarbonoclastic and generalist oil-degrading bacteria were isolated, and there was little correspondence between the isolates and the main taxa detected by pyrosequencing of sediment-extracted DNA, except for Alcanivorax, Thalassolituus, Cycloclasticus and Roseobacter spp., which were detected by both methods

Enhancing Electron Coherence via Quantum Phonon Confinement in Atomically Thin Nb3SiTe6

The extraordinary properties of two dimensional (2D) materials, such as the extremely high carrier mobility in graphene and the large direct band gaps in transition metal dichalcogenides MX2 (M = Mo or W, X = S, Se) monolayers, highlight the crucial role quantum confinement can have in producing a wide spectrum of technologically important electronic properties. Currently one of the highest priorities in the field is to search for new 2D crystalline systems with structural and electronic properties that can be exploited for device development. In this letter, we report on the unusual quantum transport properties of the 2D ternary transition metal chalcogenide - Nb3SiTe6. We show that the micaceous nature of Nb3SiTe6 allows it to be thinned down to one-unit-cell thick 2D crystals using microexfoliation technique. When the thickness of Nb3SiTe6 crystal is reduced below a few unit-cells thickness, we observed an unexpected, enhanced weak-antilocalization signature in magnetotransport. This finding provides solid evidence for the long-predicted suppression of electron-phonon interaction caused by the crossover of phonon spectrum from 3D to 2D.Comment: Accepted by Nature Physic