Genome sequence of Salarchaeum sp. Strain JOR-1, an extremely halophilic archaeon from the Dead Sea

An extremely halophilic archaeon, Salarchaeum sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb.Fil: Anton, Brian P.. New England Biolabs; Estados UnidosFil: DasSarma, Priya. University of Maryland; Estados UnidosFil: Martínez, Fabiana Lilian. University of Maryland; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto Nacional de Investigaciones para las Industrias Químicas; ArgentinaFil: DasSarma, Satyajit L.. University of Maryland; Estados UnidosFil: Madadha, Mohammad Al. University of Jordan; Jordania. University of Maryland; Estados UnidosFil: Roberts, Richard J.. New England Biolabs; Estados UnidosFil: DasSarma, Shiladitya. University of Maryland; Estados Unido

Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine

Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.Fil: DasSarma, Priya. University of Maryland; Estados UnidosFil: Anton, Brian P.. New England BioLabs; Estados UnidosFil: DasSarma, Satyajit L.. University of Maryland; Estados UnidosFil: Martínez, Fabiana Lilian. University of Maryland; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; ArgentinaFil: Guzman, Daniel. Universidad Mayor de San Simón; BoliviaFil: Roberts, Richard J.. New England BioLabs; Estados UnidosFil: DasSarma, Shiladitya. University of Maryland; Estados Unido

Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina

Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.Fil: Martínez, Fabiana Lilian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; Argentina. University of Maryland; Estados UnidosFil: Anton, B. P.. New England Biolabs; Estados UnidosFil: DasSarma, P.. University of Maryland; Estados UnidosFil: Rajal, Verónica Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; ArgentinaFil: Irazusta, Verónica Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Investigaciones para la Industria Química. Universidad Nacional de Salta. Facultad de Ingeniería. Instituto de Investigaciones para la Industria Química; ArgentinaFil: Roberts, Roy. New England Biolabs; Estados UnidosFil: DasSarma, S.. University of Maryland; Estados Unido

Conductivity in quasi two-dimensional systems

The conductivity in quasi two-dimensional systems is calculated using the quantum kinetic equation. Linearizing the Lenard-Balescu collision integral with the extension to include external field dependences allows one to calculate the conductivity with diagrams beyond the GW approximation including maximally crossed lines. Consequently the weak localization correction as an interference effect appears here from the field dependence of the collision integral (the latter dependence sometimes called intra-collisional field effect). It is shown that this weak localization correction has the same origin as the Debye-Onsager relaxation effect in plasma physics. The approximation is applied to a system of quasi two-dimensional electrons in hetero-junctions which interact with charged and neutral impurities and the low temperature correction to the conductivity is calculated analytically. It turns out that the dynamical screening due to charged impurities leads to a linear temperature dependence, while the scattering from neutral impurities leads to the usual Fermi-liquid behavior. By considering an appropriate mass action law to determine the ratio of charged to neutral impurities we can describe the experimental metal-insulator transition at low temperatures as a Mott-Hubbard transition.Comment: 7 pages 7 pages appendix 11 figure

Spin-isospin textured excitations in a double layer at filling factor ν=2\nu =2

We study the charged excitations of a double layer at filling factor 2 in the ferromagnetic regime. In a wide range of Zeeman and tunneling splittings we find that the low energy charged excitations are spin-isospin textures with the charge mostly located in one of the layers. As tunneling increases, the parent spin texture in one layer becomes larger and it induces, in the other layer, a shadow spin texture antiferromagnetically coupled to the parent texture. These new quasiparticles should be observable by measuring the strong dependence of its spin on tunneling and Zeeman couplings.Comment: 4 pages, 4 figure

Exoplanet Biosignatures: Understanding Oxygen as a Biosignature in the Context of Its Environment

Here we review how environmental context can be used to interpret whether O2 is a biosignature in extrasolar planetary observations. This paper builds on the overview of current biosignature research discussed in Schwieterman et al. (2017), and provides an in-depth, interdisciplinary example of biosignature identification and observation that serves as a basis for the development of the general framework for biosignature assessment described in Catling et al., (2017). O2 is a potentially strong biosignature that was originally thought to be an unambiguous indicator for life at high-abundance. We describe the coevolution of life with the early Earth's environment, and how the interplay of sources and sinks in the planetary environment may have resulted in suppression of O2 release into the atmosphere for several billion years, a false negative for biologically generated O2. False positives may also be possible, with recent research showing potential mechanisms in exoplanet environments that may generate relatively high abundances of atmospheric O2 without a biosphere being present. These studies suggest that planetary characteristics that may enhance false negatives should be considered when selecting targets for biosignature searches. Similarly our ability to interpret O2 observed in an exoplanetary atmosphere is also crucially dependent on environmental context to rule out false positive mechanisms. We describe future photometric, spectroscopic and time-dependent observations of O2 and the planetary environment that could increase our confidence that any observed O2 is a biosignature, and help discriminate it from potential false positives. By observing and understanding O2 in its planetary context we can increase our confidence in the remote detection of life, and provide a model for biosignature development for other proposed biosignatures.Comment: 55 pages. The paper is the second in a series of 5 review manuscripts of the NExSS Exoplanet Biosignatures Workshop. Community commenting is solicited at https://nexss.info/groups/ebww

Surface and Temporal Biosignatures

Recent discoveries of potentially habitable exoplanets have ignited the prospect of spectroscopic investigations of exoplanet surfaces and atmospheres for signs of life. This chapter provides an overview of potential surface and temporal exoplanet biosignatures, reviewing Earth analogues and proposed applications based on observations and models. The vegetation red-edge (VRE) remains the most well-studied surface biosignature. Extensions of the VRE, spectral "edges" produced in part by photosynthetic or nonphotosynthetic pigments, may likewise present potential evidence of life. Polarization signatures have the capacity to discriminate between biotic and abiotic "edge" features in the face of false positives from band-gap generating material. Temporal biosignatures -- modulations in measurable quantities such as gas abundances (e.g., CO2), surface features, or emission of light (e.g., fluorescence, bioluminescence) that can be directly linked to the actions of a biosphere -- are in general less well studied than surface or gaseous biosignatures. However, remote observations of Earth's biosphere nonetheless provide proofs of concept for these techniques and are reviewed here. Surface and temporal biosignatures provide complementary information to gaseous biosignatures, and while likely more challenging to observe, would contribute information inaccessible from study of the time-averaged atmospheric composition alone.Comment: 26 pages, 9 figures, review to appear in Handbook of Exoplanets. Fixed figure conversion error

Diurnally Entrained Anticipatory Behavior in Archaea

By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions