Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably

Multi-Scale Analysis of Magnetic Fields in Filamentary Molecular Clouds in Orion A

New visible and K-band polarization measurements on stars surrounding molecular clouds in Orion A and stars in the BN vicinity are presented. Our results confirm that magnetic fields located inside the Orion A molecular clouds and in their close neighborhood are spatially connected. On and around the BN object, we measured the angular offsets between the K-band polarization data and available submm data. We find high values of the polarization degree, P_{K}, and of the optical depth, \tau_{K}, close to an angular offset position of 90^{\circ} whereas lower values of P_{K} and \tau_{K} are observed for smaller angular offsets. We interpret these results as evidence for the presence of various magnetic field components toward lines of sight in the vicinity of BN. On a larger scale, we measured the distribution of angular offsets between available H-band polarization data and the same submm data set. Here we find an increase of with angular offset which we interpret as a rotation of the magnetic field by \lesssim 60^{\circ}. This trend generalizes previous results on small scale toward and around lines of sight to BN and is consistent with a twist of the magnetic field on a larger scale towards OMC-1. A comparison of our results with several other studies suggests that a two-component magnetic field, maybe helical, could be wrapping the OMC-1 filament.Comment: 53 pages, 21 figures, 7 tables, Accepted in the Astrophysical Journa

High-Angular Resolution Dust Polarization Measurements: Shaped B-field Lines in the Massive Star Forming Region Orion BN/KL

We present observational results of the thermal dust continuum emission and its linear polarization in one of the nearest massive star-forming sites Orion BN/KL in Orion Molecular Cloud-1. The observations were carried out with the Submillimeter Array. With an angular resolution of 1" (~2 mpc; 480 AU), we have detected and resolved the densest cores near the BN/KL region. At a wavelength of ~870 micron, the polarized dust emission can be used to trace the structure of the magnetic field in this star-forming core. The dust continuum appears to arise from a V-shaped region, with a cavity nearly coincident with the center of the explosive outflows observed on larger scales. The position angles (P.A.s) of the observed polarization vary significantly by a total of about 90 degree but smoothly, i.e., curl-like, across the dust ridges. Such a polarization pattern can be explained with dust grains being magnetically aligned instead of mechanically with outflows, since the latter mechanism would cause the P.A.s to be parallel to the direction of the outflow, i.e., radial-like. The magnetic field projected in the plane of sky is therefore derived by rotating the P.A.s of the polarization by 90 degree. We find an azimuthally symmetric structure in the overall magnetic field morphology, with the field directions pointing toward 2.5" west to the center of the explosive outflows. We also find a preferred symmetry plane at a P.A. of 36 degree, which is perpendicular to the mean magnetic field direction (120 degree) of the 0.5 pc dust ridge. Two possible interpretations of the origin of the observed magnetic field structure are discussed.Comment: 27 pages, 7 figures; ApJ in pres

Polarizing Grids, Their Assemblies and Beams of Radiation

This article gives an analysis of the behavior of polarizing grids and reflecting polarizers by solving Maxwell's equations, for arbitrary angles of incidence and grid rotation, for cases where the excitation is provided by an incident plane wave or a beam of radiation. The scattering and impedance matrix representations are derived and used to solve more complicated configurations of grid assemblies. The results are also compared with data obtained in the calibration of reflecting polarizers at the Owens Valley Radio Observatory (OVRO). From this analysis, we propose a method for choosing the optimum grid parameters (wire radius and spacing). We also provide a study of the effects of two types of errors (in wire separation and radius size) that can be introduced in the fabrication of a grid.Comment: 35 pages, 6 figure

Coexisting conical bipolar and equatorial outflows from a high-mass protostar

The BN/KL region in the Orion molecular cloud is an archetype in the study of the formation of stars much more massive than the Sun. This region contains luminous young stars and protostars, but it is difficult to study because of overlying dust and gas. Our basic expectations are shaped to some extent by the present theoretical picture of star formation, the cornerstone of which is that protostars acrete gas from rotating equatorial disks, and shed angular momentum by ejecting gas in bipolar outflows. The main source of the outflow in the BN/KL region may be an object known as radio source I, which is commonly believed to be surrounded by a rotating disk of molecular material. Here we report high-resolution observations of silicon monoxide (SiO) and water maser emission from the gas surrounding source I; we show that within 60 AU (about the size of the Solar System), the region is dominated by a conical bipolar outflow, rather than the expected disk. A slower outflow, close to the equatorial plane of the protostellar system, extends to radii of 1,000 AU.Comment: 10 pages, 2 figures. Accepted by Nature. To appear December 199

Magnetic Field Strength Maps for Molecular Clouds: A New Method Based on a Polarization - Intensity Gradient Relation

Dust polarization orientations in molecular clouds often tend to be close to tangential to the Stokes $I$ dust continuum emission contours. The magnetic field and the emission gradient orientations, therefore, show some correlation. A method is proposed, which -- in the framework of ideal magneto-hydrodynamics (MHD) -- connects the measured angle between magnetic field and emission gradient orientations to the total field strength. The approach is based on the assumption that a change in emission intensity (gradient) is a measure for the resulting direction of motion in the MHD force equation. In particular, this new method leads to maps of position-dependent magnetic field strength estimates. When evaluating the field curvature and the gravity direction locally on a map, the method can be generalized to arbitrary cloud shapes. The technique is applied to high-resolution (\sim0\farcs7) Submillimeter Array polarization data of the collapsing core W51 e2. A tentative $\sim 7.7$~mG field strength is found when averaging over the entire core. The analysis further reveals some structures and an azimuthally averaged radial profile $\sim r^{-1/2}$ for the field strength. Maximum values close to the center are around $19$~mG. The currently available observations lack higher resolution data to probe the innermost part of the core where the largest field strength is expected from the method. Application regime and limitations of the method are discussed. As a further important outcome of this technique, the local significance of the magnetic field force compared to the other forces can be quantified in a model-independent way, from measured angles only. Finally, the method can potentially also be expanded and applied to other objects (besides molecular clouds) with measurements that reveal the field morphology, as e.g. Faraday rotation measurements in galaxies.Comment: 42 pages, 14 figures, 1 table; accepted for publication in Ap

A research framework for projecting ecosystem change in highly diverse tropical mountain ecosystems

Tropical mountain ecosystems are threatened by climate and land-use changes. Their diversity and complexity make projections how they respond to environmental changes challenging. A suitable way are trait-based approaches, by distinguishing between response traits that determine the resistance of species to environmental changes and effect traits that are relevant for species\u27 interactions, biotic processes, and ecosystem functions. The combination of those approaches with land surface models (LSM) linking the functional community composition to ecosystem functions provides new ways to project the response of ecosystems to environmental changes. With the interdisciplinary project RESPECT, we propose a research framework that uses a trait-based response-effect-framework (REF) to quantify relationships between abiotic conditions, the diversity of functional traits in communities, and associated biotic processes, informing a biodiversity-LSM. We apply the framework to a megadiverse tropical mountain forest. We use a plot design along an elevation and a land-use gradient to collect data on abiotic drivers, functional traits, and biotic processes. We integrate these data to build the biodiversity-LSM and illustrate how to test the model. REF results show that aboveground biomass production is not directly related to changing climatic conditions, but indirectly through associated changes in functional traits. Herbivory is directly related to changing abiotic conditions. The biodiversity-LSM informed by local functional trait and soil data improved the simulation of biomass production substantially. We conclude that local data, also derived from previous projects (platform Ecuador), are key elements of the research framework. We specify essential datasets to apply this framework to other mountain ecosystems

Interfacial Oxide Formation Limits the Photovoltage of Alpha SnWO4 NiOx Photoanodes Prepared by Pulsed Laser Deposition

alpha SnWO4 is a promising metal oxide photoanode material for direct photoelectrochemical water splitting. With a band gap of 1.9 eV, it ideally matches the requirements as a top absorber in a tandem device theoretically capable of achieving solar to hydrogen STH efficiencies above 20 . It suffers from photoelectrochemical instability, but NiOx protection layers have been shown to help overcome this limitation. At the same time, however, such protection layers seem to reduce the photovoltage that can be generated at the solid electrolyte junction. In this study, an extensive analysis of the alpha SnWO4 NiOx interface is performed by synchrotron based hard X ray photoelectron spectroscopy HAXPES . NiOx deposition introduces a favorable upwards band bending, but also oxidizes Sn2 to Sn4 at the interface. By combining the HAXPES data with open circuit potential OCP analysis, density functional theory DFT calculations, and Monte Carlo based photoemission spectra simulation using SESSA, the presence of a thin oxide layer at the alpha SnWO4 NiOx interface is suggested and shown to be responsible for the limited photovoltage. Based on this new found understanding, suitable mitigation strategies can be proposed. Overall, this study demonstrates the complex nature of solid state interfaces in multi layer photoelectrodes, which needs to be unraveled to design efficient heterostructured photoelectrodes for solar water splittin