Complete high-quality genome sequence of Clostridium limosum (Hathewaya limosa) isolate 14S0207, recovered from a cow with suspected blackleg in Germany

Clostridium limosum can be found in soil and the intestinal tract of animals. In 2014, C. limosum was isolated from a suspected blackleg outbreak in cattle in Schleswig-Holstein, Germany. We present a complete genome sequence of a C. limosum strain represented by a circular chromosome and three plasmids

A Resonant soft x-ray powder diffraction study to determine the orbital ordering in A-site ordered SmBaMn2O6

Soft X-ray resonant powder diffraction has been performed at the Mn L2,3 edges of A-site ordered SmBaMn2O6. The energy and polarization dependence of the (1/2 1/2 0) reflection provide direct evidence for a (x2-z2)/(y2-z2) type orbital ordering in contrast to the single layer manganite. The temperature dependence of the reflection indicates an orbital reorientation transition at 210 K, below which the charge and orbital ordered MnO2 sheets show AAAA type of stacking. The concurring reduction of the ferromagnetic super exchange correlations leads to further charge localization

Doping and temperature dependence of Mn 3d states in A-site ordered manganites

We present a systematic study of the electronic structure in A-site ordered manganites as function of doping and temperature. The energy dependencies observed with soft x-ray resonant diffraction (SXRD) at the Mn L_{2,3} edges are compared with structural investigations using neutron powder diffraction as well as with cluster calculations. The crystal structures obtained with neutron powder diffraction reflect the various orbital and charge ordered phases and show an increase of the Mn-O-Mn bond angle as function of doping and temperature. Cluster calculations show that the observed spectral changes in SXRD as a function of doping are more pronounced than expected from an increase in bandwitdh due to the increase in Mn-O-Mn bond angle, and are best described by holes that are distributed at the neighbouring oxygen ions. These holes are not directly added to the Mn 3d shell, but centered at the Mn site. In contrast, the spectral changes in SXRD as function of temperature are best described by an increase of magnetic correlations. This demonstrates the strong correlations between orbitals and magnetic moments of the 3d states

Circularly polarized resonant soft x-ray diffraction study of helical magnetism in hexaferrite

Magnetic spiral structures can exhibit ferroelectric moments as recently demonstrated in various multiferroic materials. In such cases the helicity of the magnetic spiral is directly correlated with the direction of the ferroelectric moment and measurement of the helicity of magnetic structures is of current interest. Soft x-ray resonant diffraction is particularly advantageous because it combines element selectivity with a large magnetic cross-section. We calculate the polarization dependence of the resonant magnetic x-ray cross-section (electric dipole transition) for the basal plane magnetic spiral in hexaferrite Ba0.8Sr1.2Zn2Fe12O22 and deduce its domain population using circular polarized incident radiation. We demonstrate there is a direct correlation between the diffracted radiation and the helicity of the magnetic spiral.Comment: 4 pages, 4 figure

Magnetic and electronic Co states in layered cobaltate GdBaCo2O5.5-x

We have performed non-resonant x-ray diffraction, resonant soft and hard x-ray magnetic diffraction, soft x-ray absorption and x-ray magnetic circular dichroism measurements to clarify the electronic and magnetic states of the Co3+ ions in GdBaCo2O5.5. Our data are consistent with a 3+ Py Co HS state at the pyramidal sites and a 3+ Oc Co LS state at the octahedral sites. The structural distortion, with a doubling of the a axis (2ap x 2ap x 2ap cell), shows alternating elongations and contractions of the pyramids and indicates that the metal-insulator transition is associated with orbital order in the t2g orbitals of the 3+ Py Co HS state. This distortion corresponds to an alternating ordering of xz and yz orbitals along the a and c axes for the 3+ Py Co . The orbital ordering and pyramidal distortion lead to deformation of the octahedra, but the 3+ Oc Co LS state does not allow an orbital order to occur for the 3+ Oc Co ions. The soft x-ray magnetic diffraction results indicate that the magnetic moments are aligned in the ab plane but are not parallel to the crystallographic a or b axes. The orbital order and the doubling of the magnetic unit cell along the c axis support a non-collinear magnetic structure. The x-ray magnetic circular dichroism data indicate that there is a large orbital magnetic contribution to the total ordered Co moment

Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations

Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations