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High-resolution time-lapse ground-penetrating radar (GPR) observations of advancing and retreating water tables can yield a wealth of information about near-surface water content dynamics. In this study, we present and analyze a series of imbibition, drainage and infiltration experiments that have been carried out at our artificial ASSESS test site and observed with surface-based GPR. The test site features a complicated but known subsurface architecture constructed with three different kinds of sand. It allows the study of soil water dynamics with GPR under a wide range of different conditions. Here, we assess in particular (i) the feasibility of monitoring the dynamic shape of the capillary fringe reflection and (ii) the relative precision of monitoring soil water dynamics averaged over the whole vertical extent by evaluating the bottom reflection. The phenomenology of the GPR response of a dynamically changing capillary fringe is developed from a soil physical point of view. We then explain experimentally observed phenomena based on numerical simulations of both the water content dynamics and the expected GPR response.

A novel Gram-positive, aerobic, actinobacterial strain, CF5/4 T , was isolated in 2007 during an environmental screening of arid desert soil in Ouré Cassoni, Chad. The isolate grew best in a temperature range of 28–40 °C and at pH 6.0–8.5, with 0–1 % (w/v) NaCl, forming brown-coloured and nearly circular colonies on GYM agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus . The DNA G + C content of the novel strain was 75.9 mol %. The peptidoglycan contained meso -diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, diphosphatidylglycerol and a small amount of phosphatidylglycerol; MK-9(H 4 ) was identified as the dominant menaquinone and galactose as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids: iso -C 15:0 and iso -C 16:0 . The 16S rRNA gene showed 96.2–98.3 % sequence identity with the three members of the genus Geodermatophilus: G. obscurus (96.2 %), G. ruber (96.5 %), and G. nigrescens (98.3 %). Based on the chemotaxonomic results, 16S rRNA gene sequence analysis and DNA–DNA hybridization with the type strain of G. nigrescens, the isolate is proposed to represent a novel species, Geodermatophilus arenarius (type strain CF5/4 T  = DSM 45418 T  = MTCC 11413 T  = CCUG 62763 T ).

The precise determination of the SAR (synthetic aperture radar) antenna pointing is an essential task initially performed during the commissioning phase of a spaceborne SAR system and is permanently monitored during the whole mission life-time. Besides a correct illumination of the scene during data acquisition, antenna pointing is required for proper compensation of the radiation pattern for radiometric correction during SAR data processing. The Amazon rainforest is a well-established target area for antenna pointing estimation in elevation as proven by many past and current SAR missions. Several new SAR systems are now proposed which are using long wavelengths, i.e., L- and P-bands, which will be implemented using reflector-based antenna systems. These reflectors have, in contrast to planar phased array antennas, no completely rigid connection to the satellite body and, hence, a more volatile antenna pointing. Due to the huge dimensions of such reflector antennas required for the envisaged long wavelengths and the finite stiffness of the boom, the antenna pointing may change significantly along the orbit. Such variation cannot be tracked using the common Amazon rainforest approach only, as this measurement opportunity exists only at two positions along the orbit (ascending and descending). Here, the performance of an alternative technique is presented which mitigates the influence of the underlying SAR scene by employing two coherent SAR datasets acquired simultaneously with different antenna patterns. This allows the use of amplitude and phase information for pointing estimation. No assumption upon the homogeneity of the underlying scene is required and, hence, pointing estimation becomes feasible at nearly any point along the orbit. This paper outlines the technique, describes simulation results and presents outcomes from first experimental acquisitions performed with the TerraSAR-X satellite.

A novel Gram-positive, aerobic, actinobacterial strain, CF5/5, was isolated from soil in the Sahara desert, Chad. It grew best at 20–35 °C and at pH 6.0–8.0 and with 0–4 % (w/v) NaCl, forming black-colored colonies. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus . The DNA G + C content was 75.9 mol%. The peptidoglycan contained meso -diaminopimelic acid; galactose and xylose were detected as diagnostic sugars. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol; MK-9(H 4 ) was the dominant menaquinone. The major cellular fatty acids were: iso -C 16:0 and iso -C 15:0 . The 16S rRNA gene showed 95.6–98.3 % sequence similarity with the other named members of the genus Geodermatophilus . Based on the polyphasic taxonomy data, the isolate is proposed to represent a novel species, Geodermatophilus saharensis with the type strain CF5/5 T  = DSM 45423 = CCUG 62813 = MTCC 11416.

We show the potential of on-ground Ground-Penetrating Radar (GPR) to identify the parameterisation of the soil water retention curve, i.e. its functional form, with a semi-quantitative analysis based on numerical simulations of the radar signal. An imbibition and drainage experiment has been conducted at the ASSESS-GPR site to establish a fluctuating water table, while an on-ground GPR antenna recorded traces over time at a fixed location. These measurements allow to identify and track the capillary fringe in the soil. The typical dynamics of soil water content with a transient water table can be deduced from the recorded radargrams. The characteristic reflections from the capillary fringes in model soils that are described by commonly used hydraulic parameterisations are investigated by numerical simulations. The parameterisations used are (i) full van Genuchten, (ii) simplified van Genuchten with m = 1 − 1/n and (iii) Brooks–Corey. All three yield characteristically different reflections, which allows the identification of an appropriate parameterisation by comparing to the measured signals. We show that for the sand used here, these signals are not consistent with the commonly used simplified van Genuchten parameterisation with m = 1 − 1/n.

Anaerobranca gottschalkii strain LBS3 T is an extremophile living at high temperature (up to 65 degrees C) and in alkaline environments (up to pH 10.5). An assembly of 696 DNA contigs representing about 96% of the 2.26-Mbp genome of A. gottschalkii has been generated with a low-sequence-coverage shotgun-sequencing strategy. The chosen sequencing strategy provided rapid and economical access to genes encoding key enzymes of the mono- and polysaccharide metabolism, without dilution of spare resources for extensive sequencing of genes lacking potential economical value. Five of these amylolytic enzymes of considerable commercial interest for biotechnological applications have been expressed and characterized in more detail after identification of their genes in the partial genome sequence: type I pullulanase, cyclodextrin glycosyltransferase (CGTase), two alpha-amylases (AmyA and AmyB), and an alpha-1,4-glucan-branching enzyme.

Genes for DNA-dependent RNA polymerase components B, A, and C from the archaebacterium Sulfolobus acidocaldarius and for components B′ ′, B′, A, and C from the archaebacterium Halobacterium halobium were cloned and sequenced. They are organized in gene clusters in the order above, which corresponds to the order of the homologous rpoB and rpoC genes in the corresponding operon of the Escherichia coli genome. Derived amino acid sequences of archaebacterial components A and C were aligned with each other and with the sequences of corresponding (largest) subunits from the archaebacterium Methanobacterium thermoautotrophicum, with sequences of various eukaryotic nuclear RNA polymerases I, II, and III, and with the sequence of the β′component from E. coli polymerase. The archaebacterial genes for component A are homologous to about the first two-thirds of genes for the eukaryotic component A and the eubacterial component β′, and the archaebacterial genes for component C are homologous to the last third of the genes for the eukaryotic component A and the eubacterial component β′. Unrooted phylogenetic dendrograms derived from both distance matrix and parsimony analyses show the archaebacteria are a coherent group closely related to the eukaryotic nuclear RNA polymerase II and/or III lineages. The eukaryotic polymerase I lineage appears to arise separately from a bifurcation with the eubacterial β′component lineage.

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

Although its Holocene glacier history is still subject to debate, the ongoing iconic decline of Kilimanjaro's largest remaining ice body, the Northern Ice Field (NIF), has been documented extensively based on surface and photogrammetric measurements. The study presented here adds, for the first time, ground-penetrating radar (GPR) data at centre frequencies of 100 and 200 MHz to investigate bed topography, ice thickness and internal stratigraphy at NIF. The direct comparison of the GPR signal to the visible glacier stratigraphy at NIF's vertical walls is used to validate ice thickness and reveals that the major internal reflections seen by GPR can be associated with dust layers. Internal reflections can be traced consistently within our 200 MHz profiles, indicating an uninterrupted, spatially coherent internal layering within NIF's central flat area. We show that, at least for the upper 30 m, it is possible to follow isochrone layers between two former NIF ice core drilling sites and a sampling site on NIF's vertical wall. As a result, these isochrone layers provide constraints for future attempts at linking age–depth information obtained from multiple locations at NIF. The GPR profiles reveal an ice thickness ranging between (6.1 ± 0.5) and (53.5 ± 1.0) m. Combining these data with a very high resolution digital elevation model we spatially extrapolate ice thickness and give an estimate of the total ice volume remaining at NIF's southern portion as (12.0 ± 0.3) × 106 m3.

Archaeoglobus fulgidus is the first sulphur-metabolizing organism to have its genome sequence determined. Its genome of 2,178,400 base pairs contains 2,436 open reading frames (ORFs). The information processing systems and the biosynthetic pathways for essential components (nucleotides, amino acids and cofactors) have extensive correlation with their counterparts in the archaeon Methanococcus jannaschii . The genomes of these two Archaea indicate dramatic differences in the way these organisms sense their environment, perform regulatory and transport functions, and gain energy. In contrast to M. jannaschii , A. fulgidus has fewer restriction–modification systems, and none of its genes appears to contain inteins. A quarter (651 ORFs) of the A. fulgidus genome encodes functionally uncharacterized yet conserved proteins, two-thirds of which are shared with M. jannaschii (428 ORFs). Another quarter of the genome encodes new proteins indicating substantial archaeal gene diversity.