Überblick über Spurenelemente in Böden der Aue der Mittleren Elbe

Floodplain soils across the Central Elbe River, Germany, have unique features. These soils vary considerably in their properties due to rapid fluvial processes and in metal contents due to frequent industrial discharge into the river. Although there have been works studying such soils, there has never been a comprehensive study that would monitor a large number of entire soil profiles along the Elbe River. Our aim was to describe the main properties of 94 profiles representing different soils along the Elbe River, their content from 15 potentially toxic elements (PTEs) in various depths, and assess various soil contamination and health risk indices. We measured soil properties auch as pH, organic carbon (OC), particle size distribution, as well as total concentrations of aluminium (Al), arsenic (As), barium (Ba), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), lead (Pb), nickel (Ni), rubidium (Rb), strontium (Sr), tin (Sn), vanadium (V), zirconium (Zr), and zinc (Zn) in all soil profiles. We presented the data for all soil horizons and in top- (0-30 cm depth) and subsoil (>30 cm depth). We found that pH, OC, and clay differed significantly between top- and subsoil horizons reflecting different water regimes and other factors. On the other hand, Al, Fe, and Mn were not affected significantly by depth. Among the studied PTEs, Sn was found to be generating the highest values in Contamination Factor, Geoaccumulation Index, and Enrichment Factor; it was followed by As, Zn, and Pb. Other PTEs such as Ba, Rb, Sr, V, and Zr, and exhibited much lower soil contamination index values. The Pollution Load Index was very high. Health risk assessment indicated rather unexpectedly that Zr was the primary contributor to total risk. We conclude that in multi-element contamination cases, even PTEs with low soil concentrations (such as Zr here) may have predominant role in the risk related to soil contamination

Phylogenetic Evidence for Lateral Gene Transfer in the Intestine of Marine Iguanas

Background: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood. Methodology/Principal Findings: We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52 % of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT. Conclusion: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members o

Lithostratigraphy of the Palaeoproterozoic Hekpoort formation (Pretoria Group, Transvaal Supergroup), South Africa

The Palaeoproterozoic Hekpoort Formation of the Pretoria Group is a lava-dominated unit that has a basin-wide extent throughout the Transvaal sub-basin of South Africa. Additional correlative units may be present in the Kanye sub-basin of Botswana. The key characteristic of the formation is its general geochemical uniformity. Volcaniclastic and other sedimentary rocks are relatively rare throughout the succession but may be dominant in some locations. Hekpoort Formation outcrops are sporadic throughout the basin and mostly occur in the form of gentle hills and valleys, mainly encircling Archaean domes and the Palaeoproterozoic Bushveld Complex (BC). The unit is exposed in the western Pretoria Group basin, sitting unconformably either on the Timeball Hill Formation or Boshoek Formation, which is lenticular there, and on top of the Boshoek Formation in the east of the basin. The unit is unconformably overlain by the Dwaalheuwel Formation. The type-locality for the Hekpoort Formation is the Hekpoort farm (504 IQ Hekpoort), ca. 60 km to the west-southwest of Pretoria. However, no stratotype has ever been proposed. A lectostratotype, i.e., the Mooikloof area in Pretoria East, that can be enhanced by two reference stratotypes are proposed herein. The Hekpoort Formation was deposited in a cratonic subaerial setting, forming a large igneous province (LIP) in which short-termed localised ponds and small braided river systems existed. It therefore forms one of the major Palaeoproterozoic magmatic events on the Kaapvaal Craton.http://sajg.geoscienceworld.orgam2021Geolog

Pore and Grain Geometry Analysis of Sandstone Reservoir Rocks from a Well of a Northern German Basin

Pore space and grain geometry are important physical properties distinguished in reservoir rocks, particularly in sandstones, due to their influence on oil and gas reservoir quality. Therefore, a detailed study of pore space morphology and grain surface roughness in sandstone reservoir rocks is a key element in petroleum geology. It is eminent in understanding of the adhesion of hydrocarbons in rocks and coupled fluid flows in pores and along grain surfaces. In this work, sandstone samples taken from a well of a Northern German basin deposit have been analysed by thin section petrography, Confocal Raman Microscopy and Confocal Laser Scanning Microscopy (CLSM). The roughness of grain surfaces is analysed and the pore geometries of sandstone rocks are verified. Roughness and pore geometry have a significant impact on the wetting behaviour and adhesion properties of hydrocarbon fluids, water or carbon dioxide (CO2) to the pore walls. The results show the relationship between the composition of sandstones and their pore geometry and the grain surface roughness. The geometry of the pore morphology and the grain surface shows a range from very rough to flat smooth crystal facets, from few hundreds to sub-micron, depending on the scale of observation. The 50x and 100x magnifications were applied in this study. The findings offer a detailed insight into the relationship of pore space morphology and the grain surface roughness. The results add important parameters to the calculation models for hydrocarbon exploitation and to enhancement of the amount of oil recovery

Extensive bacteriocin gene shuffling in the Streptococcus bovis/Streptococcus equinus complex reveals gallocin D with activity against vancomycin resistant enterococci

peer-reviewedStreptococcus gallolyticus LL009 produces gallocin D, a narrow spectrum two component bacteriocin with potent activity against vancomycin-resistant enterococci. Gallocin D is distinct from gallocin A, a separate two component bacteriocin produced by S. gallolyticus. Although the gene clusters encoding gallocin A and gallocin D have a high degree of gene synteny, the structural genes are highly variable and appear to have undergone gene shufing with other streptococcal species. Gallocin D was analysed in laboratory-based experiments. The mature peptides are 3,343± 1 Da and 3,019 ± 1 Da and could be readily synthesized and display activity against a vancomycin resistant Enterococcus strain EC300 with a MIC value of 1.56 µM. Importantly, these bacteriocins could contribute to the ability of S. gallolyticus to colonize the colon where they have been associated with colorectal cancer.Science Foundation Irelan

The Glycobiome of the Rumen Bacterium Butyrivibrio proteoclasticus B316T Highlights Adaptation to a Polysaccharide-Rich Environment

Determining the role of rumen microbes and their enzymes in plant polysaccharide breakdown is fundamental to understanding digestion and maximising productivity in ruminant animals. Butyrivibrio proteoclasticus B316T is a Gram-positive, butyrate-forming rumen bacterium with a key role in plant polysaccharide degradation. The 4.4Mb genome consists of 4 replicons; a chromosome, a chromid and two megaplasmids. The chromid is the smallest reported for all bacteria, and the first identified from the phylum Firmicutes. B316 devotes a large proportion of its genome to the breakdown and reassembly of complex polysaccharides and has a highly developed glycobiome when compared to other sequenced bacteria. The secretion of a range of polysaccharide-degrading enzymes which initiate the breakdown of pectin, starch and xylan, a subtilisin family protease active against plant proteins, and diverse intracellular enzymes to break down oligosaccharides constitute the degradative capability of this organism. A prominent feature of the genome is the presence of multiple gene clusters predicted to be involved in polysaccharide biosynthesis. Metabolic reconstruction reveals the absence of an identifiable gene for enolase, a conserved enzyme of the glycolytic pathway. To our knowledge this is the first report of an organism lacking an enolase. Our analysis of the B316 genome shows how one organism can contribute to the multi-organism complex that rapidly breaks down plant material in the rumen. It can be concluded that B316, and similar organisms with broad polysaccharide-degrading capability, are well suited to being early colonizers and degraders of plant polysaccharides in the rumen environment

The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions

BACKGROUND: Methane (CH(4)) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO(2)). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed. METHODOLOGY/PRINCIPAL FINDINGS: The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H(2)) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species. CONCLUSIONS/SIGNIFICANCE: The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases

Exploring rumen microbe-derived fibre-degrading activities for improving feed digestibility

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evolved with their ruminant hosts over millions of years to perform this task, their enzymes are hypothesised to be optimally suited for activity at the temperature, pH range, and anaerobic environment of the rumen. However, fibre-rich diets are not fully digested, which represents a loss in potential animal productivity. Thus, there is opportunity to improve fibre utilisation through treating feeds with rumen microbe-derived fibrolytic enzymes and associated activities that enhance fibre degradation. This research aims to gain a better understanding of the key rumen microbes involved in fibre degradation and the mechanisms they employ to degrade fibre, by applying cultivation-based and culture-independent genomics approaches to rumen microbial communities of New Zealand dairy cattle. Using this knowledge, we aim to identify new opportunities for improving fibre degradation to enhance dairy productivity. Rumen content samples were taken over the course of a year from a Waikato dairy production herd. Over 1,000 rumen bacterial cultures were obtained from the plant-adherent fraction of the rumen contents. Among these cultures, two, 59 and 103 potentially new families, genera and species of rumen bacteria were identified, respectively. Many of the novel strains are being genome sequenced within the Hungate 1000 rumen microbial reference genome programme, which is providing deeper insights into the range of mechanisms used by the individual strains for fibre degradation. This information has been used to guide the selection of rumen bacterial strains with considerable potential as fibrolytic enzyme producers in vitro, with the intent of developing the strains so that their enzymes may be used as feed pre-treatments for use on farm. Culture-independent metagenomic approaches were also used to explore the activities involved in fibre degradation from the rumen microbial communities. Functional screening has revealed a range of novel enzymes and a novel fibre disrupting activity. Enrichment for the cell-secreted proteins from the community revealed evidence of a diverse range of cellulosomes, which are cell-surface associated multi-enzyme complexes that efficiently degrade plant cell wall polysaccharides. Biochemical and structural characterisation of these proteins has been conducted. In conclusion, cultivation and culture-independent genomic approaches have been applied to New Zealand bovine rumen microbial communities, and have provided considerable new insights into ruminal fibre degradation processes. Novel activities and bacterial species that display desirable activities on fibrous substrates in vitro are now being explored for their potential to improve ruminal fibre degradation, to allow the development of new technologies that will enhance dairy productivity

Codon choice in genes depends on flanking sequence information—implications for theoretical reverse translation

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75% (c-NCM). The algorithms, their applications and implications are discussed herein