Institute for Chemistry and Biology of the Marine Environment ICBM

Oldenburg, Germany

Institute for Chemistry and Biology of the Marine Environment ICBM

Oldenburg, Germany

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Kanukollu S.,Institute for Chemistry and Biology of the Marine Environment ICBM | Voget S.,University of Gottingen | Pohlner M.,Institute for Chemistry and Biology of the Marine Environment ICBM | Vandieken V.,Institute for Chemistry and Biology of the Marine Environment ICBM | And 6 more authors.
Standards in Genomic Sciences | Year: 2016

Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0-1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum (fla1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter-affiliated bacteria to the benthic environment. © 2016 Kanukollu et al.


Monien P.,Institute for Chemistry and Biology of the Marine Environment ICBM | Schnetger B.,Institute for Chemistry and Biology of the Marine Environment ICBM | Brumsack H.-J.,Institute for Chemistry and Biology of the Marine Environment ICBM | Hass H.C.,Alfred Wegener Institute for Polar and Marine Research | Kuhn G.,Alfred Wegener Institute for Polar and Marine Research
Antarctic Science | Year: 2011

Abstract During RV Polarstern cruise ANT-XXIII/4 in 2006, a gravity core (PS 69/335-2) and a giant box core (PS 69/335-1) were retrieved from Maxwell Bay off King George Island (KGI). Comprehensive geochemical (bulk parameters, quantitative XRF, Inductively Coupled Plasma Mass Spectrometry) and radiometric dating analyses (14C, 210Pb) were performed on both cores. A comparison with geochemical data from local bedrock demonstrates a mostly detrital origin for the sediments, but also points to an overprint from changing bioproductivity in the overlying water column in addition to early diagenetic processes. Furthermore, ten tephra layers that were most probably derived from volcanic activity on Deception Island were identified. Variations in the vertical distribution of selected elements in Maxwell Bay sediments further indicate a shift in source rock provenance as a result of changing glacier extents during the past c. 1750 years that may be linked to the Little Ice Age and the Medieval Warm Period. Whereas no evidence for a significant increase in chemical weathering rates was found, 210Pb data revealed that mass accumulation rates in Maxwell Bay have almost tripled since the 1940s (0.66 g cm-2 yr-1 in ad 2006), which is probably linked to rapid glacier retreat in this region due to recent warming. © Antarctic Science Ltd 2011.


Dogs M.,Institute for Chemistry and Biology of the Marine Environment ICBM | Voget S.,University of Gottingen | Teshima H.,Los Alamos National Laboratory | Petersen J.,Leibniz Institute DSMZ | And 19 more authors.
Standards in Genomic Sciences | Year: 2013

Strain T5T is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5T was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of its close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5T comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5T possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5T an facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description. © retained by original authors.


Riedel T.,Helmholtz Center for Infection Research | Teshima H.,Los Alamos National Laboratory | Petersen J.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | Fiebig A.,Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures | And 21 more authors.
Standards in Genomic Sciences | Year: 2013

Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They are a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565T together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG). © retained by original authors.


PubMed | Institute for Chemistry and Biology of the Marine environment ICBM and Max Planck Institute for Marine Microbiology
Type: Journal Article | Journal: Environmental microbiology | Year: 2016

Although fluorescence in situ hybridization (FISH) with specific ribosomal RNA (rRNA)-targeted oligonucleotides is a standard method to detect and identify microorganisms, the specific detection of genes in bacteria and archaea, for example by using geneFISH, requires complicated and lengthy (> 30 h) procedures. Here we report a much improved protocol, direct-geneFISH, which allows specific gene and rRNA detection within less than 6 h. For direct-geneFISH, catalyzed amplification reporter deposition (CARD) steps are removed and fluorochrome-labelled polynucleotide gene probes and rRNA-targeted oligonucleotide probes are hybridized simultaneously. The protocol allows quantification of gene copy numbers per cell and the signal of the directly labelled probes enables a subcellular localization of the rRNA and target gene. The detection efficiencies of direct-geneFISH were first evaluated on Escherichia coli carrying the target gene on a copy-control vector. We could show that gene copy numbers correlated to the geneFISH signal within the cells. The new protocol was then applied for the detection of the sulfate thiolhydrolase (soxB) genes in cells of the gammaproteobacterial clade SUP05 in Lake Rogoznica, Croatia. Cell and gene detection efficiencies by direct-geneFISH were statistically identical to those obtained with the original geneFISH, demonstrating the suitability of the simpler and faster protocol for environmental samples.


PubMed | Lawrence Berkeley National Laboratory, Institute for Chemistry and Biology of the Marine Environment ICBM, Los Alamos National Laboratory, U.S. Department of Energy and 2 more.
Type: Journal Article | Journal: Standards in genomic sciences | Year: 2014

Leisingera aquimarina Vandecandelaere et al. 2008 is a member of the genomically well characterized Roseobacter clade within the family Rhodobacteraceae. Representatives of the marine Roseobacter clade are metabolically versatile and involved in carbon fixation and biogeochemical processes. They form a physiologically heterogeneous group, found predominantly in coastal or polar waters, especially in symbiosis with algae, in microbial mats, in sediments or associated with invertebrates. Here we describe the features of L. aquimarina DSM 24565(T) together with the permanent-draft genome sequence and annotation. The 5,344,253 bp long genome consists of one chromosome and an unusually high number of seven extrachromosomal elements and contains 5,129 protein-coding and 89 RNA genes. It was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2010 and of the activities of the Transregional Collaborative Research Centre 51 funded by the German Research Foundation (DFG).


PubMed | Lawrence Berkeley National Laboratory, Institute for Chemistry and Biology of the Marine Environment ICBM, Los Alamos National Laboratory, U.S. Department of Energy and 3 more.
Type: Journal Article | Journal: Standards in genomic sciences | Year: 2014

Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.

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