Meinhard Simon

Carl von Ossietzky Universität Oldenburg, Oldenburg, Lower Saxony, Germany

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Publications (70)259.93 Total impact

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    ABSTRACT: The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry.The ISME Journal advance online publication, 1 August 2014; doi:10.1038/ismej.2014.134.
    The ISME Journal 08/2014; · 8.95 Impact Factor
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    ABSTRACT: In order to examine the specific role of diatoms in cycling of the trace metals manganese (Mn), molybdenum (Mo), vanadium (V), and uranium (U) Thalassiosira rotula, Skeletonema marinoi, Chaetoceros decipiens, and Rhizosolenia setigera were grown in batch cultures axenically and inoculated with three different bacterial strains isolated from the North Sea. Algal and bacterial growth, concentrations of trace metals and dissolved organic carbon (DOC) were monitored over time and showed that Mn and V were removed from the dissolved phase whereas Mo and U were not. R. setigera and T. rotula exhibited lowest growth and lowest removal whereas S. marinoi grew best and removed highest fractions of Mn and V. The high potential of Mn removal by S. marinoi was also evident from its 7x higher Mn/P elemental ratio relative to T. rotula. The presence of bacteria modified the timing of the growth of S. marinoi but not directly trace metal removal whereas bacteria enhanced trace metal removal in the cultures of T. rotula and C. decipiens. Modeling of phytoplankton growth, concentrations of Mn and DOC fraction in axenic T. rotula cultures indicated that processes of binding and desorption of Mn to excreted organic components are important to explain the varying proportions of dissolved Mn and thus must be considered as an active component in Mn cycling. The results show distinct differences in the potential of the diatoms in removal of Mn and V and that bacteria can play an active role in this context. S. marinoi presumably is an important player in Mn and V dynamics in coastal marine systems.
    Journal of Sea Research 03/2014; 87:35-45. · 1.83 Impact Factor
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    ABSTRACT: Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
    Standards in Genomic Sciences 01/2014; · 3.17 Impact Factor
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    ABSTRACT: Seawater circulation in permeable coastal sediments is driven by tidal changes in hydraulic gradients. The resulting submarine groundwater discharge is a source of nutrients and dissolved organic matter (DOM) to the water column. Yet, little is known about the cycling of DOM within tidal sediments, because the molecular DOM characterization remains analytically challenging. One technique that can dissect the multitude of molecules in DOM is ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). To aim at a high resolution DOM analysis we study the seasonal turnover and marine and terrestrial sources of DOM in an intertidal creek bank of the southern North Sea down to 3 m depth and link the biogeochemical processes to FT-ICR-MS data and the analyses of inorganic porewater chemistry, δ13C of solid-phase extracted dissolved organic carbon (SPE-DOC), dissolved black carbon (DBC) and dissolved carbohydrates (DCHO). Increasing concentrations of dissolved Fe, Mn, P, total alkalinity, dissolved nitrogen, DOC and a concomitant decrease of sulfate along the seawater circulation path from the upper tidal flat to the tidal flat margin indicate continuous microbial activity. The relative increase of Si concentrations, unsaturated aliphatics, peptide molecular formulae and isotopically more 13C-enriched SPE-DOC towards the tidal flat margin suggests that remineralization processes mobilize DOM from buried algal (diatoms) and microbial biomass. Porewater in sediments <100 cm depth contains 13C-depleted SPE-DOC and highly unsaturated compounds which are probably derived from eroded peats, suggesting rapid removal of bioavailable marine DOM such as DCHO from the water column and selective enrichment of terrestrial DOM. DBC concentrations are highest in the discharging porewater close to the tidal creek suggesting that the intertidal flat is an important DBC source to the coastal ocean. Porewater DOM accumulating at the low water line is enriched in N and S. We hypothesize that this is partly due to DOM reacting with dissolved sulfide and ammonium which may increase the refractory character of the DOM, hence making it less bioavailable for in situ active microbes.
    Geochimica et Cosmochimica Acta 01/2014; 140:418–434. · 3.88 Impact Factor
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    ABSTRACT: 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.
    Standards in Genomic Sciences 12/2013; 9(2):334-50. · 3.17 Impact Factor
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    ABSTRACT: TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
    Standards in Genomic Sciences 10/2013; 9(1):142-59. · 3.17 Impact Factor
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    ABSTRACT: Despite their importance for ecosystem functioning, little is known about the composition of active marine bacterioplankton communities. Hence, this study was focused on assessing the diversity of these communities in the southern North Sea and examining the impact of a phytoplankton spring bloom on the ambient bacterioplankton community. Community composition in and outside the bloom was assessed in 14 samples by pyrosequencing-based analysis of 16S rRNA amplicons generated from environmental RNA. The dataset comprised 211,769 16S rRNA sequences. Proteobacteria were the predominant phylogenetic group with Alphaproteobacteria and Gammaproteobacteria as the most abundant classes. Actinobacteria and Bacteroidetes were identified in minor abundances. Active bacterial communities were dominated by few lineages such as the Roseobacter RCA cluster and the SAR92 clade. Community structures of three selected samples were also assessed by direct sequencing of cDNA generated from rRNA-depleted environmental RNA. Generated datasets comprised 988,202 sequences. Taxonomic assignment of the reads confirmed the predominance of Proteobacteria. The phytoplankton spring bloom affected the bacterioplankton community structures significantly. Bacterial richness was reduced in the bloom area and the abundance of certain bacterial groups was affected by bloom presence. The SAR92 clade and the Roseobacter RCA cluster were significantly more abundant and active in the bloom. Functions affected by the bloom include photosynthesis, protein metabolism, and DNA metabolism. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 10/2013; · 3.56 Impact Factor
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    ABSTRACT: In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564(T) was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
    Standards in Genomic Sciences 07/2013; 8(3):403-19. · 3.17 Impact Factor
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    ABSTRACT: Four heterotrophic bacterial strains belonging to the globally distributed marine RCA (Roseobacter Clade Affiliated) cluster (family Rhodobacteraceae, class Alphaproteobacteria) were obtained from coastal seawater samples. Strain RCA23T was isolated from a 10-7 dilution culture inoculated with seawater from the German Wadden Sea (southern North Sea), reflecting the high abundance of RCA bacteria in this habitat. Strains IMCC1909, IMCC1923 and IMCC1933 were isolated from diluted seawater (10-3) of the Yellow Sea, South Korea. Based on 16S rRNA gene sequence comparison, Octadecabacter antarcticus strain 307T is the closest described relative of the RCA strains, with 95.4 to 95.5 % sequence similarity. Cells of RCA23T, IMCC1909, IMCC1923 and IMCC1933 are small motile rods requiring sodium ions. Optimal growth of RCA23T occurs at 25 °C and within a very narrow pH range (7 to 8, optimum 7.5). The DNA G+C base composition of RCA23T is 53.67 %. The major respiratory lipoquinone is ubiquinone-10 (Q-10) and the dominant fatty acids (>1%) are 12:1 3OH, 16:1 ω7c, 16:0, 18:1 ω7c, 18:0 and 11 methyl 18:1 ω7c. The polar lipid pattern indicated presence of phosphatidylglycerol, two unidentified aminolipids and two unidentified phospholipids. On marine agar RCA23T forms non-pigmented, transparent to light beige, small (<1 mm), circular, convex colonies. Strain RCA23T harbors all genes for the production of bacteriochlorophyll a (BChl a). Genes encoding the light-harvesting reaction center of BChl a (pufM) were identified in all RCA strains. No visible pigmentation was observed for any of the strains under laboratory conditions, but spectrophotometric analysis revealed a weak production of BChl a by RCA23T. Morphological, physiological and genotypic features of strain RCA23T suggest that it represents a novel species of a novel genus within the Rhodobacteraceae, for which we propose the name Planktomarina temperata gen. nov., sp. nov., previously described as Candidatus Planktomarina temperata by Giebel et al. (2011). The type strain of the type species is RCA23T (= DSM 22400T = JCM 18269T).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 06/2013; · 2.11 Impact Factor
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    ABSTRACT: We investigated the occurrence of Planktotalea frisia strain SH6-1(T) , a member of the Roseobacter clade, in the North Sea and interactions with phytoplankton algae with a special emphasis on the carbohydrate metabolisms. This bacterium was present in May 2006 throughout the North Sea. P. frisia SH6-1 was further present in the German Bight between February and early July with distinct peaks during and after phytoplankton blooms. Highest abundances, as detected by quantitative PCR, were 0.5-0.9% of total bacterial abundance. Comparison by CARD-FISH with a set of highly specific probes confirmed the high values in one sample. Between mid-July and October, P. frisia SH6-1 was not detected throughout the North Sea. Experimental studies in which P. frisia SH6-1 was grown in the presence of axenic cultures of the algae Phaeocystis globosa, Leptocylindrus danicus and Thalassiosira rotula exhibited distinctly different responses with the best growth together with P. globosa and T. rotula and very low growth together with L. danicus. The algae greatly differed in the composition of their exuded carbohydrates and that P. frisia SH6-1 was rather selective in their consumption, suggesting that the distinct carbohydrate metabolisms is a key feature to explain its seasonal occurrence in the North Sea. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 05/2013; · 3.56 Impact Factor
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    ABSTRACT: The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.
    PLoS ONE 01/2013; 8(5):e63422. · 3.53 Impact Factor
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    ABSTRACT: Members of the marine Roseobacter clade can degrade dimethylsulfoniopropionate (DMSP) via competing pathways releasing either methanethiol (MeSH) or dimethyl sulfide (DMS). Deuterium-labeled [(2)H6]DMSP and the synthetic DMSP analogue dimethyltelluriopropionate (DMTeP) were used in feeding experiments with the Roseobacter clade members Phaeobacter gallaeciensis DSM 17395 and Ruegeria pomeroyi DSS-3, and their volatile metabolites were analyzed by closed-loop stripping and solid-phase microextraction coupled to GC-MS. Feeding experiments with [(2)H6]DMSP resulted in the incorporation of a deuterium label into MeSH and DMS. Knockout of relevant genes from the known DMSP demethylation pathway to MeSH showed in both species a residual production of [(2)H3]MeSH, suggesting that a second demethylation pathway is active. The role of DMSP degradation pathways for MeSH and DMS formation was further investigated by using the synthetic analogue DMTeP as a probe in feeding experiments with the wild-type strain and knockout mutants. Feeding of DMTeP to the R. pomeroyi knockout mutant resulted in a diminished, but not abolished production of demethylation pathway products. These results further corroborated the proposed second demethylation activity in R. pomeroyi. Isotopically labeled [(2)H3]methionine and (34)SO4 (2-), synthesized from elemental (34)S8, were tested to identify alternative sulfur sources besides DMSP for the MeSH production in P. gallaeciensis. Methionine proved to be a viable sulfur source for the MeSH volatiles, whereas incorporation of labeling from sulfate was not observed. Moreover, the utilization of selenite and selenate salts by marine alphaproteobacteria for the production of methylated selenium volatiles was explored and resulted in the production of numerous methaneselenol-derived volatiles via reduction and methylation. The pathway of selenate/selenite reduction, however, proved to be strictly separated from sulfate reduction.
    Beilstein Journal of Organic Chemistry 01/2013; 9:942-50. · 2.80 Impact Factor
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    ABSTRACT: We investigated the occurrence of Planktotalea frisia strain SH6‐1T, a member of the Roseobacter clade, in the North Sea, and interactions with phytoplankton algae with a special emphasis on the carbohydrate metabolisms. This bacterium was present in May 2006 throughout the North Sea. Planktotalea frisia SH6‐1 was further present in the German Bight between February and early July, with distinct peaks during and after phytoplankton blooms. The highest abundances, as detected by quantitative PCR, were 0.5–0.9% of total bacterial abundance. Comparison by catalyzed reporter deposition fluorescence in situ hybridization (CARD‐FISH) with a set of highly specific probes confirmed the high values in one sample. Between mid‐July and October, P. frisia SH6‐1 was not detected throughout the North Sea. Experimental studies in which P. frisia SH6‐1 was grown in the presence of axenic cultures of the algae Phaeocystis globosa, Leptocylindrus danicus and Thalassiosira rotula exhibited distinctly different responses, with the best growth together with P. globosa and T. rotula and very low growth together with L. danicus. The algae greatly differed in the composition of their exuded carbohydrates and in the fact that P. frisia SH6‐1 was rather selective in consumption of algae, suggesting that the distinct carbohydrate metabolisms are a key feature to explain the seasonal occurrence of this bacterium in the North Sea.
    FEMS Microbiology Ecology 01/2013; 86(2). · 3.56 Impact Factor
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    ABSTRACT: Organisms of the Roseobacter clade are an important component in marine ecosystems, partially due to their metabolic variety. Not much is known, however, about the physiological diversity of different roseobacters present within one habitat. By using serial dilution cultures with low-nutrient media seven roseobacter strains, co-occurring during a phytoplankton bloom in the southern North Sea, were obtained in this study. Physiological characterization exhibited distinct substrate spectra of the isolates. Although no isolate showed growth on algal osmolyte dimethylsulfoniopropionate (DMSP), feeding experiments revealed that all new strains converted [(2)H(6)]DMSP into a variety of volatile compounds. Six strains mainly decomposed DMSP via the demethylation pathway, but four strains were also capable of cleaving DMSP to DMS and acrylate. It is hypothesized that the great physiological diversity of the roseobacters reflects their ability to inhabit different ecological niches and enables the organisms to cope differently with changing substrate supplies during phytoplankton blooms. Denaturing gradient gel electrophoresis and sequencing of excised bands resulted in detection of five additional roseobacters. Three of these sequences showed affiliation with three of the four major clusters of the Roseobacter clade, consisting predominantly of uncultured organisms (i.e. the Roseobacter clade-affiliated (RCA)), the NAC11-7 and the CHAB-I-5 clusters.
    Systematic and Applied Microbiology 12/2012; · 3.29 Impact Factor
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    ABSTRACT: Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.The ISME Journal advance online publication, 21 June 2012; doi:10.1038/ismej.2012.62.
    The ISME Journal 06/2012; · 8.95 Impact Factor
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    ABSTRACT: A heterotrophic, Gram-negative, aerobic bacterium, designated strain SH4-1T, was obtained from a seawater sample collected from the southern North Sea during a phytoplankton bloom. The 16S rRNA gene sequence comparison revealed affiliation to the Roseobacter clade (class Alphaproteobacteria) with Sulfitobacter marinus as the closest characterized species, showing 97.2% sequence similarity. Calculation of phylogenetic trees based on 16S rRNA gene sequences indicated, however, that members of the genus Roseobacter (95 and 96% sequence similarity, respectively) fall between strain SH4-1T and the Sulfitobacter cluster including Oceanibulbus indolifex (≥95.4% identities). Cells of strain SH4-1T are irregular rods with at least one flagellum. Optimal growth occurred between 28 and 32°C and at a pH between 7.0 and 8.5. Cells require the vitamin nicotinic acid amide as well as sodium ions for growth. The DNA base composition is 55.1 mol%. The fatty acids (>1%) comprised 10:0 3-OH, 12:1, 14:1 3-OH, 16:0, 18:0, 18:2, 18:1ω7c, and 11-methyl 18:1ω7c. The polar lipid pattern indicated the presence of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid (AL), one unidentified phospholipid (PL1), and one other unidentified lipid (L2). On the basis of phenotypic, chemotaxonomic and phylogenetic differences, strain SH4-1T represents a new genus and novel species within the Rhodobacteraceae, for which we propose the name Pelagimonas varians gen. nov., sp. nov. The type strain of the type species is SH4-1T (= DSM 23678T = LMG 26343T).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 05/2012; · 2.11 Impact Factor
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    05/2012: pages 49-54; , ISBN: ISSN 1866-3192
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    ABSTRACT: Production of the antibiotic tropodithietic acid (TDA) depends on the central phenylacetate catabolic pathway, specifically on the oxygenase PaaABCDE, which catalyzes epoxidation of phenylacetyl-coenzyme A (CoA). Our study was focused on genes of the upper part of this pathway leading to phenylacetyl-CoA as precursor for TDA. Phaeobacter gallaeciensis DSM 17395 encodes two genes with homology to phenylacetyl-CoA ligases (paaK1 and paaK2), which were shown to be essential for phenylacetate catabolism but not for TDA biosynthesis and phenylalanine degradation. Thus, in P. gallaeciensis another enzyme must produce phenylacetyl-CoA from phenylalanine. Using random transposon insertion mutagenesis of a paaK1-paaK2 double mutant we identified a gene (ior1) with similarity to iorA and iorB in archaea, encoding an indolepyruvate:ferredoxin oxidoreductase (IOR). The ior1 mutant was unable to grow on phenylalanine, and production of TDA was significantly reduced compared to the wild-type level (60%). Nuclear magnetic resonance (NMR) spectroscopic investigations using (13)C-labeled phenylalanine isotopomers demonstrated that phenylalanine is transformed into phenylacetyl-CoA by Ior1. Using quantitative real-time PCR, we could show that expression of ior1 depends on the adjacent regulator IorR. Growth on phenylalanine promotes production of TDA, induces expression of ior1 (27-fold) and paaK1 (61-fold), and regulates the production of TDA. Phylogenetic analysis showed that the aerobic type of IOR as found in many roseobacters is common within a number of different phylogenetic groups of aerobic bacteria such as Burkholderia, Cupriavidis, and Rhizobia, where it may also contribute to the degradation of phenylalanine.
    Applied and Environmental Microbiology 03/2012; 78(10):3539-51. · 3.95 Impact Factor
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    ABSTRACT: Humic substances (HS) constitute 50–80% of total dissolved organic matter (DOM) in freshwaters but in the open ocean<3%, indicating that large fractions of DOM and HS are removed in the estuarine and coastal zone. In order to assess the role of bacteria in this removal, we conducted experiments in flow-through cultures to examine the decomposition of peat bog-born humic acids (HA) by marine (salinity 30, Exp1) and estuarine (salinity 10, Exp2) bacterial communities. After~70days 40–>60% of the HA were decomposed. Highest fractions were decomposed in treatments in which the bacterial communities were fed by HA media of a foreign salinity, e.g., of 14 in Exp1 and of 28 in Exp2. Some of the HA material was not decomposed but broken down to smaller moieties entering the fulvic acid (FA) fraction. The analysis of the HA media and their residuals after bacterial decomposition by pyrolysis GC/MS showed that individual organic compounds were decomposed. In Exp1, 32 aliphatic and aromatic compounds, including lignin biomarkers, were detected in the HA medium of which mainly aliphatic compounds were decomposed. In Exp2, 49 compounds were detected of which~40–60% were not detected any more after bacterial decomposition in the HA fraction but still in the FA fraction. The results show that estuarine and marine bacterial communities can decompose large amounts of HA and that this process is important in reducing the amount of terrestrial HS and DOM entering the estuarine and coastal region. KeywordsHumic matter–DOC–Bacteria–Flow-through culture–Pyrolysis-GC/MS
    Biogeochemistry 01/2012; · 3.53 Impact Factor
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    ABSTRACT: Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.
    The ISME Journal 12/2011; 6(6):1260-72. · 8.95 Impact Factor

Publication Stats

1k Citations
259.93 Total Impact Points

Institutions

  • 2001–2014
    • Carl von Ossietzky Universität Oldenburg
      • Department of Chemistry and Biology of the Marine Environment (ICBM)
      Oldenburg, Lower Saxony, Germany
  • 2011–2012
    • Technische Universität Braunschweig
      • Institute of Organic Chemistry
      Brunswyck, Lower Saxony, Germany
  • 2009
    • Helmholtz Centre for Infection Research
      Brunswyck, Lower Saxony, Germany
  • 2007–2009
    • Forschungsinstitut für biologischen Landbau
      Frick, Aargau, Switzerland
  • 2006
    • Institut Hiscia
      Basel-Landschaft, Switzerland
  • 2005
    • National Institute of Oceanography
      Nova Goa, Goa, India