Meinhard Simon

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

Are you Meinhard Simon?

Claim your profile

Publications (84)348.36 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Dissolved organic matter (DOM) is the main substrate and energy source for heterotrophic bacterioplankton. To understand the interactions between DOM and the bacterial community (BC), it is important to identify the key factors on both sides in detail, chemically distinct moieties in DOM and the various bacterial taxa. Next-generation sequencing facilitates the classification of millions of reads of environmental DNA and RNA amplicons and ultrahigh-resolution mass spectrometry yields up to 10[thinsp]000 DOM molecular formulae in a marine water sample. Linking this detailed biological and chemical information is a crucial first step toward a mechanistic understanding of the role of microorganisms in the marine carbon cycle. In this study, we interpreted the complex microbiological and molecular information via a novel combination of multivariate statistics. We were able to reveal distinct relationships between the key factors of organic matter cycling along a latitudinal transect across the North Sea. Total BC and DOM composition were mainly driven by mixing of distinct water masses and presumably retain their respective terrigenous imprint on similar timescales on their way through the North Sea. The active microbial community, however, was rather influenced by local events and correlated with specific DOM molecular formulae indicative of compounds that are easily degradable. These trends were most pronounced on the highest resolved level, that is, operationally defined /`species/', reflecting the functional diversity of microorganisms at high taxonomic resolution.
    No preview · Article · Jan 2016 · The ISME Journal
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The diversity of macro-organisms increases towards the equator, with almost no exceptions. It is the most conserved biogeographical pattern on earth and is thought to be related to the increase of temperature and productivity in the tropics. The extent and orientation of a latitudinal gradient of marine bacterioplankton diversity is controversial. Here we studied the euphotic zone of the Atlantic Ocean based on a transect covering ~12.000 km from 51°S to 47 °N. Water samples were collected at 26 stations at five depths between 20 and 200 m and sequentially filtered through 8 μm, 3 μm and 0,22 μm filters, resulting in a total of 359 samples. Illumina sequencing of the V5–V6 region of the 16S rRNA gene revealed a clear biogeographic pattern with a double inverted latitudinal gradient. Diversity was higher in mid-latitudinal regions of the Atlantic Ocean and decreased towards the equator. This pattern was conserved for bacteria from all three planktonic size fractions. Diversity showed a non-linear relationship with temperature and was negatively correlated with bacterial cell numbers in the upper depth layers (<100 m). The latitudinal gradients of marine bacterial diversity and the mechanisms that govern them are distinct from those found in macro-organisms.
    Full-text · Article · Jan 2016 · Scientific Reports
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The marine metabolite tropodithietic acid (TDA), produced by several Roseobacter clade bacteria, is known for its broad antimicrobial activity. TDA is of interest not only as a probiotic in aquaculture, but also because it might be of use as an antibacterial agent in non-marine or non-aquatic environments, and thus the potentially cytotoxic influences on eukaryotic cells need to be evaluated. The present study was undertaken to investigate its effects on cells of the mammalian nervous system, i.e., neuronal N2a cells and OLN-93 cells as model systems for nerve cells and glia. The data show that in both cell lines TDA exerted morphological changes and cytotoxic effects at a concentration of 0.3–0.5 �g/mL (1.4–2.4 �M). Furthermore, TDA caused a breakdown of the mitochondrial membrane potential, the activation of extracellular signal-regulated kinases ERK1/2, and the induction of the small heat shock protein HSP32/HO-1, which is considered as a sensor of oxidative stress. The cytotoxic effects were accompanied by an increase in intracellular Ca2+-levels, the disturbance of the microtubule network, and the reorganization of the microfilament system. Hence, mammalian cells are a sensitive target for the action of TDA and react by the activation of a stress response resulting in cell death.
    Full-text · Article · Nov 2015 · Marine Drugs
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Roseobacter group is one of the predominant lineages in the marine environment. While most investigations focus on pelagic roseobacters, the distribution and metabolic potential of benthic representatives is less understood. In this study, the diversity of the Roseobacter group was characterized in sediment and water samples along the German/Scandinavian North Sea coast by 16S rRNA gene analysis and cultivation-based methods. Molecular analysis indicated an increasing diversity between communities of the Roseobacter group from the sea surface to the seafloor and revealed distinct compositions of free-living and attached fractions. Culture media containing dimethyl sulfide (DMS), dimethyl sulfonium propionate (DMSP) or dimethyl sulfoxide (DMSO) stimulated growth of roseobacters showing highest most probable numbers (MPN) in DMSO-containing dilutions of surface sediments (2.1×10(7) roseobacters cm(-3)). Twenty roseobacters (12 from sediments) were isolated from DMSP- and DMS-containing cultures. Sequences of the isolates represented 0.04% of all Bacteria and 4.7% of all roseobacters in the pyrosequencing dataset from sediments. Growth experiments with the isolate Shimia sp. SK013 indicated that benthic roseobacters are able to switch between aerobic and anaerobic utilization of organic sulfur compounds. This response to changing redox conditions might be an adaptation to specific environmental conditions on particles and in sediments.
    Full-text · Article · Nov 2015 · FEMS Microbiology Ecology
  • Source
    Sonja Voget · Sara Billerbeck · Meinhard Simon · Rolf Daniel
    [Show abstract] [Hide abstract]
    ABSTRACT: The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878) belongs to the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the genus Octadecabacter and the type strain of the species.
    Preview · Article · Sep 2015 · Genome Announcements
  • [Show abstract] [Hide abstract]
    ABSTRACT: Subterranean estuaries (STEs) are important biogeochemical land-sea interfaces, where fresh groundwater mixes with seawater in coastal aquifers. However, the sources of dissolved organic matter (DOM) and the connection of its molecular-level processing to pore water chemistry and redox conditions in these ecosystems are still not well understood. We studied the cycling of DOM in the STE of an intertidal sandy beach of the North Sea on spatial and seasonal scales. Ultrahigh-resolution mass spectrometry was used to identify thousands of DOM molecular formulae. These data were interpreted in the context of inorganic pore water chemistry, stable carbon isotope composition of solid-phase extracted (SPE) DOM and chemical tracers for bioavailable (dissolved carbohydrates, DCHOs) as well as biorefractory DOM (dissolved black carbon, DBC). Numerical modelling was used to estimate pore water residence times indicating relatively young pore water in the upper saline plume (USP, <4 years) and decades-old groundwater in the freshwater discharge tube. The detected levels of dissolved Fe and ammonium in the USP at sediment depths exceeding 50cm demonstrated suboxic conditions. Statistical analyses revealed complex biotic and abiotic DOM processing apart from conservative mixing of marine and terrestrial endmembers. We propose that the input of bioavailable marine and terrestrial DOM, such as DCHOs, by percolating seawater and meteoric groundwater and its degradation by microbes caused oxygen depletion favoring Fe oxide/hydroxide reduction. In the freshwater discharge tube, the presence of highly aromatic compounds, DBC, and 13C-depleted SPE-DOM indicated the intrusion of meteoric groundwater containing terrestrial DOM. The discharge of this groundwater appears to be a significant source of nutrients (e.g., ammonium) and biorefractory, e.g. combustion-derived, DOM to the adjacent water column.
    No preview · Article · Sep 2015 · Marine Chemistry
  • [Show abstract] [Hide abstract]
    ABSTRACT: Dissolved organic matter (DOM) in the oceans constitutes a major carbon pool involved in global biogeochemical cycles. More than 96% of the marine DOM resists microbial degradation for thousands of years. The composition of this refractory DOM (RDOM) exhibits a molecular signature ubiquitously detected in the deep oceans. Surprisingly efficient microbial transformation of labile into stable forms of DOM has been shown previously, implying that microorganisms apparently produce far more RDOM than needed to sustain the global pool. Here we show, by assessing the microbial formation and transformation of DOM in unprecedented molecular detail for 3 years, that most of the microbial DOM is different from RDOM in the ocean. Only <0.4% of the net community production is channelled into a form of DOM that is undistinguishable from oceanic RDOM. Our study provides a molecular background for global models on the production, turnover and accumulation of marine DOM.
    No preview · Article · Jun 2015 · Nature Communications
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The marine bacterium Alteromonas macleodii is a copiotrophic r-strategist, but little is known about its potential to degrade polysaccharides. Here, we studied the degradation of alginate and other algal polysaccharides by A. macleodii strain 83-1 in comparison to other A. macleodii strains. Cell densities of strain 83-1 with alginate as sole carbon source were comparable to those with glucose, but the exponential phase was delayed. The genome of 83-1 was found to harbor an alginolytic system comprising five alginate lyases, whose expression was induced by alginate. The alginolytic system contains additional CAZymes, including two TonB-dependent receptors, and is part of a 24 kb genomic island unique to the A. macleodii "surface clade" ecotype. In contrast, strains of the "deep clade" ecotype contain only a single alginate lyase in a separate 7 kb island. This difference was reflected in a eightfold greater efficiency of surface clade strains to grow on alginate. Strain 83-1 furthermore hydrolyzed laminarin, pullulan, and xylan, and corresponding polysaccharide utilization loci were detected in the genome. A. macleodii alginate lyases were predominantly detected in Atlantic Ocean metagenomes. The demonstrated hydrolytic capacities are likely of ecological relevance and represent another level of adaptation among A. macleodii ecotypes. This article is protected by copyright. All rights reserved.
    Full-text · Article · Apr 2015 · Environmental Microbiology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Marine planktonic bacteria often live in habitats with extremely low concentrations of dissolved organic matter (DOM). To study the use of trace amounts of DOM by the facultatively oligotrophic Pseudovibrio sp. FO-BEG1, we investigated the composition of artificial and natural seawater before and after growth. We determined the concentrations of dissolved organic carbon (DOC), total dissolved nitrogen (TDN), free and hydrolysable amino acids, and the molecular composition of DOM by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR-MS). The DOC concentration of the artificial seawater we used for cultivation was 4.4 μmol C L<sup>-1</sup>, which was eight times lower compared to the natural oligotrophic seawater we used for parallel experiments (36 μmol C L <sup>-1</sup>). During the three-week duration of the experiment, cell numbers increased from 40 cells mL<sup>-1</sup> to 2x10<sup>4</sup> cells mL <sup>-1</sup> in artificial and to 3x10<sup>5</sup> cells mL <sup>-1</sup> in natural seawater. No nitrogen fixation and minor CO<sub>2</sub> fixation (< 1% of cellular carbon) was observed. Our data show that in both media, amino acids were not the main substrate for growth. Instead, FT-ICR-MS analysis revealed usage of a variety of different dissolved organic molecules, belonging to a wide range of chemical compound groups, also containing nitrogen. The present study shows that marine heterotrophic bacteria are able to proliferate with even lower DOC concentrations than available in natural ultra-oligotrophic seawater, using unexpected organic compounds to fuel their energy, carbon and nitrogen requirements.
    Full-text · Article · Mar 2015 · PLoS ONE
  • [Show abstract] [Hide abstract]
    ABSTRACT: A heterotrophic, Gram negative, aerobic bacterium, designated strain SB1T, was isolated from surface water of the southern North Sea. Comparison of 16S rRNA gene sequences revealed that strain SB1T is affiliated to the genus Octadecabacter within the marine Roseobacter clade (family Rhodobacteraceae) with Octadecabacter antarcticus as the closest described species (98.2% sequence similarity). DNA-DNA hybridization indicated that SB1T is a distinct species within this genus. On marine agar, strain SB1T forms beige, circular and convex colonies. Cells are irregular, motile rods. Growth occurs between 4 and 25°C and is optimal at 20°C. pH ranges from 7-9 (optimum 7.5-8.5), NaCl concentrations between 1 and 6% are tolerated (optimum 2-4%). The DNA G+C base content of SB1T is 54.7 mol%. The fatty acids (>1%) comprise 10:0 3-OH, 12:1 3-OH, 16:1ω7c, 16:0, 18:2ω7, 12, 18:1ω7c, 18:0, and 11-methyl 18:1ω7c. The sole respiratory lipoquinone is ubiquinone Q-10 and the polar lipid pattern indicates the presence of the phospholipids phosphatidylglycerol and phosphatidylcholine, as well as the unidentified aminolipid AL1, phospholipids PL1 and PL3 and the lipids L1, L2 and L4. On the basis of phylogenetic and phenotypic differences strain SB1T represents a novel species in the genus Octadecabacter, for which we propose the name Octadecabacter temperatus sp. nov. The type strain is SB1T (= DSM 26878T = LMG 27946T). Furthermore, our results suggest reclassification of Octadecabacter jejudonensis as type species of a new genus, Pseudooctadecabacter, as Pseudooctadecabacter jejudonensis comb. nov. (type strain SSK2-1T = KCTC 32535T = CECT 8397T).
    No preview · Article · Mar 2015 · International Journal of Systematic and Evolutionary Microbiology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The bacterial degradation of polysaccharides is central to marine carbon cycling, but little is known about the bacterial taxa that degrade specific marine polysaccharides. Here, bacterial growth and community dynamics were studied during the degradation of the polysaccharides chitin, alginate and agarose in microcosm experiments at four contrasting locations in the Southern and Atlantic Oceans. At the Southern polar front, chitin-supplemented microcosms were characterized by higher fractions of actively growing cells and a community shift from Alphaproteobacteria to Gammaproteobacteria and Bacteroidetes. At the Antarctic ice shelf, chitin degradation was associated with growth of Bacteroidetes, with 24% higher cell numbers compared with the control. At the Patagonian continental shelf, alginate and agarose degradation covaried with growth of different Alteromonadaceae populations, each with specific temporal growth patterns. At the Mauritanian upwelling, only the alginate hydrolysis product guluronate was consumed, coincident with increasing abundances of Alteromonadaceae and possibly cross-feeding SAR11. 16S rRNA gene amplicon libraries indicated that growth of the Bacteroidetes-affiliated genus Reichenbachiella was stimulated by chitin at all cold and temperate water stations, suggesting comparable ecological roles over wide geographical scales. Overall, the predominance of location-specific patterns showed that bacterial communities from contrasting oceanic biomes have members with different potentials to hydrolyse polysaccharides.
    Full-text · Article · Mar 2015 · Environmental Microbiology
  • [Show abstract] [Hide abstract]
    ABSTRACT: Marine bacteria form one of the largest living surfaces on Earth, and their metabolic activity is of fundamental importance for global nutrient cycling. Here, we explored the largely unknown intracellular pathways in twenty-five microbes representing different classes of glucose-using marine bacteria: Alphaproteobacteria, Gammaproteobacteria and Flavobacteriia of the Bacteriodetes phylum. We applied (13)C-isotope experiments to infer metabolic fluxes through their carbon core pathways. Notably, 90% of all studied strains use the Entner-Doudoroff (ED) pathway for glucose catabolism, whereas only 10% rely on the Embden-Meyerhof-Parnas (EMP) pathway. This result differed dramatically from the studied terrestrial model strains, which preferentially used the high-ATP-yielding EMP pathway. ED pathway using strains exhibited a more robust resistance against the oxidative stress, typically found in this environment. An important feature contributing to the preferential use of the ED pathway in the oceans could therefore be enhanced supply of NADPH through this pathway. The studied marine bacteria did not specifically rely on a distinct anaplerotic route, but the carboxylation of PEP or pyruvate for fueling of the TCA cycle was evenly distributed. The studied marine isolates belong to clades that dominate the uptake of glucose, a major carbon source for bacteria in seawater. Therefore, the ED pathway may play a significant role in the cycling of mono- and polysaccharides by bacterial communities in marine ecosystems. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    No preview · Article · Jan 2015 · Applied and Environmental Microbiology
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Diatom-dominated phytoplankton blooms in neritic seas are typically terminated by aggregation. Despite extensive studies, it is still unknown how temperature controls aggregation. Therefore, we studied aggregation in a 750 liter mesocosm experiment under simulated in situ conditions during a spring diatom bloom in the southern North Sea at Helgoland Roads. In the early phase, at the peak, and in the late phase, aggregation was examined in rolling tanks at the ambient temperature (6uC) and at 11uC. In a second set of rolling tanks, cells of Thalassiosira rotula were added to examine how this readily aggregating diatom affects aggregation. In the treatments with the natural phytoplankton, a significant effect of temperature on aggregation was detected only in the late bloom, when the aggregate area increased at 11uC relative to 6uC. In contrast, in the T. rotula–supplemented treatments, aggregation was enhanced by the elevated temperature at the peak but not in the late bloom. The aggregate area per microgram particulate organic carbon, a normalized measure to assess the aggregation potential, indicated that the aggregation potential in the natural phytoplankton community decreased from the peak to the late bloom, independent of temperature. This was presumably due to the reduced stickiness of the particles and lower concentrations of transparent exopolymer particles in the late phase. In the T. rotula–supplemented treatments, aggregation potential increased from the peak to the late bloom at the ambient temperature, whereas it decreased at the elevated temperature. Flavobacteria and Sphingobacteria of the Bacteroidetes phylum and Gammaproteobacteria were the dominant bacterial groups colonizing the aggregates.
    Full-text · Article · Nov 2014 · Limnology and Oceanography
  • [Show abstract] [Hide abstract]
    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.
    No preview · Article · Sep 2014 · Geochimica et Cosmochimica Acta
  • [Show abstract] [Hide abstract]
    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.
    No preview · Article · Aug 2014 · The ISME Journal
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Heterotrophic bacterial communities are major drivers of organic matter remineralization in the World’s Oceans. As much of organic matter consists of polymers, investigating the hydrolytic potential among marine bacteria is crucial for the understanding of marine nutrient cycles and their linkages with bacterial community structure. The present study characterized the response of bacterioplankton communities to polymeric carbohydrates at four locations in the Southern and Atlantic Oceans using natural seawater microcosms amended with chitin, alginate, and agarose. Cell numbers as determined by flow cytrometry increased markedly in temperate water microcosms (Patagonian Shelf), yielding almost double cell numbers with alginate and chitin compared to the control regime (3 × 106 cells mL-1). In warm water microcosms (Mauritanian Upwelling), only alginate distinctly stimulated bacterial growth, yielding almost double cell numbers (2.3 × 106 cells mL-1). Cell numbers remained almost unchanged in polar water microcosms (Polar Front, Antarctic Ice Shelf). 454 pyrosequencing as well as CARD-FISH revealed that Gammaproteobacteria were significantly stimulated across all locations and regimes (p < 0.05). Agarose and alginate strongly stimulated Alteromonadaceae in temperate waters, reaching relative abundances of 63 and 78%, respectively. This was largely due to single OTUs related to Pseudoalteromonas atlantica and Alteromonas macleodii, respectively. The response of Colwellia was determined by both location and substrate, being stimulated by agarose and alginate in polar waters and by chitin at all locations except the Antarctic Ice Shelf. The latter instead featured a significant stimulation of Fibrobacteres (reaching 28%). Chitin strongly stimulated Reichenbachiella (Cytophagales) in polar and temperate waters, with relative abundances increasing by 300- to 1500-fold (p < 0.005). At present, several alginate-degrading strains from the Gammaproteobacteria and Bacteroidetes are investigated by physiological and whole-genome analyses, indicating that closely related strains have distinct alginate utilization modes. In conclusions, this study presents a comprehensive picture of bacterial polysaccharide degradation in different oceanic regions and contributes to the understanding of fundamental marine nutrient cycles across wide geographical scales.
    Full-text · Conference Paper · Jun 2014
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Mar 2014 · Journal of Sea Research
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Jan 2014 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Dec 2013 · Standards in Genomic Sciences
  • Source
    [Show abstract] [Hide abstract]
    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.
    Full-text · Article · Oct 2013 · Standards in Genomic Sciences

Publication Stats

3k Citations
348.36 Total Impact Points

Institutions

  • 2001-2016
    • 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
    • Leibniz-Institute of Freshwater Ecology and Inland Fisheries
      Berlín, Berlin, Germany
  • 1993-1997
    • Universität Konstanz
      Constance, Baden-Württemberg, Germany