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consumption of tropospheric levels of methyl bromide by c(1) compound-utilizing bacteria and comparison to saturation kinetics.pure cultures of methylotrophs and methanotrophs are known to oxidize methyl bromide (mebr); however, their ability to oxidize tropospheric concentrations (parts per trillion by volume [pptv]) has not been tested. methylotrophs and methanotrophs were able to consume mebr provided at levels that mimicked the tropospheric mixing ratio of mebr (12 pptv) at equilibrium with surface waters ( approximately 2 pm). kinetic investigations using picomolar concentrations of mebr in a continuously stirred t ...200111722890
diverse organization of genes of the beta-ketoadipate pathway in members of the marine roseobacter lineage.members of the roseobacter lineage, an ecologically important marine clade within the class alpha-proteobacteria, harbor genes for the protocatechuate branch of the beta-ketoadipate pathway, a major catabolic route for lignin-related aromatic compounds. the genes of this pathway are typically clustered, although gene order varies among organisms. here we characterize genes linked to pcah and -g, which encode protocatechuate 3,4-dioxygenase, in eight closely related members of the roseobacter lin ...200415006791
genome organization and localization of the puflm genes of the photosynthesis reaction center in phylogenetically diverse marine alphaproteobacteria.genome organization, plasmid content and localization of the puflm genes of the photosynthesis reaction center were studied by pulsed-field gel electrophoresis (pfge) in marine phototrophic alphaproteobacteria. both anaerobic phototrophs (rhodobacter veldkampii and rhodobacter sphaeroides) and strictly aerobic anoxygenic phototrophs from the roseobacter-sulfitobacter-silicibacter clade (roseivivax halodurans, roseobacter litoralis, staleya guttiformis, roseovarius tolerans, and five new strains ...200415184132
jannaschia cystaugens sp. nov., an alexandrium (dinophyceae) cyst formation-promoting bacterium from hiroshima bay, japan.heterotrophic bacteria isolated from water samples taken from hiroshima bay, japan, and referred to as alexandrium (dinophyceae) cyst formation-promoting bacteria, were assigned to the roseobacter-sulfitobacter-silicibacter group within the alpha-proteobacteria on the basis of nearly complete 16s rrna gene sequences. phylogenetic analyses showed that two strains, cfpb-a9t and cfpb-a5, are closely related to each other and that their closest relative was jannaschia helgolandensis (95.9 % sequence ...200415388729
tfam detects co-evolution of trna identity rules with lateral transfer of histidyl-trna synthetase.we present tfam, an automated, statistical method to classify the identity of trnas. tfam, currently optimized for bacteria, classifies initiator trnas and predicts the charging identity of both typical and atypical trnas such as suppressors with high confidence. we show statistical evidence for extensive variation in trna identity determinants among bacterial genomes due to variation in overall tdna base content. with tfam we have detected the first case of eukaryotic-like trna identity rules i ...200616473847
yangia pacifica gen. nov., sp. nov., a novel member of the roseobacter clade from coastal sediment of the east china sea.an aerobic, gram-negative bacterial isolate, strain dx5-10t, was isolated from coastal sediment of the east china sea. the taxonomy of strain dx5-10t was studied by phenotypic and phylogenetic methods. strain dx5-10t was motile, formed faint-yellowish colonies and was positive for catalase reaction and weakly positive for oxidase reaction. the nearly complete 16s rrna gene of strain dx5-10t was obtained and sequence analysis indicated that strain dx5-10t represented an independent lineage within ...200616514022
dissimilation of c3-sulfonates.cysteate and sulfolactate are widespread natural products in the environment, while propanesulfonate, 3-aminopropanesulfonate and propane-1,3-disulfonate are xenobiotics. while some understanding of the bacterial assimilation of cysteate sulfur has been achieved, details of the dissimilation of cysteate and sulfolactate by microbes together with information on the degradation of the xenobiotics have only recently become available. this minireview centres on bacterial catabolism of the carbon moi ...200616341843
thalassobius mediterraneus gen. nov., sp. nov., and reclassification of ruegeria gelatinovorans as thalassobius gelatinovorus comb. nov.a gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from sea water off the western mediterranean coast near valencia (spain). this strain was able to grow on several organic acids and amino acids added to a minimal medium as carbon sources, but used few carbohydrates or yielded slight growth when sugars were used. phylogenetic analysis based on an almost complete 16s rrna gene sequence revealed that strain xsm19t was a member of the r ...200516280499
strain variability in the dna immigration control region (icr) of xylella fastidiosa.the genome of the bacterium xylella fastidiosa contains four orfs (xf2721, xf2725, xf2739 and xf0295) related to the restriction modification type i system, ordinarily named r-m. this system belongs to the dna immigration control region (icr). each orf is related to different operon structures, which are homologues among themselves and with subunit hsd r from the endonuclease coding genes. in addition, these orfs are highly homologous to genes in pseudomonas aeruginosa, methylococcus capsulatus ...200616125907
dinoroseobacter shibae gen. nov., sp. nov., a new aerobic phototrophic bacterium isolated from dinoflagellates.a novel group of aerobic anoxygenic phototrophic bacteria was isolated from marine dinoflagellates, and two strains were characterized in detail. cells were gram-negative cocci or ovoid rods and were motile by means of a single, polarly inserted flagellum. they were obligate aerobes requiring 1-7 % salinity. the optimal ph range for growth was 6.5-9.0 and the temperature optimum was 33 degrees c. the bacteria contained bacteriochlorophyll a and spheroidenone as the only carotenoid. the in vivo a ...200515879238
roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll a-producing alpha-proteobacterium isolated from hypersaline ekho lake, antarctica.a gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic ekho lake (east antarctica). the strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. cells had an absolute requirement for artificial sea water, which could not be replaced by nacl. a large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. the predominant fatty acids of this or ...200515653851
genome sequence of silicibacter pomeroyi reveals adaptations to the marine environment.since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. here we describe the genome sequence of silicibacter pomeroyi, a member of the marine roseobacter clade (fig. 1), the relatives of which c ...200415602564
chemotaxis of silicibacter sp. strain tm1040 toward dinoflagellate products.the alpha-proteobacteria phylogenetically related to the roseobacter clade are predominantly responsible for the degradation of organosulfur compounds, including the algal osmolyte dimethylsulfoniopropionate (dmsp). silicibacter sp. strain tm1040, isolated from a dmsp-producing pfiesteria piscicida dinoflagellate culture, degrades dmsp, producing 3-methylmercaptopropionate. tm1040 possesses three lophotrichous flagella and is highly motile, leading to a hypothesis that tm1040 interacts with p. p ...200415294804
cyclic peptides from a ruegeria strain of bacteria associated with the sponge suberites domuncula.two new cyclic peptides, cyclo-(glycyl-l-seryl-l-prolyl-l-glutamyl) and cyclo-(glycyl-l-prolyl-l-glutamyl), have been isolated from the cell extract of a ruegeria strain associated with cell cultures of suberites domuncula. three other cyclopeptides have been isolated for the first time from a natural source. additionally, a new diastereoisomer of a known compound is reported. the structures of isolated compounds have been elucidated by means of spectroscopic data (1d-, 2d-nmr, hresims) and chir ...200415270577
a superfamily of voltage-gated sodium channels in bacteria.nachbac, a six-alpha-helical transmembrane-spanning protein cloned from bacillus halodurans, is the first functionally characterized bacterial voltage-gated na(+)-selective channel. as a highly expressing ion channel protein, nachbac is an ideal candidate for high resolution structural determination and structure-function studies. the biological role of nachbac, however, is still unknown. in this report, another 11 structurally related bacterial proteins are described. two of these functionally ...200414665618
three new chlorine containing antibiotics from a marine-derived fungus aspergillus ostianus collected in pohnpei.a marine bacterium ruegeria atlantica (designated as strain tuf-d) was isolated from a glass plate submerged in the coastal water. three new chlorine containing compounds (1 to approximately 3), together with penicillic acid (4) were obtained from a marine-derived fungus aspergillus ostianus strain tuf 01f313 isolated from a marine sponge at pohnpei as antibacterial components against r. atlantica. the structures of three new antibiotics were determined based on their spectral data as 8-chloro-9 ...200314632284
exocellular cyclic dipeptides from a ruegeria strain associated with cell cultures of suberites domuncula.from cell cultures of suberites domuncula was isolated a bacterial strain, sdc-1, which was identified by 16s ribosomal rna sequence analysis as an alpha-proteobacterium of the genus ruegeria. the occurrence of the strain in sponge cell culture could be explained by its resistance to the antibiotics used in the isolation of sponge cell cultures or by the preservation of sdc-1 by host sponge cells. the fatty acid composition of sdc-1 is characterized by branched c-12 methyl fatty acids. two new a ...200414586767
silicibacter pomeroyi sp. nov. and roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments.three gram-negative, rod-shaped, aerobic bacteria that were capable of degrading dimethylsulfoniopropionate (dmsp) were isolated from marine waters. these isolates (dss-3(t), dss-10 and ism(t)) exhibited the ability to demethylate and cleave dmsp, as well as to degrade other sulfur compounds related to dmsp that are cycled in marine environments. intracellular poly-beta-hydroxybutyrate inclusions, surface blebs and one polar, complex flagellum that rotated exclusively in the clockwise direction ...200313130004
jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine roseobacter clade from the north sea.heterotrophic bacteria were isolated from a water sample taken from the north sea, 2 km off the coast of the island of helgoland, by direct plating of the serially diluted sample on complex marine media. sixteen of 80 strains from the highest sample dilution belonged to the 'roseobacter-sulfitobacter-silicibacter' group within the 2-subclass of the proteobacteria on the basis of partial 16s rdna sequence analysis. phylogenetic analysis of nearly complete 16s rdna sequences showed that the closes ...200312807194
transcriptional response of silicibacter pomeroyi dss-3 to dimethylsulfoniopropionate (dmsp).dimethylsufoniopropionate (dmsp) is an abundant organic sulfur compound in the ocean and an important substrate for marine bacterioplankton. the roseobacter clade of marine alphaproteobacteria, including silicibacter pomeroyi strain dss-3, are known to be involved in dmsp degradation in situ. the fate of dmsp has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. s. pomeroyi is capable of performing two major pathw ...200717922758
phylogenomics and signature proteins for the alpha proteobacteria and its main groups.alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. however, for these bacteria as a whole and for all of its major subgroups (viz. rhizobiales, rhodobacterales, rhodospirillales, rickettsiales, sphingomonadales and caulobacterales), very few or no distinctive molecular or biochemical characteristics are known.200718045498
mesaconyl-coenzyme a hydratase, a new enzyme of two central carbon metabolic pathways in bacteria.the coenzyme a (coa)-activated c5-dicarboxylic acids mesaconyl-coa and beta-methylmalyl-coa play roles in two as yet not completely resolved central carbon metabolic pathways in bacteria. first, these compounds are intermediates in the 3-hydroxypropionate cycle for autotrophic co2 fixation in chloroflexus aurantiacus, a phototrophic green nonsulfur bacterium. second, mesaconyl-coa and beta-methylmalyl-coa are intermediates in the ethylmalonyl-coa pathway for acetate assimilation in various bacte ...200818065535
nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium ruegeria isolate pr1b.two plasmids, 76 and 148 kb in size, isolated from ruegeria strain pr1b were entirely sequenced. these are the first plasmids to be characterized from this genus of marine bacteria. sequence analysis revealed a biased distribution of function among the putative proteins encoded on the two plasmids. the smaller plasmid, designated psd20, encodes a large number of putative proteins involved in polysaccharide biosynthesis and export. the larger plasmid, designated psd25, primarily encodes putative ...200312749836
diversity and quorum-sensing signal production of proteobacteria associated with marine sponges.marine sponges are hosts to diverse and dense bacterial communities and thus provide a potential environment for quorum sensing. quorum sensing, a key factor in cell-cell communication and bacterial colonization of higher animals, might be involved in the symbiotic interactions between bacteria and their sponge hosts. given that marine proteobacteria are known to produce n-acyl homoserine lactone (ahl) signal molecules, we tested the production of ahls by alpha- and gammaproteobacteria isolated ...200818211268
reclassification of marine agrobacterium species: proposals of stappia stellulata gen. nov., comb. nov., stappia aggregata sp. nov., nom. rev., ruegeria atlantica gen. nov., comb. nov., ruegeria gelatinovora comb. nov., ruegeria algicola comb. nov., and ahrensia kieliense gen. nov., sp. nov., nom. rev.the bootstrapped 16s rdna sequence-based neighbor-joining phylogeny has suggested that the marine species of the genus agrobacterium have no relation to the terrestrial agrobacterium species. agrobacterium atlanticum iam 14463(t) (a superscript (t)=type strain), agrobacterium ferrugineum iam 12616(t), agrobacterium gelatinovorum iam 12617(t), agrobacterium meteori iam 14464(t), agrobacterium stellulatum iam 12621(t) and iam 12614, and the invalidly published marine species "agrobacterium kielien ...199812501429
leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide.a marine methylotroph, designated strain mb2t, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. a limited amount of growth was observed with dimethyl sulfide. growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and casamino acids. no growth was observed on methylated amines, methanol, formate, acetate, gluco ...200212054249
microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition.quantitative and qualitative changes in bacterial communities from the mediterranean sea were compared in duplicate batch mesocosms with or without addition of inorganic nutrients. methods including traditional microbial ecology techniques, molecular biology and flow cytometry were combined to determine abundances, production, cell size, activity, culturability and taxonomic diversity of bacterial cells. addition of nutrients and confinement resulted in an increase of bacterial densities which w ...200111137605
microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations.a mesocosm experiment was performed to study the influence of nutrients on activity and diversity of bacterial assemblages from the mediterranean sea. changes in the diversity of the predominant bacterial populations were monitored by dgge fingerprinting of pcr products derived from 16s rrna encoding genes. fluctuations in the diversity of the most active populations was inferred by performing the dgge fingerprinting on the basis of the cellular rrna after reverse transcription and pcr amplifica ...200111137604
phylogenetic analysis of bacterial communities associated with leaves of the seagrass halophila stipulacea by a culture-independent small-subunit rrna gene approach.the phylogenetic diversity of the bacterial community associated with leaves of the marine plant halophila stipulacea in the northern gulf of elat was examined by 16s rrna gene (rdna) sequence analyses of a clone library. for 59 clones corresponding to 51 ardra (amplified rdna restriction analysis) groups, the sequence of approximately 1 kb was determined, and the fraction of the corresponding ardra groups of the leaf library was calculated. the class proteobacteria was represented by 62.6% of t ...200010790514
differentiation of newly described antarctic bacterial isolates related to roseobacter species based on 16s-23s rdna internal transcribed spacer sequences.the 16s-23s rdna internal transcribed spacer (its) of roseobacter denitrificans, roseobacter litoralis, ruegeria algicola and strains of the recently described species antarctobacter heliothermus and roseovarius tolerans were analysed in order to examine dna sequence variations and to draw conclusions about inter- and intraspecific relationships. a. heliothermus included four strains with an its fragment length of 1092 bp. roseovarius tolerans was described on the basis of eight strains. five of ...200010758903
silicibacter lacuscaerulensis gen. nov., sp. nov., a mesophilic moderately halophilic bacterium characteristic of the blue lagoon geothermal lake in iceland.mesophilic, moderately halophilic bacteria were isolated from a silica-rich geothermal lake, the blue lagoon in iceland. the isolates are strictly aerobic, but reduce nitrate to nitrite, and are oxidase- and catalase-positive. the nonsporeforming and nonmotile gram negative rods are 0.6-0.8 microm in diameter and variable in length (9-18 microm), and contain gas vacuoles. the gc content in their dna is 66.15%. the minimum, optimum, and maximum temperatures for growth are 22 degrees c, 45 degrees ...19979680308
reclassification of roseobacter gallaeciensis ruiz-ponte et al. 1998 as phaeobacter gallaeciensis gen. nov., comb. nov., description of phaeobacter inhibens sp. nov., reclassification of ruegeria algicola (lafay et al. 1995) uchino et al. 1999 as marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera roseobacter, ruegeria and leisingera.a heterotrophic, antibiotic-producing bacterium, strain t5(t), was isolated from the german wadden sea, located in the southern region of the north sea. sequence analysis of the 16s rrna gene of this strain demonstrated close affiliation with roseobacter gallaeciensis bs107(t) (99 % similarity), but the results of genotypic (dna-dna hybridization and dna g + c content) and phenotypic characterization revealed that strain t5(t) represents a novel species. the novel organism is strictly aerobic, g ...200616738106
environmental biology of the marine roseobacter lineage.the roseobacter lineage is a phylogenetically coherent, physiologically heterogeneous group of alpha-proteobacteria comprising up to 25% of marine microbial communities, especially in coastal and polar oceans, and it is the only lineage in which cultivated bacteria are closely related to environmental clones. currently 41 subclusters are described, covering all major marine ecological niches (seawater, algal blooms, microbial mats, sediments, sea ice, marine invertebrates). members of the roseob ...200616719716
inducible transcription of genes involved in taurine uptake and dissimilation by silicibacter pomeroyi dss-3t.a largely untested hypothesis for the bacterial dissimilation of taurine was explored in silicibacter pomeroyi dss-3, whose genome has been sequenced. substrate-specific transcription of candidate genes encoding taurine uptake and dissimilation (tauabc, tpa, ald, xsc, pta) was found, which corresponded to the induction of tpa, ald, xsc and pta, that was observed.200616541231
induction of multiple prophages from a marine bacterium: a genomic approach.approximately 70% of sequenced bacterial genomes contain prophage-like structures, yet little effort has been made to use this information to determine the functions of these elements. the recent genomic sequencing of the marine bacterium silicibacter sp. strain tm1040 revealed five prophage-like elements in its genome. the genomes of these prophages (named prophages 1 to 5) are approximately 74, 30, 39, 36, and 15 kb long, respectively. to understand the function of these prophages, cultures of ...200616820498
l-cysteate sulpho-lyase, a widespread pyridoxal 5'-phosphate-coupled desulphonative enzyme purified from silicibacter pomeroyi dss-3(t).quantitative utilization of l-cysteate (2-amino-3-sulphopropionate) as the sole source of carbon and energy for growth of the aerobic, marine bacterium silicibacter pomeroyi dss-3(t) was observed. the sulphonate moiety was recovered in the medium largely as sulphite, and the appropriate amount of the ammonium ion was also observed. genes [suyab (3-sulpholactate sulpho-lyase)] encoding the known desulphonation reaction in cysteate degradation were absent from the genome, but a homologue of a puta ...200616302849
motility is involved in silicibacter sp. tm1040 interaction with dinoflagellates.silicibacter sp. tm1040, originally isolated from a culture of the dinoflagellate pfiesteria piscicida, senses and responds to the dinoflagellate secondary metabolite dimethylsulfoniopropionate (dmsp) by flagella-mediated chemotaxis behaviour. in this report we show that swimming motility is important for initiating the interaction between the bacterium and dinoflagellate. following transposon mutagenesis, three mutants defective in wild-type swimming motility (mot-) were identified. the defects ...200616913924
phylogenetic analysis of a biofilm bacterial population in a water pipeline in the gulf of mexico.the aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the gulf of mexico used to inject marine water into the oil reservoir. several aerobic and heterotrophic bacteria were isolated and identified by 16s rrna gene sequence analysis. metagenomic dna was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16s rrna gene metagenomic library. denaturing gradient gel electr ...200616958915
comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria hyphomonas neptunium and caulobacter crescentus.the dimorphic prosthecate bacteria (dpb) are alpha-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism caulobacter crescentus. here we describe the genome sequence of hyphomonas neptunium, a marine member of the dpb that differs from c. crescentus in that h. neptunium uses its stalk as a re ...200616980487
production of antibacterial compounds and biofilm formation by roseobacter species are influenced by culture conditions.bacterial communities associated with marine algae are often dominated by members of the roseobacter clade, and in the present study, we describe roseobacter phenotypes that may provide this group of bacteria with selective advantages when colonizing this niche. nine of 14 members of the roseobacter clade, of which half were isolated from cultures of the dinoflagellate pfiesteria piscicida, produced antibacterial compounds. many non-roseobacter marine bacteria were inhibited by sterile filtered ...200717098910
pseudoruegeria aquimaris gen. nov., sp. nov., isolated from seawater of the east sea in korea.a gram-negative, non-motile, rod-shaped bacterial strain, sw-255(t), was isolated from seawater from hwajinpo, on the coast of the east sea, korea, and subjected to a polyphasic taxonomic study. strain sw-255(t) grew optimally at ph 7.0-8.0 and 37 degrees c in the presence of 2 % (w/v) nacl. it contained q-10 as the predominant ubiquinone and c(18 : 1)omega7c as the major fatty acid. the dna g+c content was 67.0 mol%. a neighbour-joining phylogenetic tree based on 16s rrna gene sequences showed ...200717329781
taxonomic evaluation of the genera ruegeria and silicibacter: a proposal to transfer the genus silicibacter petursdottir and kristjansson 1999 to the genus ruegeria uchino et al. 1999.the taxonomic positions of the genera ruegeria and silicibacter were evaluated by a polyphasic investigation. it was evident from 16s rrna gene sequence analysis that both genera are closely related as they formed a monophyletic clade with high sequence similarities (96.9-98.2 %). several properties commonly found in these taxa strongly suggest that they should be classified in the same genus. further, a comparative study based on dna-dna hybridization, phenotypic characterization and chemotaxon ...200717392212
hthp: a novel class of hexameric, tyrosine-coordinated heme proteins.we have cloned, expressed, isolated and characterized a hexameric tyrosine-coordinated heme protein (hthp) from the marine bacterium silicibacter pomeroyi. hthp shows peroxidase and catalase activity and has a high thermal stability. as-isolated hthp has absorption maxima at 407, 495, 504, 532 and 622 nm wavelength. upon reduction maxima at 430, 564 and 596 nm wavelength are discernible. the crystal structure of hthp reveals a hexameric, ring-like arrangement of six monomers. each monomer binds ...200717395199
ruegeria mobilis sp. nov., a member of the alphaproteobacteria isolated in japan and palau.the taxonomic positions of two bacterial strains, mbic01146(t) and mbic01099, isolated from marine environments of japan and palau, respectively, were determined by using a polyphasic approach. the bacteria were aerobic, motile, gram-negative rods and formed star-shaped aggregations. the g+c content of the genomic dna ranged from 58.5 to 58.7 mol%. the major respiratory quinone was ubiquinone-10 and the predominant cellular fatty acids were c(16 : 0), c(18 : 1)omega6c and c(18 : 1)omega7c. 16s r ...200717551047
2,3-dihydroxypropane-1-sulfonate degraded by cupriavidus pinatubonensis jmp134: purification of dihydroxypropanesulfonate 3-dehydrogenase.2,3-dihydroxypropane-1-sulfonate (dhps) is a widespread intermediate in plant and algal transformations of sulfoquinovose (sq) from the plant sulfolipid sulfoquinovosyl diacylglycerol. further, dhps is recovered quantitatively during bacterial degradation of sq by klebsiella sp. strain abr11. dhps is also a putative precursor of sulfolactate in e.g. ruegeria pomeroyi dss-3. a bioinformatic approach indicated that some 28 organisms with sequenced genomes might degrade dhps inducibly via sulfolact ...201020150239
wenxinia marina gen. nov., sp. nov., a novel member of the roseobacter clade isolated from oilfield sediments of the south china sea.an aerobic and heterotrophic, gram-negative bacterial isolate, strain hy34(t), was isolated from sediment of an oilfield in the south china sea, china. the taxonomy of strain hy34(t) was studied by phenotypic and phylogenetic methods. strain hy34(t) formed faint-pink colonies on marine agar 2216. cells of strain hy34(t) were non-motile, ovoid or short rods. strain hy34(t) was positive for catalase and oxidase, and nitrate was reduced to nitrite. the nearly complete 16s rrna gene sequence of stra ...200717684242
ruegeria pelagia sp. nov., isolated from the sargasso sea, atlantic ocean.gram-negative, facultatively aerobic, chemoheterotrophic, short rod-shaped marine bacterial strains htcc2662(t) and htcc2663, isolated from the sargasso sea by using a dilution-to-extinction culturing method, were investigated to determine their taxonomic position. characterization of the two strains by phenotypic and phylogenetic analyses revealed that they belonged to the same species. the dna g+c content of strain htcc2662(t) was 58.4 mol% and the predominant cellular fatty acids were c(18 : ...200717684263
identification of a novel gentisate 1,2-dioxygenase from silicibacter pomeroyi.a 1,125-bp long orf encoding a novel gentisate 1,2-dioxygenase with two-domain bicupins was cloned from silicibacter pomeroyi dss-3 and expressed in escherichia coli. the resulting product was purified to homogeneity and partially characterized. non-reductive sds-page and gel filtration showed that the active recombinant gentisate 1,2-dioxygenase had an estimated molecular mass of 132 kda, and reductive sds-page indicated an approximate size of 45 kda. the enzyme thus appears to be a homotrimeri ...200717684705
genetic dissection of tropodithietic acid biosynthesis by marine roseobacters.the symbiotic association between the roseobacter silicibacter sp. strain tm1040 and the dinoflagellate pfiesteria piscicida involves bacterial chemotaxis to dinoflagellate-produced dimethylsulfoniopropionate (dmsp), dmsp demethylation, and ultimately a biofilm on the surface of the host. biofilm formation is coincident with the production of an antibiotic and a yellow-brown pigment. in this report, we demonstrate that the antibiotic is a sulfur-containing compound, tropodithietic acid (tda). us ...200818192410
occurrence and expression of gene transfer agent genes in marine bacterioplankton.genes with homology to the transduction-like gene transfer agent (gta) were observed in genome sequences of three cultured members of the marine roseobacter clade. a broader search for homologs for this host-controlled virus-like gene transfer system identified likely gta systems in cultured alphaproteobacteria, and particularly in marine bacterioplankton representatives. expression of gta genes and extracellular release of gta particles ( approximately 50 to 70 nm) was demonstrated experimental ...200818359833
crystal structure and mutagenic analysis of gdosp, a gentisate 1,2-dioxygenase from silicibacter pomeroyi.dioxygenases catalyze dioxygen incorporation into various organic compounds and play a key role in the complex degradation pathway of mono- and polycyclic aromatic and hetero-aromatic compounds. here we report the crystal structure of gentisate 1,2-dioxygenase from silicibacter pomeroyi (gdosp) at a 2.8 a resolution. the enzyme possessed a conserved three-dimensional structure of the bicupin family, forming a homotetramerization. however, each subunit of gdosp unusually contained two ferrous cen ...200818505738
a new class of homoserine lactone quorum-sensing signals.quorum sensing is a term used to describe cell-to-cell communication that allows cell-density-dependent gene expression. many bacteria use acyl-homoserine lactone (acyl-hsl) synthases to generate fatty acyl-hsl quorum-sensing signals, which function with signal receptors to control expression of specific genes. the fatty acyl group is derived from fatty acid biosynthesis and provides signal specificity, but the variety of signals is limited. here we show that the photosynthetic bacterium rhodops ...200818563084
dimethylsulfoniopropionate-dependent demethylase (dmda) from pelagibacter ubique and silicibacter pomeroyi.the ubiquitous algal metabolite dimethylsulfoniopropionate (dmsp) is a major source of carbon and reduced sulfur for marine bacteria. recently, the enzyme responsible for the demethylation of dmsp, designated dmda, was identified, and homologs were found to be common in marine bacterioplankton cells. the recombinant dmda proteins from the cultured marine bacteria pelagibacter ubique htcc1062 and silicibacter pomeroyi dss-3 were purified with a three-step procedure using anion-exchange, hydrophob ...200818849431
genome sequence of strain tw15, a novel member of the genus ruegeria belonging to the marine roseobacter clade.ruegeria sp. tw15, which belongs to the family rhodobacteraceae, was isolated from an ark clam in the south sea of korea. here is presented the draft genome sequence of ruegeria sp. tw15 (4,490,771 bp, with a g+c content of 55.7%), a member of the marine roseobacter clade, which comprises up to 20% of bacterioplankton in the coastal and oceanic mixed layer.201121551304
phaeobacter and ruegeria species of the roseobacter clade colonize separate niches in a danish turbot (scophthalmus maximus)-rearing farm and antagonize vibrio anguillarum under different growth conditions.members of the roseobacter clade colonize a spanish turbot larval unit, and one isolate (phaeobacter strain 27-4) is capable of disease suppression in in vivo challenge trials. here, we demonstrate that roseobacters with antagonistic activity against vibrio anguillarum also colonize a danish turbot larval farm that relies on a very different water source (the danish fiord limfjorden as opposed to the galician atlantic ocean). phylogenetic analyses based on 16s rrna and gyrase b gene sequences re ...200818952864
the crystal structure of ueha in complex with ectoine-a comparison with other trap-t binding proteins.substrate-binding proteins or extracellular solute receptors (esrs) are components of both abc (atp binding cassette) and trap-t (tripartite atp-independent periplasmic transporter). the trap-t system uehabc from silicibacter pomeroyi dss-3 imports the compatible solutes ectoine and 5-hydroxyectoine as nutrients. ueha, the esr of the uehabc operon, binds both ectoine and 5-hydroxyectoine with high affinity (k(d) values of 1.4+/-0.1 and 1.1+/-0.1 microm, respectively) and delivers them to the tra ...200919362561
genetic determinants of silicibacter sp. tm1040 motility.silicibacter sp. tm1040 is a member of the marine roseobacter clade of alphaproteobacteria that forms symbioses with unicellular eukaryotic phytoplankton, such as dinoflagellates. the symbiosis is complex and involves a series of steps that physiologically change highly motile bacteria into cells that readily form biofilms on the surface of the host. the initial phases of symbiosis require bacterial motility and chemotaxis that drive the swimming bacteria toward their planktonic host. cells lack ...200919482930
phylogenetic characterization of the heterotrophic bacterial communities inhabiting a marine recirculating aquaculture system.the aim of the present work was to characterize the heterotrophic bacterial community of a marine recirculating aquaculture system (ras).200919508294
genome sequences of two novel phages infecting marine roseobacters.two bacteriophages, dss3phi2 and ee36phi1, which infect marine roseobacters silicibacter pomeroyi dss-3 and sulfitobacter sp. ee-36, respectively, were isolated from baltimore inner harbor water. these two roseophages resemble bacteriophage n4, a large, short-tailed phage infecting escherichia coli k12, in terms of their morphology and genomic structure. the full genome sequences of dss3phi2 and ee36phi1 reveal that their genome sizes are 74.6 and 73.3 kb, respectively, and they both contain a h ...200919689706
analysis of the unique geothermal microbial ecosystem of the blue lagoon.cultivation and culture-independent techniques were used to describe the geothermal ecosystem of the blue lagoon in iceland. the lagoon contains both seawater and freshwater of geothermal origin and is extremely high in silica content. water samples were collected repeatedly in summer and autumn in 2003 and 2005 and in winter 2006 were analyzed for species composition. the study revealed the typical traits of an extreme ecosystem characterized by dominating species and other species represented ...200919709176
genetic diversity of 'satellite' bacteria present in cultures of marine diatoms.abstract uni-algal, non-axenic cultures of six marine diatoms were screened by polymerase chain reaction-denaturing gradient gel electrophoresis for the diversity of the accompanying bacterial communities ('satellite' bacteria) in order to test the hypothesis that algal cells constitute niches for specific bacterial species. the complexity of the satellite assemblages, as judged from the number of detected phylotypes, was low when compared to the complexity of bacterial assemblages in nature. ge ...200219709263
celeribacter neptunius gen. nov., sp. nov., a new member of the class alphaproteobacteria.a whitish gram-negative, motile, aerobic bacterium, designated strain h 14(t), was isolated from seawater collected at st kilda beach in port phillip bay, melbourne, australia. analysis of 16s rrna gene sequences revealed that the organism belonged to the roseobacter lineage of the class alphaproteobacteria, forming a distinct evolutionary lineage at the genus level. strain h 14(t) was distantly related to the genera nautella, ruegeria and pseudoruegeria (family rhodobacteraceae). strain h 14(t) ...201019717584
ruegeria pelagia is a later heterotypic synonym of ruegeria mobilis.the 16s rrna genes of ruegeria pelagia nbrc 102038t and ruegeria mobilis nbrc 101030t were resequenced and the results confirmed that they differ by only one base in their almost full-length sequences (1425 nt). the gyrb gene sequence similarity between the two strains was also high (97.7%). the outcome of api 20ne, api zym and antibiotic susceptibility tests showed that the two strains show only one difference, in beta-galactosidase activity, in api tests and five differences in susceptibility ...201019783609
antibacterial activity of marine culturable bacteria collected from a global sampling of ocean surface waters and surface swabs of marine organisms.the purpose of the present study was to isolate marine culturable bacteria with antibacterial activity and hence a potential biotechnological use. seawater samples (244) and 309 swab samples from biotic or abiotic surfaces were collected on a global danish marine research expedition (galathea 3). total cell counts at the seawater surface were 5 x 10(5) to 10(6) cells/ml, of which 0.1-0.2% were culturable on dilute marine agar (20 degrees c). three percent of the colonies cultured from seawater i ...201019823914
microbial diversity associated with algae, ascidians and sponges from the north coast of são paulo state, brazil.little is known about the microbial diversity associated with marine macroorganisms, despite the vital role microorganisms may play in marine ecosystems. the aim of the present study was to investigate the diversity of bacteria and fungi isolated from eight marine invertebrate and one algae samples. data derived from ardra and sequencing analyses allowed the identification of marine-derived microorganisms isolated from those samples. microbial strains identified up to the genus level revealed 14 ...201019879115
diversity of sulfur-oxidizing bacteria in greenwater system of coastal aquaculture.reduced sulfur compounds produced by the metabolism are the one of the major problems in aquaculture. in the present study, herbivorous fishes have been cultured as biomanipulators for secretions of slime, which enhanced the production of greenwater containing beneficial bacteria. the genes encoding soxb which is largely unique to sulfur-oxidizing bacteria (sob) due to its hydrolytic function has been targeted for examining the diversity of sob in the green water system of coastal aquaculture. n ...201020069462
selection of candidate probionts by two different screening strategies from atlantic cod (gadus morhua l.) larvae.two primary selection criteria were used to collect a pool of nearly 500 candidate probiotic bacteria from atlantic cod (gadus morhua l.) larvae, i.e. the dominant intestinal bacterial flora and isolates with antagonistic activity against vibrio anguillarum. bacteria were isolated from cod larvae from five rearing groups with variable rearing technologies. the bacteria were brought to pure culture and characterized phenotypically. based on properties such as uniqueness, dominance and fermentativ ...201020097491
ruegeria marina sp. nov., isolated from marine sediment.a gram-negative, neutrophilic and rod-shaped bacterium, strain zh17(t), was isolated from a marine sediment of the east china sea and subjected to a polyphasic taxonomic characterization. the isolate grew in the presence of 0-7.5 % (w/v) nacl and at ph 6.5-9.0; optimum growth was observed with 0.5-3.0 % (w/v) nacl and at ph 7.5. chemotaxonomic analysis showed ubiquinone-10 as predominant respiratory quinone and c(18 : 1)ω7c, 11-methyl c(18 : 1)ω7c, c(16 : 0), c(12 : 0) 3-oh and c(16 : 0) 2-oh as ...201120228209
ruegeria faecimaris sp. nov., isolated from a tidal flat sediment.a gram-negative-staining, non-motile and rod-shaped bacterial strain, hd-28(t), was isolated from a tidal flat of the yellow sea, korea. strain hd-28(t) grew optimally at ph 7.0-8.0 and 30 °c in the presence of 2-3 % (w/v) nacl. phylogenetic analyses based on 16s rrna gene sequences showed that strain hd-28(t) was most closely related to species of the genus ruegeria and exhibited 95.5-96.9 % 16s rrna gene sequence similarity to the type strains of ruegeria species. a neighbour-joining phylogene ...201120562248
expression of tropodithietic acid biosynthesis is controlled by a novel autoinducer.the interactions between marine prokaryotic and eukaryotic microorganisms are crucial to many biological and biogeochemical processes in the oceans. often the interactions are mutualistic, as in the symbiosis between phytoplankton, e.g., the dinoflagellate pfiesteria piscicida and silicibacter sp. tm1040, a member of the roseobacter taxonomic lineage. it is hypothesized that an important component of this symbiosis is bacterial production of tropodithietic acid (tda), a biologically active tropo ...201020601479
[effects of rice straw on the diversity of nitrifying genes (amoa and hao) in paddy soil].the effects of long-term (16 years) fertilization on the diversity and community structure of soil ammonia-oxidizing gene (amoa) and hydroxylamine-oxidizing gene (hao) in paddy soil were evaluated using the methods of polymerase chain reaction, cloning and sequencing. the soil samples were collected from the treatments of npk (ck) and npk plus rice straw (sr) of the long-term field fertilization experiment in taoyuan agro-ecological experimental station. the shannon indices showed that the diver ...201020698282
dddq, a novel, cupin-containing, dimethylsulfoniopropionate lyase in marine roseobacters and in uncultured marine bacteria.ruegeria (previously silicibacter) pomeroyi dss-3, a marine roseobacter, can catabolize dimethylsulfoniopropionate (dmsp), a compatible solute that is made in large amounts by marine plankton and algae. this strain was known to demethylate dmsp via a demethylase, encoded by the dmda gene, and it can also cleave dmsp, releasing the environmentally important volatile dimethyl sulfide (dms) in the process. we found that this strain has two different genes, dddp and dddq, which encode enzymes that c ...201020880330
temperature induced bacterial virulence and bleaching disease in a chemically defended marine macroalga.host-pathogen interactions have been widely studied in humans and terrestrial plants, but are much less well explored in marine systems. here we show that a marine macroalga, delisea pulchra, utilizes a chemical defence - furanones - to inhibit colonization and infection by a novel bacterial pathogen, ruegeria sp. r11, and that infection by r11 is temperature dependent. ruegeria sp. r11 formed biofilms, invaded and bleached furanone-free, but not furanone-producing d. pulchra thalli, at high (24 ...201020946533
in-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: the ruegeria pomeroyi dss-3 case-study.microorganisms secrete into their extracellular environment numerous compounds that are required for their survival. many of these compounds could be of great interest for biotechnology applications and their genes used in synthetic biology design. the secreted proteins and the components of the translocation systems themselves can be scrutinized in-depth by the most recent proteomic tools. while the secretomes of pathogens are well-documented, those of non-pathogens remain largely to be establi ...201020948905
simplified bacterial "pore" channel provides insight into the assembly, stability, and structure of sodium channels.eukaryotic sodium channels are important membrane proteins involved in ion permeation, homeostasis, and electrical signaling. they are long, multidomain proteins that do not express well in heterologous systems, and hence, structure/function and biochemical studies on purified sodium channel proteins have been limited. bacteria produce smaller, homologous tetrameric single domain channels specific for the conductance of sodium ions. they consist of n-terminal voltage sensor and c-terminal pore s ...201121454659
ruegeria scottomollicae sp. nov., isolated from a marine electroactive biofilm.seventy isolates were obtained from a marine electroactive biofilm that was generated on a cathodically polarized stainless steel electrode (genoa, italy). the genetic diversity was investigated by means of box-pcr fingerprinting and two clusters of isolates with similar box-pcr profiles were delineated. whole-cell fatty acid methyl ester analysis and 16s rrna gene sequence analysis showed that the isolates belonged to the roseobacter lineage of the class alphaproteobacteria. dna-dna hybridizati ...200819060048
new alk genes detected in antarctic marine sediments.alkane monooxygenases (alk) are the key enzymes for alkane degradation. in order to understand the dispersion and diversity of alk genes in antarctic marine environments, this study analysed by clone libraries the presence and diversity of alk genes (alkb and alkm) in sediments from admiralty bay, king george island, peninsula antarctica. the results show a differential distribution of alk genes between the sites, and the predominant presence of new alk genes, mainly in the pristine site. sequen ...200919207566
the alkaline phosphatase phox is more widely distributed in marine bacteria than the classical phoa.phosphorus (p) is a vital nutrient for all living organisms and may control the growth of bacteria in the ocean. bacteria induce alkaline phosphatases when inorganic phosphate (p(i)) is insufficient to meet their p-requirements, and therefore bulk alkaline phosphatase activity measurements have been used to assess the p-status of microbial assemblages. in this study, the molecular basis of marine bacterial phosphatases and their potential role in the environment were investigated. we found that ...200919212430
ruegeria halocynthiae sp. nov., isolated from sea squirt halocynthia roretzi.a gram-negative, non-motile, and rod-shaped bacterial strain, ma1-6(t), which was isolated from a sea squirt (halocynthia roretzi) collected from the south sea, korea, was characterised here taxonomically. strain ma1-6(t) grew optimally at ph 7.0-8.0, at 30 ┬░c and in presence of 2-3 % (w/v) nacl. phylogenetic analysis based on 16s rrna gene sequences showed that strain ma1-6(t) fell within the clade comprising ruegeria species and exhibited 95.3-96.5 % 16s rrna gene sequence similarity to the t ...201121669923
genome sequence of ruegeria sp. strain klh11, an n-acylhomoserine lactone-producing bacterium isolated from the marine sponge mycale laxissima.ruegeria sp. strain klh11, isolated from the marine sponge mycale laxissima, produces a complex profile of n-acylhomoserine lactone quorum-sensing (qs) molecules. the genome sequence provides insights into the genetic potential of klh11 to maintain complex qs systems, and this is the first genome report of a cultivated symbiont from a marine sponge.201121742885
dddw, a third dmsp lyase in a model roseobacter marine bacterium, ruegeria pomeroyi dss-3.ruegeria pomeroyi dss-3 is a model roseobacter marine bacterium, particularly regarding its catabolism of dimethylsulfoniopropionate (dmsp), an abundant anti-stress molecule made by marine phytoplankton. we found a novel gene, dddw, which encodes a dmsp lyase that cleaves dmsp into acrylate plus the environmentally important volatile dimethyl sulfide (dms). mutations in dddw reduced, but did not abolish dms production. transcription of dddw was greatly enhanced by pre-growth of cells with dmsp, ...201121677693
effects of stimulation of copper bioleaching on microbial community in vineyard soil and copper mining waste.long-term copper application in vineyards and copper mining activities cause heavy metal pollution sites. such sites need remediation to protect soil and water quality. bioremediation of contaminated areas through bioleaching can help to remove copper ions from the contaminated soils. thus, the aim of this work was to evaluate the effects of different treatments for copper bioleaching in two diverse copper-contaminated soils (a 40-year-old vineyard and a copper mining waste) and to evaluate the ...201121947860
Tropodithietic acid production in Phaeobacter gallaeciensis is regulated by N-acyl homoserine lactone-mediated quorum sensing.The production of N-acyl homoserine lactones (AHLs) is widely distributed within the marine Roseobacter clade, and it was proposed that AHL-mediated quorum sensing (QS) is one of the most common cell-to-cell communication mechanisms in roseobacters. The traits regulated by AHL-mediated QS are yet not known for members of the Roseobacter clade, but production of the antibiotic tropodithietic acid (TDA) was supposed to be controlled by AHL-mediated QS in Phaeobacter spp. We describe here for the f ...201121949069
Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies amongst these marine bacteria.Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically-encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the e ...201122122883
novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria.dimethylsulphoniopropionate (dmsp) accounts for up to 10% of carbon fixed by marine phytoplankton in ocean surface waters, producing an estimated 11.7-103 tmol s per year, most of which is processed by marine bacteria through the demethylation/demethiolation pathway. this pathway releases methanethiol (mesh) instead of the climatically active gas dimethylsulphide (dms) and enables marine microorganisms to assimilate the reduced sulphur. despite recognition of this critical microbial transformati ...201121562561
tdaa regulates tropodithietic acid synthesis by binding to the tdac promoter region.silicibacter sp. tm1040, a member of the marine roseobacter clade, produces the antibiotic and quorum signaling molecule tropodithietic acid (tda), encoded by tdaabcdef. here we showed that a lysr-type transcriptional regulator, tdaa, is a positive regulator of tdacde gene expression and binds to the tdac promoter region.201121622742
voltage-gated sodium channel (nav) protein dissection creates a set of functional pore-only proteins.many voltage-gated ion channel (vgic) superfamily members contain six-transmembrane segments in which the first four form a voltage-sensing domain (vsd) and the last two form the pore domain (pd). studies of potassium channels from the vgic superfamily together with identification of voltage-sensor only proteins have suggested that the vsd and the pd can fold independently. whether such transmembrane modularity is common to other vgic superfamily members has remained untested. here we show, usin ...201121746903
proteomic insights into the lifestyle of an environmentally relevant marine bacterium.in terms of lifestyle, free-living bacteria are classified as either oligotrophic/specialist or opportunist/generalist. heterogeneous marine environments such as coastal waters favour the establishment of marine generalist bacteria, which code for a large pool of functions. this is basically foreseen to cope with the heterogeneity of organic matter supplied to these systems. nevertheless, it is not known what fraction of a generalist proteome is needed for house-keeping functions or what fractio ...201121776030
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