| phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, loihi seamount, hawaii. | the phylogenetic diversity of small-subunit rrna genes associated with the domain bacteria was examined (by using previously defined operational taxonomic units [c. l. moyer, f.c. dobbs, and d. m. karl, appl. environ. microbiol. 60:871-879, 1994]; those for pele's vents bacteria are hereafter abbreviated pvb otus) with samples from a microbial mat at an active, deep-sea hydrothermal vent system. a cluster of phylogenetically related pvb otus (otus 2, 3, 6, and 8) was closely affiliated with thio ... | 1995 | 7538279 |
| diversity and association of psychrophilic bacteria in antarctic sea ice. | the bacterial populations associated with sea ice sampled from antarctic coastal areas were investigated by use of a phenotypic approach and a phylogenetic approach based on genes encoding 16s rrna (16s rdna). the diversity of bacteria associated with sea ice was also compared with the bacterial diversity of seawater underlying sea ice. psychrophilic (optimal growth temperature, < or = 15 degrees c; no growth occurring at 20 degrees c) bacterial diversity was found to be significantly enriched i ... | 1997 | 9251193 |
| genetic diversity of the biofilm covering montacuta ferruginosa (mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of pcr-amplified gene fragments coding for 16s rrna. | the shell of the bivalve montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. this biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. the aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their ... | 1998 | 9726898 |
| assignment of vibrio sp. strain abe-1 to colwellia maris sp. nov., a new psychrophilic bacterium. | a psychrophilic bacterium, previously described as vibrio sp. strain abe-1t, has been reassigned by phenotypic characterization, chemotaxonomic analysis and 16s rrna phylogenetic analysis. the organism was curved rods and it could reduce nitrate to nitrite and hydrolyse gelatin and dna, but not chitin. nacl was required for growth. this strain was susceptible to the vibriostatic compound o/129. the major isoprenoid quinone was ubiquinone-8 and the dna g + c content was 39.4 mol%. the whole-cell ... | 1998 | 9828437 |
| idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the pacific ocean, including descriptions of two species, idiomarina abyssalis sp. nov. and idiomarina zobellii sp. nov. | two bacterial strains, kmm 227t and 231t, were isolated from seawater samples collected from the north-western pacific ocean at a depth of 4000-5000 m and were characterized using polyphasic taxonomy. both were gram-negative, psychrotolerant, heterotrophic, aerobic and required nacl for growth (0.6-15.0%). the temperature for growth was 4-30 degrees c. both strains were rod-shaped, with a single flagellum. however, strain kmm 231t revealed a single long fimbrium. cellular fatty acids detected in ... | 2000 | 10758902 |
| succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts. | enrichment experiments with north sea bacterioplankton were performed to test if rapid incubation-induced changes in community structure explain the frequent isolation of members of a few particular bacterial lineages or if readily culturable bacteria are common in the plankton but in a state of dormancy. a metabolic inhibitor of cell division (nalidixic acid [na]) was added to substrate-amended (s+) and unamended (s-) grazer-free seawater samples, and shifts in community composition and per cel ... | 2000 | 11055904 |
| [a new family of alteromonadaceae fam. nov., including the marine proteobacteria species alteromonas, pseudoalteromonas, idiomarina i colwellia]. | the taxonomic position of the marine genera alteromonas, pseudoalteromonas, idiomarina, and colwellia within the gamma subclass of the class proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. gram-negative aerobic bacteria of the genera alteromonas, pseudoalteromonas, and idiomarina and facultatively anaerobic bacteria of the genus colwellia were found to form a phylogenetic cluster with a 16s rrna sequence homology of 90% or higher. the ... | 2001 | 11338830 |
| purification and characterization of a cold-adapted isocitrate lyase and a malate synthase from colwellia maris, a psychrophilic bacterium. | isocitrate lyase (icl) and malate synthase (ms) of a psychrophilic marine bacterium, colwellia maris, were purified to electrophoretically homogeneous state. the molecular mass of the icl was found to be 240 kda, composed of four identical subunits of 64.7 kda. ms was a dimeric enzyme composed of 76.3 kda subunits. n-terminal amino acid sequences of the icl and ms were analyzed. purified icl had its maximum activity at 20 degrees c and was rapidly inactivated at the temperatures above 30 degrees ... | 2001 | 11440123 |
| thalassomonas viridans gen. nov., sp. nov., a novel marine gamma-proteobacterium. | a new genus and species are proposed for two halophilic, strictly aerobic, chemo-organotrophic, marine bacterial strains. these bacteria are gram-negative, motile rods isolated from oysters cultivated off the mediterranean coast at valencia (spain). they produce green/blue-green diffusible pigment. the g+c content of the dna of the proposed type strain (xom25t) is 48.4 mol %. a 16s rrna gene sequence analysis of the two strains has shown that the new isolates represent a branch within the gamma- ... | 2001 | 11491324 |
| phylogenetic diversity of numerically important arctic sea-ice bacteria cultured at subzero temperature. | heterotrophic bacteria in sea ice play a key role in carbon cycling, but little is known about the predominant players at the phylogenetic level. in a study of both algal bands and clear ice habitats within summertime arctic pack ice from the chukchi sea, we determined the abundance of total bacteria and actively respiring cells in melted ice samples using epifluorescence microscopy and the stains 4', 6'-diamidino-2-phenylindole 2hcl (dapi) and 5-cyano-2,3-ditolyl tetrazolium chloride (ctc), res ... | 2002 | 12037610 |
| the cold-inducible icl gene encoding thermolabile isocitrate lyase of a psychrophilic bacterium, colwellia maris. | the gene encoding isocitrate lyase (icl; ec 4.1.3.1) of a psychrophilic bacterium, colwellia maris, was cloned and sequenced. the orf of the gene (icl) was 1584 bp long, and the predicted gene product consisted of 528 aa (molecular mass 58150 da) and showed low homology with the corresponding enzymes from other organisms. the analyses of amino acid content and primary structure of the c. maris icl suggested that it possessed many features of a cold-adapted enzyme. primer extension and northern b ... | 2002 | 12177352 |
| purification and characterization of a cold-adapted isocitrate lyase and expression analysis of the cold-inducible isocitrate lyase gene from the psychrophilic bacterium colwellia psychrerythraea. | isocitrate lyase (icl) from colwellia psychrerythraea, a psychrophilic bacterium, was purified and characterized. the subunit molecular mass was 64 kda, which is larger than that of other bacterial icls. the optimal temperature for its activity was 25 degrees c, the value of k(m) for the substrate ( dl-isocitrate) was minimum at 15 degrees c, and the catalytic efficiency ( k(cat)/ k(m)) value was maximum at 20 degrees c. furthermore, the enzyme was remarkably thermolabile and completely inactiva ... | 2002 | 12382116 |
| isolation and characterization of marine psychrophilic phage-host systems from arctic sea ice. | phage-host systems from extreme cold environments have rarely been surveyed. this study is concerned with the isolation and characterization of three different phage-host systems from arctic sea ice and melt pond samples collected north-west of svalbard (arctic). on the basis of 16s rdna sequences, the three bacterial phage hosts exhibited the greatest similarity to the species shewanella frigidimarina (96.0%), flavobacterium hibernum (94.0%), and colwellia psychrerythraea (98.4%), respectively. ... | 2003 | 12820036 |
| motility of colwellia psychrerythraea strain 34h at subzero temperatures. | we examined the arctic bacterium colwellia psychrerythraea strain 34h for motility at temperatures from -1 to -15 degrees c by using transmitted-light microscopy in a temperature-controlled laboratory. the results, showing motility to -10 degrees c, indicate much lower temperatures to be permissive of motility than previously reported (5 degrees c), with implications for microbial activity in frozen environments. | 2003 | 12839815 |
| gene structure and transcriptional regulation specific to the groesl operon from the psychrophilic bacterium colwellia maris. | the groesl operon of a psychrophilic bacterium, colwellia maris, was cloned and sequenced. the operon contains two orfs of 291 bp and 1,650 bp separated by 210 bp. northern blot analysis suggested that the groesl operon was transcribed as a bicistronic mrna, and that the amount of mrna markedly increased after the temperature was raised from 10 degrees c to 20 degrees c. although the optimum temperatures for groesl function are different in psychrophilic, mesophilic, and thermophilic bacteria, t ... | 2003 | 12898133 |
| thalassomonas ganghwensis sp. nov., isolated from tidal flat sediment. | a gram-negative, aerobic, halophilic bacterium, designated strain jc2041(t), was isolated from a sediment sample of getbol, the korean tidal flat. results of 16s rdna sequence analyses indicated a moderate relationship to thalassomonas viridans within the gamma-proteobacteria (94.9 % similarity). depending on the tree-making algorithm used, the isolate either formed a monophyletic clade with t. viridans or was recovered as a sister group of a class containing the genera thalassomonas and colwell ... | 2004 | 15023946 |
| characterization of chimeric isocitrate dehydrogenases of a mesophilic nitrogen-fixing bacterium, azotobacter vinelandii, and a psychrophilic bacterium, colwellia maris. | several properties of chimeric enzymes between a mesophilic isocitrate dehydrogenase (idh) from a nitrogen-fixing bacterium, azotobacter vinelandii, and a cold-adapted idh isozyme (idh-ii) from a psychrophilic bacterium, colwellia maris, were examined. each of the genes encoding the idhs was divided into four regions of almost equal lengths, and each region was ligated with different combinations to construct various chimeric genes. the resultant wild-type and chimeric genes were overexpressed i ... | 2004 | 15060737 |
| gene structure and transcriptional regulation of dnak and dnaj genes from a psychrophilic bacterium, colwellia maris. | the dnak and dnaj genes, encoding heat shock proteins, were cloned from a psychrophilic bacterium, colwellia maris. significant homology was evident comparing dnak and dnaj of the psychrophilile with the counterparts of mesophilic and thermophilic bacteria. in the dnaj protein, three conserved regions of the hsp40 family were observed. a putative promoter similar to the sigma32 consensus sequence was found upstream of the dnak gene. the g+c content in the 5'-untranslated region of the dnak gene ... | 2004 | 15085417 |
| design of 16s rrna-targeted oligonucleotide probes and microbial community analysis in the denitrification process of a saline industrial wastewater treatment system. | three 16s rrna-targeted oligonucleotide probes, namely, psmg437 targeting several members of the genus pseudomonas, hlm474 targeting several members of the genus halomonas, and clw844 targeting several members of the genus colwellia, were designed. the microbial community structure and nitrogen removal ability of nitrate-containing saline wastewater treatment systems with anaerobic packed bed and fluidized bed were monitored. direct cell counting using fluorescence in situ hybridization (fish) i ... | 2004 | 15158280 |
| purification, characterization, and sequencing of an extracellular cold-active aminopeptidase produced by marine psychrophile colwellia psychrerythraea strain 34h. | the limited database on cold-active extracellular proteases from marine bacteria was expanded by successful purification and initial biochemical and structural characterization of a family m1 aminopeptidase (designated colap) produced by the marine psychrophile colwellia psychrerythraea strain 34h. the 71-kda enzyme displayed a low optimum temperature (19 degrees c) and narrow ph range (ph 6 to 8.5) for activity and greater thermolability than other extracellular proteases. sequencing of the gen ... | 2004 | 15184127 |
| colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the japan trench. | two strains of obligately piezophilic bacteria were isolated from sediment collected from the bottom surface of a small canyon on the seaward slope of the japan trench at a depth of 6278 m. the isolated strains, y223gt and y251e, are closely affiliated with members of the genus colwellia on the basis of 16s rrna gene sequence analysis. the g + c contents of both strains were about 39 mol%. dna-dna hybridization values between these strains and colwellia reference strains were significantly lower ... | 2004 | 15388720 |
| phylogenetic relationships among marine alteromonas-like proteobacteria: emended description of the family alteromonadaceae and proposal of pseudoalteromonadaceae fam. nov., colwelliaceae fam. nov., shewanellaceae fam. nov., moritellaceae fam. nov., ferrimonadaceae fam. nov., idiomarinaceae fam. nov. and psychromonadaceae fam. nov. | the phylogenetic relationships among marine alteromonas-like bacteria of the genera alteromonas, pseudoalteromonas, glaciecola, thalassomonas, colwellia, idiomarina, oceanimonas, oceanisphaera, shewanella, moritella, ferrimonas, psychromonas and several other genera of the 'gammaproteobacteria' were studied. results of 16s rrna gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. characteristic signature oligonucleotides for studie ... | 2004 | 15388743 |
| amino acid residues involved in cold adaptation of isocitrate lyase from a psychrophilic bacterium, colwellia maris. | to investigate the mechanism of cold adaptation of isocitrate lyase (icl; ec 4.1.3.1) from the psychrophilic bacterium colwellia maris, gln207 and gln217 of this enzyme were substituted by his and lys, respectively, by site-directed mutagenesis. his184 and lys194 of icl from escherichia coli, corresponding to the two gln residues of c. maris icl, are highly conserved in the icls of many organisms and are known to be essential for catalytic function. the mutated icls (cm-q207h and cm-q217k, respe ... | 2004 | 15470117 |
| widespread presence of "bacterial-like" ppp phosphatases in eukaryotes. | in eukaryotes, ppp (protein phosphatase p) family is one of the two known protein phosphatase families specific for ser and thr. the role of ppp phosphatases in multiple signaling pathways in eukaryotic cell has been extensively studied. unlike eukaryotic ppp phosphatases, bacterial members of the family have broad substrate specificity or may even be tyr-specific. moreover, one group of bacterial ppps are diadenosine tetraphosphatases, indicating that bacterial ppp phosphatases may not necessar ... | 2004 | 15555063 |
| rapid screening and dereplication of bacterial isolates from marine sponges of the sula ridge by intact-cell-maldi-tof mass spectrometry (icm-ms). | rapid grouping of bacterial isolates is critical in comprehensive microbial studies of environmental samples or screening programmes e.g. in unknown marine environments where large numbers of strains have to be isolated on different growth media. sets of bacteria have been cultured from the marine sponges isops phlegraei, haliclona sp. 1, phakellia ventilabrum and plakortis sp. growing at a depth of about 300 m on the sula ridge close to the norwegian coast. we employed intact-cell maldi-tof (ic ... | 2004 | 15614563 |
| incorporation of glucose under anoxic conditions by bacterioplankton from coastal north sea surface waters. | it has been hypothesized that the potential for anaerobic metabolism might be a common feature of bacteria in coastal marine waters (l. riemann and f. azam, appl. environ. microbiol. 68: 5554-5562, 2002). therefore, we investigated whether different phylogenetic groups of heterotrophic picoplankton from the coastal north sea were able to take up a simple carbon source under anoxic conditions. oxic and anoxic incubations (4 h) or enrichments (24 h) of seawater with radiolabeled glucose were perfo ... | 2005 | 15811993 |
| elucidation of stability determinants of cold-adapted monomeric isocitrate dehydrogenase from a psychrophilic bacterium, colwellia maris, by construction of chimeric enzymes. | to elucidate determinants of differences in thermostability between mesophilic and psychrophilic monomeric isocitrate dehydrogenases (idhs) from azotobacter vinelandii (avidh) and colwellia maris (cmidh), respectively, chimeric enzymes derived from the two idhs were constructed based on the recently resolved three-dimensional structure of avidh, and several characteristics of the two wild-type and six chimeric idhs were examined. these characteristics were then compared with those of dimeric idh ... | 2005 | 15817777 |
| the psychrophilic lifestyle as revealed by the genome sequence of colwellia psychrerythraea 34h through genomic and proteomic analyses. | the completion of the 5,373,180-bp genome sequence of the marine psychrophilic bacterium colwellia psychrerythraea 34h, a model for the study of life in permanently cold environments, reveals capabilities important to carbon and nutrient cycling, bioremediation, production of secondary metabolites, and cold-adapted enzymes. from a genomic perspective, cold adaptation is suggested in several broad categories involving changes to the cell membrane fluidity, uptake and synthesis of compounds confer ... | 2005 | 16043709 |
| purification and characterization of an extracellular cold-active serine protease from the psychrophilic bacterium colwellia sp. nj341. | colwellia sp. nj341, isolated from antarctic sea ice, secreted a cold-active serine protease. the purified protease had an apparent mr of 60 kda by sds-page and maldi-tof ms. it was active from ph 5-12 with maximum activity at 35 degrees c (assayed over 10 min). activity at 0 degrees c was nearly 30% of the maximum activity. it was completely inhibited by phenylmethylsulfonyl fluoride. | 2005 | 16158263 |
| the rpoh gene encoding heat shock sigma factor sigma32 of psychrophilic bacterium colwellia maris. | the rpoh gene encoding a heat shock sigma factor, sigma(32), was cloned from the psychrophilic bacterium colwellia maris. the deduced amino acid sequence of sigma(32) from c. maris is more than 60% homologous to that of sigma(32) from mesophilic bacteria. the rpoh box, a 9-amino-acid sequence region (qrklffnlr) specific to sigma(32), and two downstream box sequences complementary to a part of 16s rrna were identified. primer extension analysis showed that the c. maris rpoh is expressed from only ... | 2006 | 16362517 |
| colwellia aestuarii sp. nov., isolated from a tidal flat sediment in korea. | a novel colwellia-like bacterial strain, smk-10t, was isolated from a tidal flat sediment in korea and subjected to a polyphasic taxonomic analysis. cells of strain smk-10t were gram-negative, motile, greyish yellow-pigmented, curved rods. optimal growth occurred at 25-30 degrees c and in the presence of 2-3 % (w/v) nacl. strain smk-10t contained q-8 as the predominant ubiquinone and c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh, c(17 : 1), c(15 : 1) and iso-c(16 : 0) as major fatty acids. the dna ... | 2006 | 16403863 |
| two isocitrate dehydrogenases from a psychrophilic bacterium, colwellia psychrerythraea. | two structurally different monomeric and dimeric types of isocitrate dehydrogenase (idh; ec 1.1.1.42) isozymes were confirmed to exist in a psychrophilic bacterium, colwellia psychrerythraea, by western blot analysis and the genes encoding them were cloned and sequenced. open reading frames of the genes (icd-m and icd-d) encoding the monomeric and dimeric idhs of this bacterium, idh-m and idh-d, were 2,232 and 1,251 bp in length and corresponded to polypeptides composed of 743 and 416 amino acid ... | 2006 | 16418792 |
| evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. | evolutionary relationships of cultivated barophilic bacteria were determined. all psychrophilic and barophilic isolates were affiliated with one of five genera of the gamma subdivision of the class proteobacteria ((gamma)-proteobacteria): shewanella, photobacterium, colwellia, moritella, and a new group containing strain cnpt3. the data indicate that the barophilic phenotype has evolved independently in different (gamma)-proteobacteria genera. | 1997 | 16535621 |
| bacterial incorporation of leucine into protein down to -20 degrees c with evidence for potential activity in sub-eutectic saline ice formations. | direct evidence for metabolism in a variety of frozen environments has pushed temperature limits for bacterial activity to increasingly lower temperatures, so far to -20 degrees c. to date, the metabolic activities of marine psychrophilic bacteria, important components of sea-ice communities, have not been studied in laboratory culture, not in ice and not below -12 degrees c. we measured [3h]-leucine incorporation into macromolecules (further fractionated biochemically) by the marine psychrophil ... | 2006 | 16647051 |
| [phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, artic]. | the phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'n - 81 degrees 12'n), canadian basin and greenland sea arctic, was investigated. a total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microl of each dilution ice-melt sample was spreaded onto the surface of marine 2216 agar (difco laboratories, detroit, mi) and incubated for 2 to 6 weeks at 4 degrees c; ( ii ) b ... | 2006 | 16736573 |
| distribution and genetic diversity of bacterial thiopurine methyltransferases in soils emitting dimethyl selenide. | dimethyl selenide (dmse) and dimethyl diselenide (dmdse) emissions by soil samples spiked with selenite or (methyl)selenocysteine, with or without a supplement of nutrient broth and glucose were measured. dmse was the main form of volatile se produced, and was observed for both se-substrates. dmdse was only emitted from soils spiked with (methyl)selenocysteine. two bacterial thiopurine methyltransferases (tpmts), tpmt-i and tpmt-e, have been reported to be involved in dmse and dmdse emissions [j ... | 2006 | 17007990 |
| predominance of roseobacter, sulfitobacter, glaciecola and psychrobacter in seawater collected off ushuaia, argentina, sub-antarctica. | bacterial diversity in sub-antarctic seawater, collected off ushuaia, argentina, was examined using a culture independent approach. the composition of the 16s rrna gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (p value 0.001). in both libraries, clones representing the alphaproteobacteria, gammaproteobacteria, the cytophaga-flavobacterium-bacteroidetes group and unculturable bacteria were dominant. clones associate ... | 2007 | 17026513 |
| plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. | tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ... | 2007 | 17311090 |
| identification of the acea gene encoding isocitrate lyase required for the growth of pseudomonas aeruginosa on acetate, acyclic terpenes and leucine. | pseudomonas aeruginosa pao1 mutants affected in acyclic monoterpenes, n-octanol, and acetate assimilation were isolated using transposon mutagenesis. the isocitrate lyase gene (acea) corresponding to orf pa2634 of the pao1 strain genome was identified in one of these mutants. the acea gene encodes a protein that is 72% identical to the isocitrate lyase (icl) characterized from colwellia maris, but is less than 30% identical to their homologues from pseudomonads. the genetic arrangement of acea s ... | 2007 | 17319879 |
| diversity and enzyme properties of protease-producing bacteria isolated from sub-antarctic sediments of isla de los estados, argentina. | protease-producing bacteria isolated from sub-antarctic marine sediments of isla de los estados (argentina) were characterized, and the thermal inactivation kinetics of their extracellular proteases compared. isolates were affiliated with the genera pseudoalteromonas, shewanella, colwellia, planococcus, and a strain to the family flavobacteriaceae. colwellia strains were moderate psychrophiles (optimal growth at about 15 degrees c, maximum growth temperature at around 25 degrees c). 16s rrna phy ... | 2007 | 17487446 |
| optimization of cold-active protease production by the psychrophilic bacterium colwellia sp. nj341 with response surface methodology. | culture conditions were optimized for an extracellular cold-active protease production by the psychrophilic bacterium colwellia sp. nj341. response surface methodology was applied for the most significant fermentation parameters (casein, citrate sodium, temperature and tween-80) identified earlier by one-factor-at-a-time approach. a 2(4) full factorial central composite design was employed to determine the maximum protease production. using this methodology, the quadratic regression model of pro ... | 2008 | 17499500 |
| structure of phenylalanine hydroxylase from colwellia psychrerythraea 34h, a monomeric cold active enzyme with local flexibility around the active site and high overall stability. | the characteristic of cold-adapted enzymes, high catalytic efficiency at low temperatures, is often associated with low thermostability and high flexibility. in this context, we analyzed the catalytic properties and solved the crystal structure of phenylalanine hydroxylase from the psychrophilic bacterium colwellia psychrerythraea 34h (cppah). cppah displays highest activity with tetrahydrobiopterin (bh(4)) as cofactor and at 25 degrees c (15 degrees c above the optimal growth temperature). alth ... | 2007 | 17537732 |
| an ice-binding protein from an antarctic sea ice bacterium. | an antarctic sea ice bacterium of the gram-negative genus colwellia, strain slw05, produces an extracellular substance that changes the morphology of growing ice. the active substance was identified as a approximately 25-kda protein that was purified through its affinity for ice. the full gene sequence was determined and was found to encode a 253-amino acid protein with a calculated molecular mass of 26,350 da. the predicted amino acid sequence is similar to predicted sequences of ice-binding pr ... | 2007 | 17651136 |
| responses of microbial communities in arctic sea ice after contamination by crude petroleum oil. | microbial communities associated with arctic fjord ice polluted with petroleum oils were investigated in this study. a winter field experiment was conducted in the van mijen fjord (svalbard) from february to june 2004, in which the ice was contaminated with a north sea paraffinic oil. holes were drilled in the ice and oil samples frozen into the ice at the start of the experiment. samples, including cores of both oil-contaminated and clean ice, were collected from the field site 33, 74, and 112 ... | 2008 | 17805918 |
| gene cloning of cold-adapted isocitrate lyase from a psychrophilic bacterium, colwellia psychrerythraea, and analysis of amino acid residues involved in cold adaptation of this enzyme. | the gene (icl) encoding cold-adapted isocitrate lyase (icl) of a psychrophilic bacterium, colwellia psychrerythraea, was cloned and sequenced. open reading frame of the gene was 1,587 bp in length and corresponded to a polypeptide composed of 528 amino acids. the deduced amino acid sequence showed high homology with that of cold-adapted icl from other psychrophilic bacterium, c. maris (88% identity), but the sequential homology with that of the escherichia coli icl was low (28% identity). primer ... | 2008 | 17965824 |
| impact of nitrate on the structure and function of bacterial biofilm communities in pipelines used for injection of seawater into oil fields. | we studied the impact of no(3)(-) on the bacterial community composition, diversity, and function in in situ industrial, anaerobic biofilms by combining microsensor profiling, (15)n and (35)s labeling, and 16s rrna gene-based fingerprinting. biofilms were grown on carbon steel coupons within a system designed to treat seawater for injection into an oil field for pressurized oil recovery. no(3)(-) was added to the seawater in an attempt to prevent bacterial h(2)s generation and microbially influe ... | 2008 | 18344353 |
| crystal structure of the cold-active aminopeptidase from colwellia psychrerythraea, a close structural homologue of the human bifunctional leukotriene a4 hydrolase. | the crystal structure of a cold-active aminopeptidase (colap) from colwellia psychrerythraea strain 34h has been determined, extending the number of crystal structures of the m1 metallopeptidase family to four among the 436 members currently identified. in agreement with their sequence similarity, the overall structure of colap displayed a high correspondence with leukotriene a4 hydrolase (lta4h), a human bifunctional enzyme that converts leukotriene a4 (lta4) in the potent chemoattractant leuko ... | 2008 | 18539590 |
| epiphytic bacteria on the antarctic ice diatom amphiprora kufferathii manguin cleave hydrogen peroxide produced during algal photosynthesis. | the antarctic ice diatom amphiprora kufferathii manguin is always accompanied by epiphytic bacteria in its natural habitat. to investigate the nature of this relationship, axenic cultures of a. kufferathii were obtained by ampicillin treatment. diatom cultures without bacteria were less dense. the bacteria were shown to consume hydrogen peroxide produced by the diatom during photosysnthesis and algal photosynthesis after a hydrogen peroxide shock recovered faster in the presence of bacteria. thr ... | 2008 | 18557912 |
| cold adaptation of enzymes: structural, kinetic and microcalorimetric characterizations of an aminopeptidase from the arctic psychrophile colwellia psychrerythraea and of human leukotriene a(4) hydrolase. | the relationships between structure, activity, stability and flexibility of a cold-adapted aminopeptidase produced by a psychrophilic marine bacterium have been investigated in comparison with a mesophilic structural and functional human homolog. differential scanning calorimetry, fluorescence monitoring of thermal- and guanidine hydrochloride-induced unfolding and fluorescence quenching were used to show that the cold-adapted enzyme is characterized by a high activity at low temperatures, a low ... | 2008 | 18599387 |
| colwellia polaris sp. nov., a psychrotolerant bacterium isolated from arctic sea ice. | a novel psychrotolerant, gram-negative, aerobic bacterium, designated strain 537t, was isolated from sea-ice samples from the arctic. strain 537t was able to grow at 4-26 degrees c, with optimum growth occurring at 20-21 degrees c. strain 537t had q-8 as the major respiratory quinone and contained iso-c15:0 2-oh and/or c16:1 omega7c (22.95 %), c15:1 (17.64 %) and c17:1 omega8c (13.74 %) as the predominant cellular fatty acids. the genomic dna g+c content was 38.9 mol%. a phylogenetic analysis ba ... | 2008 | 18676483 |
| production of cryoprotectant extracellular polysaccharide substances (eps) by the marine psychrophilic bacterium colwellia psychrerythraea strain 34h under extreme conditions. | extracellular polysaccharide substances (eps) play critical roles in microbial ecology, including the colonization of extreme environments in the ocean, from sea ice to the deep sea. after first developing a sugar-free growth medium, we examined the relative effects of temperature, pressure, and salinity on eps production (on a per cell basis) by the obligately marine and psychrophilic gamma-proteobacterium, colwellia psychrerythraea strain 34h. over growth-permissive temperatures of approximate ... | 2009 | 19190702 |
| the nonrandom microheterogeneity of 16s rrna genes in vibrio splendidus may reflect adaptation to versatile lifestyles. | 16s rrna molecules in a microbial strain can differ due to nucleotide variation between their genes. this is a typical trait of fast-growing bacteria to cope with different niches. we investigated characteristics of 16s rrna genes in vibrio splendidus strain pb1-10, from the normal flora of atlantic halibut. sequencing of 16s rrna gene clones detected 35 variable positions in a total of 13 different gene copies. more than two-thirds of the substitutions occurred in regions corresponding to helix ... | 2009 | 19341395 |
| colwellia asteriadis sp. nov., a marine bacterium isolated from the starfish asterias amurensis. | a marine bacterial strain, kmd 002t, was isolated from an amur starfish, asterias amurensis, collected in the east sea of korea. strain kmd 002t was a gram-negative, beige-pigmented, rod-shaped bacterium. the strain was capable of growth at relatively low temperatures (4-25 degrees c) and over a broad ph range (ph 4.0-10.0). the major fatty acids were c16:1omega7c and/or iso-c15:0 2-oh and c16:0 and the predominant isoprenoid quinone was q-8. the dna g+c content of strain kmd 002t was 40.3 mol%. ... | 2010 | 19801395 |
| bacterial diversity in water injection systems of brazilian offshore oil platforms. | biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in brazil. to achieve this goal, we used a cul ... | 2010 | 19830416 |
| cold adaptation in dead-box proteins. | spontaneous rearrangements of rna structures are usually characterized by large activation energies and thus become very slow at low temperatures, yet rna structure must remain dynamic even in cold-adapted (psychrophilic) organisms. dead-box proteins constitute a ubiquitous family of rna-dependent atpases that can often unwind short rna duplexes in vitro (helicase activity), hence the belief that one of their major (though not exclusive) roles in vivo is to assist in rna rearrangements. here, we ... | 2010 | 20166751 |
| persistence of bacterial and archaeal communities in sea ice through an arctic winter. | the structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. we tested these hypotheses by weekly sampling (january-march 2004) of first-year winter sea ice (franklin bay, western arctic) that experienced temperatures from -9 degrees c to -26 degrees c, generating community fingerprints and clone libraries for bacteria and archaea. des ... | 2010 | 20192970 |
| preliminary x-ray crystallographic analysis of the breakage-reunion domain of the gyra subunit of dna gyrase from colwellia psychrerythraea strain 34h. | dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal breakage-reunion domain of the gyra subunit of dna gyrase from colwellia psychrerythraea 34h was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.60 a resolution using a synchrotron-radiation source. the crystal belonged to space group p2(1)2(1)2(1 ... | 2010 | 20383017 |
| colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the arctic ocean. | a novel psychrotolerant bacterial strain, bcw111(t), was isolated from seawater samples from the chukchi sea in the arctic ocean. cells of strain bcw111(t) were gram-negative, motile, facultatively anaerobic, curved rods and were able to grow at 0-30 °c (optimum 23-25 °c). strain bcw111(t) had q-8 as the major respiratory quinone and contained iso-c(15 : 0) 2-oh and/or c(16 : 1)ω7c (28.13 %), c(16 : 0) (13.28 %) and c(17 : 1) (12.90 %) as the major cellular fatty acids. the genomic dna g+c conte ... | 2011 | 20495042 |
| isocitrate dehydrogenase isozymes from a psychrotrophic bacterium, pseudomonas psychrophila. | the genes encoding monomer- and dimer-type isocitrate dehydrogenase (idh) isozymes from a psychrotrophic bacterium, pseudomonas psychrophila, were cloned and sequenced. open reading frames of the genes were 2,226 and 1,257 bp in length and corresponded to polypeptides composed of 741 and 418 amino acids, respectively. the deduced amino acid sequences showed high sequence identity with those of psychrophilic bacteria, colwellia maris and colwellia psychrerythraea, (about 70% identity) and the res ... | 2010 | 20549192 |
| high bicarbonate assimilation in the dark by arctic bacteria. | although both autotrophic and heterotrophic microorganisms incorporate co₂ in the dark through different metabolic pathways, this process has usually been disregarded in oxic marine environments. we studied the significance and mediators of dark bicarbonate assimilation in dilution cultures inoculated with winter arctic seawater. at stationary phase, bicarbonate incorporation rates were high (0.5-2.5 μg c l⁻¹ d⁻¹) and correlated with rates of bacterial heterotrophic production, suggesting that m ... | 2010 | 20555365 |
| characterization of a bacterial community from a northeast siberian seacoast permafrost sample. | a combination of culture-dependent and -independent techniques was used to characterize a bacterial community, examine cold adaptation of isocitrate lyase (icl) genes, and detect genes with important ecological functions in a permafrost sample from the bykovsky peninsula on the laptev sea coast of northeast siberia. according to the 16s rrna gene sequence, 47 of the cultured isolates were members of the phyla firmicutes, proteobacteria, and actinobacteria, with 85% of the isolates belonging to t ... | 2010 | 20695892 |
| exopolymer alteration of physical properties of sea ice and implications for ice habitability and biogeochemistry in a warmer arctic. | the physical properties of arctic sea ice determine its habitability. whether ice-dwelling organisms can change those properties has rarely been addressed. following discovery that sea ice contains an abundance of gelatinous extracellular polymeric substances (eps), we examined the effects of algal eps on the microstructure and salt retention of ice grown from saline solutions containing eps from a culture of the sea-ice diatom, melosira arctica. we also experimented with xanthan gum and with ep ... | 2011 | 21368216 |
| favourable effects of eicosapentaenoic acid on the late step of the cell division in a piezophilic bacterium, shewanella violacea dss12, at high-hydrostatic pressures. | shewanella violacea dss12, a deep-sea bacterium, produces eicosapentaenoic acid (epa) as a component of membrane phospholipids. although various isolates from the deep sea, such as photobacterium profundum ss9, colwellia psychrerythraea 34h and various shewanella strains, produce epa- or docosahexaenoic acid-containing phospholipids, the physiological role of these polyunsaturated fatty acids remains unclear. in this article, we illustrate the physiological importance of epa for high-pressure ad ... | 2011 | 21518217 |
| genome-level homology and phylogeny of shewanella (gammaproteobacteria: lteromonadales: shewanellaceae). | abstract: | 2011 | 21569439 |
| a survey of culturable aerobic and anaerobic marine bacteria in de novo biofilm formation on natural substrates in st. andrews bay, scotland. | this study reports a novel study of marine biofilm formation comprising aerobic and anaerobic bacteria. samples of quartz and feldspar, minerals commonly found on the earth, were suspended 5 m deep in the north sea off the east coast of st. andrews, scotland for 5 weeks. the assemblage of organisms attached to these stones was cultivated under aerobic and anaerobic conditions in the laboratory. bacteria isolated on marine agar 2216 were all gram-negative and identified to genus level by sequenci ... | 2011 | 21638112 |
| Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. | Microbial communities present in the Gulf of Mexico rapidly responded to the Deepwater Horizon oil spill. In deep water plumes, these communities were initially dominated by members of Oceanospirillales, Colwellia, and Cycloclasticus. None of these groups were abundant in surface oil slick samples, and Colwellia was much more abundant in oil-degrading enrichment cultures incubated at 4 °C than at room temperature, suggesting that the colder temperatures at plume depth favored the development of ... | 2011 | 21969552 |