Publications

identification of culturable bacteria present in haemodialysis water and fluid.	water used to prepare haemodialysis fluid is not sterile, and its microbiological control is important for the prevention of haemodialysis-associated illness. bacterial populations inhabiting a distribution system for haemodialysis water were studied over an 18-month period. 203 planktonic bacteria isolated on r2a medium were identified by restriction analysis and sequencing of 16s rrna gene. a diverse bacterial community was detected, containing predominantly gram-negative members of the alphap ...	2004	16329897
hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica.	a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ...	2004	16329936
green fluorescent protein as a marker for monitoring a pentachlorophenol degrader sphingomonas chlorophenolica atcc39723.	sphingomonas chlorophenolica atcc39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpb gene by homologous recombination. as the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. their population density dropped from 10(8) to 10(6) (cfu/ml) in the non-sterilized soil microcosms during the first 6 days. moreover, the gfp recombinant wa ...	2004	15459656
degradation of the radioactive and non-labelled branched 4(3',5'-dimethyl 3'-heptyl)-phenol nonylphenol isomer by sphingomonas ttnp3.	the degradation of the 4(3',5'-dimethyl-3'-heptyl)-phenol (p353np) nonylphenol isomer in cultures of sphingomonas ttnp3 supplemented with the technical mixture of nonylphenol was first assessed. then the radioactive and non-labelled form of these diastereomers were both synthesised. the radioactive isomers were synthesised using [ring-u-14c]-labelled phenol and 3,5-dimethyl-3-heptanol by friedel and crafts alkylation. the time-course of degradation was performed with and without 14c-p353np; bala ...	2004	14971853
[investigation of the bacteria in the seawater of xisha in the south china sea and their antibiotic sensitivity profile].	to investigate the distribution and antibiotic sensitivity of the bacteria in the seawater of xisha in the south china sea.	2004	15041561
evaluation of bacterial strategies to promote the bioavailability of polycyclic aromatic hydrocarbons.	polycyclic aromatic hydrocarbon (pahs)-degrading bacteria may enhance the bioavailability of pahs by excreting biosurfactants, by production of extracellular polymeric substances, or by forming biofilms. we tested these hypotheses in pure cultures of pahs-degrading bacterial strains. most of the strains did not substantially reduce the surface tension when grown on pahs in liquid shaken cultures. thus, pseudo-solubilization of pahs in biosurfactant micelles seems not to be a general strategy for ...	2004	14716468
sphingomonas yabuuchiae sp. nov. and brevundimonas nasdae sp. nov., isolated from the russian space laboratory mir.	on the basis of phenotypic and genotypic characteristics and 16s rrna gene sequence analysis, novel species belonging to the genera sphingomonas and brevundimonas were identified from samples taken from the russian space laboratory mir. strain a1-18(t) was isolated from the air. 16s rdna sequence analysis showed that strain a1-18(t) formed a coherent cluster with sphingomonas sanguinis, sphingomonas parapaucimobilis, sphingomonas paucimobilis and sphingomonas roseiflava with sequence similarity ...	2004	15143030
are some putative glycogen accumulating organisms (gao) in anaerobic : aerobic activated sludge systems members of the alpha-proteobacteria?	activated sludge plants designed to remove phosphorus microbiologically often perform unreliably. one suggestion is that the polyphosphate-accumulating organisms (pao) are out-competed for substrates by another group of bacteria, the glycogen-accumulating organisms (gao) in the anaerobic zones of these processes. this study used fluorescence in situ hybridization (fish) and denaturing gradient gel electrophoresis (dgge) to analyse the communities from laboratory-scale anaerobic : aerobic sequenc ...	2004	15256569
bacterial diversity of a soil sample from schirmacher oasis, antarctica.	the bacterial diversity of a soil sample collected in the vicinity of lake zub, schirmacher oasis, antarctica, was determined both by establishing pure colonies of culturable bacteria and by cloning the total 16s rdna of the soil and establishing the phylogeny of the clones. analysis of the 16s rrna gene clones indicated that the bacteria belonged to the classes alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, gemmatimonas, bacteriodetes, actinobacteria, chloroflexi and chlamydia ...	2004	15559969
a previously unexposed forest soil microbial community degrades high levels of the pollutant 2,4,6-trichlorophenol.	2,4,6-trichlorophenol (2,4,6-tcp) is a hazardous pollutant that is efficiently degraded by some aerobic soil bacterial isolates under laboratory conditions. the degradation of this pollutant in soils and its effect on the soil microbial community are poorly understood. we report here the ability of a previously unexposed forest soil microbiota to degrade high levels of 2,4,6-tcp and describe the changes in the soil microbial community found by terminal restriction fragment length polymorphism (t ...	2004	15574963
mtbe biodegradation in a gravity flow, high-biomass retaining bioreactor.	the aerobic biodegradation of methyl tert-butyl ether (mtbe), a widely used fuel oxygenate, was investigated using a pilot-scale biomass-retaining bioreactor called a biomass concentrator reactor (bcr). the reactor was operated for a year at a flow rate of 2500 l/d on cincinnati dechlorinated tap water and an influent mtbe concentration of 5 mg/l. treatment efficiency of mtbe in the reactor during stable operations exceeded 99.9%. the upper 95% confidence levels of effluent mtbe concentrations a ...	2004	15260347
origin and diversity of alginate lyases of families pl-5 and -7 in sphingomonas sp. strain a1.	sphingomonas sp. strain a1 has three endotype alginate lyases (a1-i, a1-ii [family pl-7], and a1-iii [family pl-5]), each of which is encoded by a single gene. in addition to those of these lyases, a gene (the a1-ii' gene) showing significant identity with the a1-ii gene was present in the bacterial genome and coded for an alginate lyase with broad substrate specificity. since no expression of a1-ii' was observed even in bacterial cells grown on alginate, the a1-ii' gene was thought to be a sile ...	2004	15090531
a sphingomonas bacterium interacting with epithelial cells.	bacteria of the genus sphingomonas are environmental organisms that have recently been implicated in a variety of community-acquired and nosocomial infections. during studies on bacteria-cell interactions, we incurred a microorganism contaminating our hela cell culture, possibly from water utilized for reagent preparation; this bacterium appeared to tightly adhere to cell monolayers and to survive, with only limited growth rate, which did not seem to alter cells as far as shape, growth rate or s ...	2004	15380551
divergent structures of carbazole degradative car operons isolated from gram-negative bacteria.	southern hybridization analysis of the genomes from the newly-isolated 10 carbazole (car)-utilizing bacteria revealed that 8 of the isolates carried gene clusters homologous to the car-catabolic car operon of pseudomonas resinovorans strain ca10. sequencing analysis showed that two car operons and the neighboring regions of pseudomonas sp. strain k23 are nearly identical to that of strain ca10. in contrast to strains ca10 and k23, caref genes did not exist downstream of the car gene cluster of j ...	2004	15277751
detection and characterization of conjugative degradative plasmids in xenobiotic-degrading sphingomonas strains.	a systematic survey for the presence of plasmids in 17 different xenobiotic-degrading sphingomonas strains was performed. in almost all analyzed strains, two to five plasmids with sizes of about 50 to 500 kb were detected by using pulsed-field gel electrophoresis. a comparison of plasmid preparations untreated or treated with s1 nuclease suggested that, in general, sphingomonas plasmids are circular. hybridization experiments with labeled gene probes suggested that large plasmids are involved in ...	2004	15175300
regulation of tetralin biodegradation and identification of genes essential for expression of thn operons.	the tetralin biodegradation genes of sphingomonas macrogolitabida strain tfa are clustered in two closely linked and divergent operons. to analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacz have been constructed in plasmids unable to replicate in sphingomonas and integrated by recombination into the genome of strain tfa. expression analysis indicated that the transcription of both genes is ...	2004	15342579
electrokinetic transport of pah-degrading bacteria in model aquifers and soil.	an investigation of the mobility, viability, and activity of polycyclic aromatic hydrocarbon (pah) degrading bacteria in an electric field is presented. bench-scale model aquifers were used to test electrophoresis and electroosmosis as potential mechanisms for bacterial dispersion in contaminated sites. glass beads, alluvial sand from lake geneva, and historically polluted clayey soil were used as packing materials. the green-fluorescent protein labeled pah-degrading bacteria sphingomonas sp. l1 ...	2004	15461168
degradation of aromatic hydrocarbons by sphingomonas paucimobilis strain epa505.	to determine the substrate range capability of sphingomonas paucimobilis strain epa505, a number of aromatic compounds were tested as potential growth substrates. strain epa505 grew on phenanthrene, naphthalene, fluoranthene, toluene, benzoic acid, 2,3- and 3,4-dihydroxybenzoic acids, 1-chloro-2,4-dinitrobenzene, anthracene, 2-hydroxy-3-naphthoic acid and 1-hydroxy- 2-naphthoic acid, salicylic acid, and catechol. strain epa505 was unable to grow on coumarine 3-carboxylic acid, naphthalene dicarb ...	2004	15386141
thermophilic, reversible gamma-resorcylate decarboxylase from rhizobium sp. strain mtp-10005: purification, molecular characterization, and expression.	we found the occurrence of thermophilic reversible gamma-resorcylate decarboxylase (gamma-rdc) in the cell extract of a bacterium isolated from natural water, rhizobium sp. strain mtp-10005, and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be about 151 kda by gel filtration, and that of the subunit was 37.5 kda by sodium dodecyl sulfate-polyacrylamide gel electrophoresis; in other words, the enzyme was a homotetramer. the enzyme was induced specifically ...	2004	15466039
genetic analysis of phenoxyalkanoic acid degradation in sphingomonas herbicidovorans mh.	phenoxyalkanoic acid degradation is well studied in beta- and gammaproteobacteria, but the genetic background has not been elucidated so far in alphaproteobacteria. we report the isolation of several genes involved in dichlor- and mecoprop degradation from the alphaproteobacterium sphingomonas herbicidovorans mh and propose that the degradation proceeds analogously to that previously reported for 2,4-dichlorophenoxyacetic acid (2,4-d). two genes for alpha-ketoglutarate-dependent dioxygenases, sd ...	2004	15466552
the gellan gum biosynthetic genes gelc and gele encode two separate polypeptides homologous to the activator and the kinase domains of tyrosine autokinases.	the high-molecular-weight exopolysaccharide gellan is an important commercial gelling agent produced in high yield by the gram-negative bacterium sphingomonas elodea atcc 31461. the cluster of genes required for gellan biosynthesis contains the genes gelc and gele. these encode for two polypeptides homologous to the activator domain and the kinase domain, respectively, of bacterial autophosphorylating tyrosine kinases involved in polysaccharide chain length determination. the gelc/gele pair is a ...	2004	15741740
enzymatic hydrolysis of alpha- and beta-oligo(l-aspartic acid)s by poly(aspartic acid) hydrolases-1 and 2 from sphingomonas sp. kt-1.	the enzymatic hydrolysis of alpha- and beta-oligo(l-aspartic acid)s by paa hydrolase-1 and paa hydrolase-2 (purified from sphingomonas sp. kt-1) was performed to elucidate the mechanism of the microbial degradation by sphingomonas sp. kt-1 of the thermally synthesized alpha,beta-poly(d,l-aspartic acid) (tpaa). gpc analysis of the hydrolyzed products of alpha- and beta-tetra(l-aspartic acid)s by paa hydrolase-1 has showed that paa hydrolase-1 is capable of hydrolyzing only the specific amide bond ...	2004	15468224
biodegradation of phthalate esters by two bacteria strains.	in this study two aerobic phthalic acid ester (pae) degrading bacteria strains, dk4 and o18, were isolated from river sediment and petrochemical sludge, respectively. the two strains were found to rapidly degrade pae with shorter alkyl-chains such diethyl phthalate (dep), dipropyl phthalate (dprp), di-n-butyl phthalate (dbp), benzylbutyl phthalate (bbp) and diphenyl phthalate (dpp) are very easily biodegraded, while pae with longer alkyl-chains such as dicyclohexyl phthalate (dcp) and dihexyl ph ...	2004	15006506
dynamics of multiple lin gene expression in sphingomonas paucimobilis b90a in response to different hexachlorocyclohexane isomers.	sphingomonas paucimobilis b90a is able to degrade the alpha-, beta-, gamma-, and delta-isomers of hexachlorocyclohexane (hch). it contains the genes lina, linb, linc, lind, line, and linr, which have been implicated in hch degradation. in this study, dynamic expression of the lin genes was measured in chemostat-grown s. paucimobilis b90a by rna dot blot hybridization and real-time reverse transcriptase pcr upon exposure to a pulse of different hch isomers. irrespective of the addition of hch, li ...	2004	15528530
isolation and characterization of polycyclic aromatic hydrocarbons-degrading sphingomonas sp. strain zl5.	a bacterial strain zl5, capable of growing on phenanthrene as a sole carbon and energy source but not naphthalene, was isolated by selective enrichment from crude-oil-contaminated soil of liaohe oil field in china. the isolate was identified as a sphingomonas sp. strain on the basis of 16s ribosomal dna analysis. strain zl5 grown on phenanthrene exhibited catechol 2,3-dioxygenase (c23o) activity but no catechol 1,2-dioxygenase, gentisate 1,2-dioxygenase, protocatechuate 3,4-dioxygenase and proto ...	2004	15228078
degradation of a nonylphenol single isomer by sphingomonas sp. strain ttnp3 leads to a hydroxylation-induced migration product.	sphingomonas sp. strain ttnp3 degrades 4(3',5'-dimethyl-3'-heptyl)-phenol and unidentified metabolites that were described previously. the chromatographic analyses of the synthesized reference compound and the metabolites led to their identification as 2(3',5'-dimethyl-3'-heptyl)-1,4-benzenediol. this finding indicates that the nonylphenol metabolism of this bacterium involves unconventional degradation pathways where an nih shift mechanism occurs.	2004	15528560
molecular analysis of shower curtain biofilm microbes.	households provide environments that encourage the formation of microbial communities, often as biofilms. such biofilms constitute potential reservoirs for pathogens, particularly for immune-compromised individuals. one household environment that potentially accumulates microbial biofilms is that provided by vinyl shower curtains. over time, vinyl shower curtains accumulate films, commonly referred to as "soap scum," which microscopy reveals are constituted of lush microbial biofilms. to determi ...	2004	15240300
comparative biochemical analysis of three bacterial prolyl endopeptidases: implications for coeliac sprue.	prolyl endopeptidases have potential for treating coeliac sprue, a disease of the intestine caused by proteolytically resistant peptides from proline-rich prolamins of wheat, barley and rye. we compared the properties of three similar bacterial prolyl endopeptidases, including the known enzymes from flavobacterium meningosepticum (fm) and sphingomonas capsulate (sc) and a novel enzyme from myxococcus xanthus (mx). these enzymes were interrogated with reference chromogenic substrates, as well as ...	2004	15245330
bioavailability of pentachlorophenol to acclimatised bacteria under batch and flow-through conditions.	biodegradation of organic contaminants in multi-phase systems, such as soils and aquifers, is often limited by the extent and the rate of contaminant sorption onto the solid matrix. however, information about biodegradation in complex matrices is largely limited to studies of closed systems under batch conditions in which potential bioavailability is characterised by the aqueous-phase concentration of a contaminant. there is little knowledge regarding the influence of flow-through conditions on ...	2004	14716469
study of enzymatic reaction by electrophoretically mediated microanalysis in a partially filled capillary with indirect or direct detection.	electrophoretically mediated microanalysis (emma), in combination with a partial filling technique and indirect or direct detection, is described for the study of enzymes reacting with the high mobility inorganic or organic anions as substrates or products. part of the capillary is filled with a buffer optimized for the enzymatic reaction, the rest of the capillary with the background electrolyte being optimal for the separation of substrates and products. with haloalkane dehalogenase, chosen as ...	2004	14743481
characterization of degradation process of cyanobacterial hepatotoxins by a gram-negative aerobic bacterium.	a bacterium termed 7cy, capable of decomposing cyanobacterial toxins, was isolated from surface water sample of lake suwa and degradation of microcystin-rr and nodularin-har was investigated. the isolated 7cy was a gram-negative, aerobic bacillus, and a member of a genus sphingomonas. the strain degraded microcystin-ly, -lw, and -lf completely as well as microcystin-lr within 4 days after their addition (6 microg/ml) whereas degradation of nodularin-har did not occur at all during experiment. on ...	2004	15207597
treatment of atrazine by integrating photocatalytic and biological processes.	this research examines the degradation of atrazine by photocatalytic oxidation (pco) under different experimental conditions. deisopropylatrazine, deethylatrazine and deethyldeisopropylatrazine were formed as major intermediates based on gas chromatography-mass spectrometry. the reaction mixture was found to be toxic towards two bioassays, i.e. the microtox and amphipods survival tests even when atrazine was completely degraded by pco within 2 h under optimized conditions. the results indicate t ...	2004	15210274
isolation of adda from microcystin-lr by microbial degradation.	the intact adda was isolated from microcystin-lr by a microbial degradation using an isolated sphingomonas strain, b-9. the reaction of microcystin-lr with cell extract of this strain proceeded smoothly to give the final degradation product by way of two intermediates, linearized microcystin-lr and a tetrapeptide. the purified adda that was structurally characterized using various spectral data did not show the toxicity to mice or inhibition to protein phosphatase activity in contrast to the nat ...	2004	15225569
crystal structure of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 at 0.95 a resolution: dynamics of catalytic residues.	we present the structure of linb, a 33-kda haloalkane dehalogenase from sphingomonas paucimobilis ut26, at 0.95 a resolution. the data have allowed us to directly observe the anisotropic motions of the catalytic residues. in particular, the side-chain of the catalytic nucleophile, asp108, displays a high degree of disorder. it has been modeled in two conformations, one similar to that observed previously (conformation a) and one strained (conformation b) that approached the catalytic base (his27 ...	2004	14744129
organization of genes required for gellan polysaccharide biosynthesis in sphingomonas elodea atcc 31461.	sphingomonas elodea atcc 31461 produces gellan, a capsular polysaccharide that is useful as a gelling agent for food and microbiological media. complementation of nonmucoid s. elodea mutants with a gene library resulted in identification of genes essential for gellan biosynthesis. a cluster of 18 genes spanning 21 kb was isolated. these 18 genes are homologous to genes for synthesis of sphingan polysaccharide s-88 from sphingomonas sp. atcc 31554, with predicted amino acid identities varying fro ...	2004	14767675
reactions of serine palmitoyltransferase with serine and molecular mechanisms of the actions of serine derivatives as inhibitors.	serine palmitoyltransferase (spt) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a to 3-ketodihydrosphingosine. we have succeeded in the overproduction of a water-soluble homodimeric spt from sphingomonas paucimobilis ey2395(t) in escherichia coli. the recombinant spt showed the characteristic absorption and circular dichroism spectra derived from its coenzyme pyridoxal 5'-phosphate. on the basis of the spectral chan ...	2004	14744154
biodegradation kinetics of volatile hydrophobic organic compounds in cultures with variable fractional volumes.	an extension of the models developed by guha and jaffé (biotechnol bioeng [1996] 50:693-699) to describe the phenanthrene biodegradation kinetics for the cultures with variable fractional volumes is presented. batch experiments were conducted with a culture capable of degrading the phenanthrene using a single culture vessel from which samples were withdrawn over time to monitor the disappearance of phenanthrene. for accurate measurement of phenanthrene concentrations, a sampling procedure design ...	2004	14966799
estimation of kinetic parameter for the biotransformation of three-ring azaarenes by the phenanthrene-degrading strain sphingomonas sp. lh128.	we examined the biotransformation of several azaarenes to get information on their rate of removal from contaminated soil by cometabolic degradation. acridine, 9-methyl-acridine, phenanthridine, benzo[f]quinoline, and benzo[h]quinoline were found to be cometabolized by phenanthrene-degrading sphingomonas sp. strain lh128. the transformation of acridine and benzo[h]quinoline was shown to be inhibited at relatively high concentrations (24.9 mg/l and 58.2 mg/l, respectively). maximum biotransformat ...	2004	14982379
hydrocarbon spills on antarctic soils: effects and management.	antarctic exploration and research have led to some significant although localized impacts on the environment. human impacts occur around current or past scientific research stations, typically located on ice-free areas that are predominantly soils. fuel spills, the most common occurrence, have the potential to cause the greatest environmental impact in the antarctic through accumulation of aliphatic and aromatic compounds. effective management of hydrocarbon spills is dependent on understanding ...	2004	15046325
isolation of a beta-carotene over-producing soil bacterium, sphingomonas sp.	a carotenoid-accumulating bacterium isolated from soil, identified as a sphingomonas sp., grew at 0.18 h(-1) and produced 1.7 mg carotenoids g(-1) dry cell, among which beta-carotene (29% of total carotenoids) and nostoxanthin (36%). a mutant strain, obtained by treatment with ethyl methanesulfonate, accumulated up to 3.5 mg carotenoids g(-1) dry cell. accumulation of beta-carotene by this strain depended on the oxygenation of the growth medium, with maximal accumulation (89%) occurring under li ...	2004	15049373
microbiological influences in 'blue water' copper corrosion.	to investigate the influence of micro-organisms associated with copper corrosion on 'blue water' corrosion in drinking water.	2004	15281940
a 19f nmr study of fluorobenzoate biodegradation by sphingomonas sp. hb-1.	while several microorganisms readily degrade 2- and 4-fluorobenzoates, only a very small number appear to catabolise the 3-fluoro isomer, owing to the accumulation of toxic intermediates. here we describe the isolation of a bacterium capable of using 3-fluorobenzoate as a sole source of carbon and energy, and the experiments conducted to define the steps involved in the biodegradation of this compound. the organism was identified as a strain belonging to the genus sphingomonas by sequence analys ...	2004	15321683
comparison of n-eicosane and phenanthrene removal by pure and mixed cultures of two marine bacteria.	the biotransformation activities of two hydrocarbonoclastic marine bacteria, corynebacterium sp. and sphingomonas sp. 2mpii, on n-eicosane and phenanthrene were investigated. during a 56-day experiment, in pure and mixed cultures, corynebacterium sp. and sphingomonas sp. 2mpii removed about 70% of the initial n-eicosane and phenanthrene concentrations (1 and 0.4 g l(-1), respectively). in pure cultures, culturable cell abundances increased over time, from 0.8 to 8.6 x 10(-11) cfu l(-1) (coryneba ...	2004	15325883
microbial characterization during the early habitation of the international space station.	an evaluation of the microbiota from air, water, and surface samples provided a baseline of microbial characterization onboard the international space station (iss) to gain insight into bacterial and fungal contamination during the initial stages of construction and habitation. using 16s genetic sequencing and rep-pcr, 63 bacterial strains were isolated for identification and fingerprinted for microbial tracking. of the bacterial strains that were isolated and fingerprinted, 19 displayed similar ...	2004	14749908
electrophoretically mediated microanalysis with partial filling technique and indirect or direct detection as a tool for inhibition studies of enzymatic reaction.	the inhibition of the model enzyme, haloalkane dehalogenase from sphingomonas paucimobilis, was investigated by a combination of electrophoretically mediated microanalysis with a partial filling technique, followed by indirect or direct detection. in this setup, part of the capillary is filled with a buffer suitable for the enzymatic reaction (20 mm glycine buffer, ph 8.6) whereas the rest of the capillary is filled with the background electrolyte optimal for separation of substrates and product ...	2004	15095444
requirement of a relatively high threshold level of mg(2+) for cell growth of a rhizoplane bacterium, sphingomonas yanoikuyae ec-s001.	mg(2+) is one of the essential elements for bacterial cell growth. the presence of the magnesium cation (mg(2+)) in various concentrations often affects cell growth restoration in plant-associating bacteria. this study attempted to determine whether mg(2+) levels in sphingomonas yanoikuyae ec-s001 affected cell growth restoration in the host plant and what the threshold level is. s. yanoikuyae ec-s001, isolated from the rhizoplane of spinach seedlings grown from surface-sterilized seeds under as ...	2004	15345402
structure and function of a hypothetical pseudomonas aeruginosa protein pa1167 classified into family pl-7: a novel alginate lyase with a beta-sandwich fold.	structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in pseudomonas aeruginosa and in the development of therapeutic agents for bacterial disease. most alginate lyases are classified into polysaccharide lyase (pl) family-5 and -7 based on their primary structures. family pl-7 enzymes are still poorly characterized especially in structural properties. among family pl-7, a gene coding for a hypothetical protein (pa1167) homolog ...	2004	15136569
isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading sphingomonas sp. strain a4.	sphingomonas sp. strain a4 is capable of utilizing acenaphthene and acenaphthylene as sole carbon and energy sources, but it is unable to grow on other polycyclic aromatic hydrocarbons (pahs). the genes encoding terminal oxygenase components of ring-hydroxylating dioxygenase (arha1 and arha2) were isolated from this strain by means of the ability to oxidize indole to indigo of the escherichia coli clone containing electron transport proteins from phenanthrene-degrading sphingobium sp. strain p2. ...	2004	15358414
organization of lin genes and is6100 among different strains of hexachlorocyclohexane-degrading sphingomonas paucimobilis: evidence for horizontal gene transfer.	the organization of lin genes and is6100 was studied in three strains of sphingomonas paucimobilis (b90a, sp+, and ut26) which degraded hexachlorocyclohexane (hch) isomers but which had been isolated at different geographical locations. dna-dna hybridization data revealed that most of the lin genes in these strains were associated with is6100, an insertion sequence classified in the is6 family and initially found in mycobacterium fortuitum. eleven, six, and five copies of is6100 were detected in ...	2004	15060023
occurrence and phylogenetic diversity of sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons.	bacterial strains of the genus sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (pah) as the sole source of carbon and energy. the direct detection of sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. in this study, a culture-independent pcr-based detection method using specific primers targeting the sphingomonas 16s rrna gene combined with denaturing ...	2004	15066784
distribution of nevskia ramosa and other rosette-forming neustonic bacteria.	samples from 27 natural and artificial aquatic environments were analyzed for the presence of rosette-forming bacteria by a combined cultivation and molecular biological approach. rosette-forming bacteria developed in 20 enrichment cultures with ammonia-free medium under air. three morphotypes could be distinguished. the most abundant type i resembled nevskia ramosa and formed hydrophobic, flat, and dichotomously branching rosettes. type ii rosettes were three-dimensional and were observed in 10 ...	2004	15054677
genetic and phenotypic diversity of (r/s)-mecoprop [2-(2-methyl-4-chlorophenoxy)propionic acid]-degrading bacteria isolated from soils.	twelve mecoprop-degrading bacteria were isolated from soil samples, and their genetic and phenotypic characteristics were investigated. analysis of 16s rdna sequences indicated that the isolates were related to members of the genus sphingomonas. ten different chromosomal dna patterns were obtained by polymerase-chain-reaction (pcr) amplification of repetitive extragenic palindromic (rep) sequences from the 12 isolates. the isolates were found to be able to utilize the chiral herbicide mecoprop a ...	2004	15357300
microbial characterization of organic carrier colonization during a model biofiltration experiment.	dynamic microbial characterization of the colonization of organic carrier during a model biofiltration experiment using methanol as air pollutant.	2004	15130150
heterologous gene expression in thermus thermophilus: beta-galactosidase, dibenzothiophene monooxygenase, pnb carboxy esterase, 2-aminobiphenyl-2,3-diol dioxygenase, and chloramphenicol acetyl transferase.	enzymes from thermophiles are preferred for industrial applications because they generally show improved tolerance to temperature, pressure, solvents, and ph as compared with enzymes from mesophiles. however, nearly all thermostable enzymes used in industrial applications or available commercially are produced as recombinant enzymes in mesophiles, typically escherichia coli. the development of high-temperature bioprocesses, particularly those involving cofactor-requiring enzymes and/or multi-ste ...	2004	15138843
catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus sphingomonas for vigorous growth.	a bacterial strain, designated ast4(t), was isolated from activated sludge. the bacterium did not show significant growth on nutrient broth, but growth was clearly stimulated by addition of supernatant from other bacterial cultures. culture filtrate of a strain related to the genus sphingomonas in particular increased the cell yield and growth rate of strain ast4(t). phylogenetic analysis based on the 16s rrna gene sequences showed that strain ast4(t) is located within the 'rhodobacter group' in ...	2004	15143049
isolation of an exopolysaccharide-producing bacterium, sphingomonas sp. cs101, which forms an unusual type of sphingan.	an exopolysaccharide-producing gram negative bacterium was isolated and determined to be a sphingomonas sp. (cs101). a sugar composition analysis of an exopolysaccharide indicated that the sphingomonas sp. cs101 secreted an exopolysaccharide composed of glucose, mannose, fucose, and rhamnose in the ratio of 2.1:1.1:1.0:0.1, suggesting that this exoplysaccharide is an unusual type of sphingan family. the mean molecular weight of the exopolysaccharide was determined to be 4.2x10(5) da by size excl ...	2004	15170124
cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, sphingopyxis alaskensis.	sphingopyxis (formerly sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation). it has a unique physiology which is fundamentally different to that of the well studied bacteria such as escherichia coli. to begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-de) methods and determined the identity of 12 proteins from a total ...	2004	15174144
molecular identification and characterization of an alginate-binding protein on the cell surface of sphingomonas sp. a1.	cells of sphingomonas sp. a1 (strain a1) directly incorporate a macromolecule, alginate, into cytoplasm through a biosystem, or "super-channel," consisting of a pit on the cell surface, alginate-binding proteins in periplasm, and an abc transporter in the inner membrane. the pit functions as a concentrator for extracellular alginate. through differential display analysis, a protein (p8) with a molecular mass of 20kda and a pi of 7.4 was found to be inducibly expressed in the outer membrane of al ...	2004	15336522
overexpression, purification, and characterization of atp-nad kinase of sphingomonas sp. a1.	the nad kinase gene (nadk) of sphingomonas sp. a1 was cloned and then overexpressed in escherichia coli, and the gene product (nadk) was purified from the e. coli cells through five steps with a 25% yield of activity. nadk was a homodimer of 32 kda subunits, utilized atp or other nucleoside triphosphates, but not inorganic polyphosphates, as phosphoryl donors for the phosphorylation of nad, most efficiently at ph 8.0 and 50-55 degrees c, and was designated as atp-nad kinase (nadk). nadk showed n ...	2004	15177293
root nodule bradyrhizobium spp. harbor tfdaalpha and cada, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins.	the distribution of tfdaalpha and cada, genes encoding 2,4-dichlorophenoxyacetate (2,4-d)-degrading proteins which are characteristic of the 2,4-d-degrading bradyrhizobium sp. isolated from pristine environments, was examined by pcr and southern hybridization in several bradyrhizobium strains including type strains of bradyrhizobium japonicum usda110 and bradyrhizobium elkanii usda94, in phylogenetically closely related agromonas oligotrophica and rhodopseudomonas palustris, and in 2,4-d-degradi ...	2004	15066803
sphingomonas sp. strain sb5 degrades carbofuran to a new metabolite by hydrolysis at the furanyl ring.	microorganisms capable of degrading carbofuran were isolated from soils and examined for the degradation of this pesticide at ring structure. an isolate that could degrade carbofuran and carbofuran-7-phenol was selected for further studies. the 16s rrna analysis results showed that the isolate belongs to the genus of sphingomonas, close to dioxin and dicamba degraders, and is named sphingomonas sp. sb5. sb5 did not show any similarity of 16s rrna to known carbofuran degraders. when time-course d ...	2004	15080638
a novel tetrahydrofolate-dependent o-demethylase gene is essential for growth of sphingomonas paucimobilis syk-6 with syringate.	sphingomonas paucimobilis syk-6 degrades syringate to 3-o-methylgallate (3mga), which is finally converted to pyruvate and oxaloacetate via multiple pathways in which protocatechuate 4,5-dioxygenase, 3mga dioxygenase, and gallate dioxygenase are involved. here we isolated the syringate o-demethylase gene (desa), which complemented the growth deficiency on syringate of a tn5 mutant of the syk-6 derivative strain. the desa gene is located 929 bp downstream of fera, encoding feruloyl-coenzyme a syn ...	2004	15090517
bacteriophages and insertion sequences of chromobacterium violaceum atcc 12472.	a fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. a substantial portion of these sudden changes is mediated by lateral gene transfer (lgt), through genetic recombination mechanisms, such as transformation, conjugation and transduction. the recent sequencing of several organisms has offered a new approach to the study of lgt, using comparison and analysis of nucleotide sequences dis ...	2004	15100989
bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense.	thlaspi goesingense is able to hyperaccumulate extremely high concentrations of ni when grown in ultramafic soils. recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. in this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing t. goesingense were characterized in detail by using both cultivation and cultivation-independent te ...	2004	15128517
purification and characterization of arylsulfatase from sphingomonas sp. as6330.	arylsulfatase was purified from sphingomonas sp. as6330 through ionic exchange, hydrophobic- and gel-chromatographies. the purity increased 12,800-fold with approximately 19.1% yield against cell homogenate. the enzyme was a monomeric protein with apparent molecular weight of 62 kda as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis, and 41 kda as determined by gel filtration. the enzyme had optimum reaction conditions for hydrolysis of sulfate ester bonds in agar and p-ni ...	2004	14600791
phosphonium ionic liquids for degradation of phenol in a two-phase partitioning bioreactor.	six ionic liquids (ils), which are organic salts that are liquid at room temperature, were tested for their biocompatibility with three xenobiotic-degrading bacteria, pseudomonas putida, achromobacter xylosoxidans, and sphingomonas aromaticivorans. of the 18 pairings, seven were found to demonstrate biocompatibility, with one il (trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl) amide) being biocompatible with all three organisms. this il was then used in a two-phase partitioning bior ...	2005	15549289
influence of the carbon/nitrogen/phosphorus ratio on polycyclic aromatic hydrocarbon degradation by mycobacterium and sphingomonas in soil.	biodegradation of polycyclic aromatic hydrocarbons (pahs) in the environment is often limited due to unfavorable nutrient conditions for the bacteria that use these pahs as sole source of carbon and energy. mycobacterium and sphingomonas are 2 pah-degrading specialists commonly present in pah-polluted soil, but not much is known about their specific nutrient requirements. by adding different inorganic supplements of nitrogen (n) and phosphorus (p), affecting the overall carbon/nitrogen/phosphoru ...	2005	15549290
9,10-phenanthrenequinone photoautocatalyzes its formation from phenanthrene, and inhibits biodegradation of naphthalene.	polycyclic aromatic hydrocarbons (pahs) have earned considerable attention due to their widespread environmental distribution and toxicity. in the environment, pahs decompose by a variety of biotic and abiotic pathways. in both polar and nonpolar environments, phenanthrene (phe, a common, three-ring pah) is converted by sunlight to more polar products such as 9,10-phenanthrenequinone (pheq) and subsequent oxidation products such as the corresponding open-ring dicarboxylic acid product. biodegrad ...	2005	15758098
characterization of micro-organisms isolated from dairy industry after cleaning and fogging disinfection with alkyl amine and peracetic acid.	to characterize micro-organisms isolated from norwegian dairy production plants after cleaning and fogging disinfection with alkyl amine/peracetic acid and to indicate reasons for survival.	2005	15610421
cis-dihydrodiol, arene oxide and phenol metabolites of dictamnine: key intermediates in the biodegradation and biosynthesis of furoquinoline alkaloids.	biotransformation of the parent furoquinoline alkaloid dictamnine and its 4-chlorofuroquinoline precursor, using the b8/36 bacterial mutant strain of sphingomonas yanoikuyae, yielded, via biphenyl dioxygenase-catalysed dihydroxylation, the first isolable alkaloid cis-dihydrodiol metabolites; these metabolites were used in the chemoenzymatic synthesis of postulated arene oxide and phenol intermediates, and a range of derived furoquinoline alkaloids.	2005	16075095
purification of cytochrome p450 and ferredoxin, involved in bisphenol a degradation, from sphingomonas sp. strain ao1.	in a previous study (m. sasaki, j. maki, k. oshiman, y. matsumura, and t. tsuchido, biodegradation 16:449-459, 2005), the cytochrome p450 monooxygenase system was shown to be involved in bisphenol a (bpa) degradation by sphingomonas sp. strain ao1. in the present investigation, we purified the components of this monooxygenase, cytochrome p450 (p450bisd), ferredoxin (fd(bisd)), and ferredoxin reductase (red(bisd)). we demonstrated that p450bisd and fd(bisd) are homodimeric proteins with molecular ...	2005	16332782
a structural basis for depolymerization of alginate by polysaccharide lyase family-7.	alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-l-guluronate and beta-d-mannuronate, through a beta-elimination reaction. their structure/function relationships are expected to provide information valuable to future industrial alginate processing and drug design for pseudomonas aeruginosa alginate biofilm-dependent infection, but much remains unknown. here, we present the crystal structure at 1.0 a resolution and the results of mutational analysis of sphingomona ...	2005	16081095
degradation of chlorophenols using pentachlorophenol-degrading bacteria sphingomonas chlorophenolica in a batch reactor.	chlorophenols are common environmental contaminants that have been used as the major component in wide-spectrum biocides in industry and agriculture. many chlorophenols tend to persist in the environment and may become public health hazards. this research studied the ability of the pentachlorophenol (pcp)-degrading bacterium sphingomonas chlorophenolica to degrade and dechlorinate other chlorophenols. in addition, the characteristics of s. chlorophenolica were also investigated. when s. chloroph ...	2005	16086107
culture-dependent and -independent approaches establish the complexity of a pah-degrading microbial consortium.	a microbial consortium (am) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (pah) mixture of three- and four-ringed pahs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (dgge), and the screening of 16s and 18s rrna gene clone libraries. eleven different sequences by culture-dependent techniques and seven by both dgge and clone libraries wer ...	2005	16333329
[isolation and characterization of a hch degradation sphingomanas sp. stain bhc-a].	an aerobic bacterium was isolated successfully from a long-term contaminated upland field, which was named bhc-a. the bacterium can utilize hexachlorocycloexane as a sole carbon source and decompose this substance rapidly and completely. according to its physiological & biochemical characters and the homology analysis of its 16s rdna sequence, this strain was identified as sphingomonas sp. stain bhc-a canmineralize not only alpha, gamma and delta-hch rapidly, but also 5 mg/l beta-hch in 12h comp ...	2005	16342765
[metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane].		2005	16218450
proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities.	the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ...	2005	16085866
[rare bacteria species found in wounds of tsunami patients. predominance of gram-negative rods, increased antibiotic resistance].	microbiological cultures from 229 patients seeking medical advise in stockholm after the tsunami catastrophe december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative rods were the most common findings from wound cultures. common human pathogens as escherichia coli, proteus species, klebsiella spp, and pseudomonas aeruginosa were isolated. however, more rare species of gram-negative rods were also isolated, e.g. myroides ...	2005	16416946
biofilm formation characteristics of bacterial isolates retrieved from a reverse osmosis membrane.	high-quality water purification systems using reverse osmosis (ro) membrane separation have faced a major challenge related to biofilm formation on the membrane surface, or biofouling. to understand this issue, the biofilm formation characteristics of four bacterial isolates previously retrieved from an ro membrane treating potable water were investigated. biofilm formation of all four isolates occurred to different extents in microtiter plates and could be related to one or more cell properties ...	2005	16245826
biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1.	the ability of sphingomonas wittichii strain rw1 to remove polychlorinated dibenzo-p-dioxins (pcdds) from fly ash was investigated. all experiments were carried out in a slurry-phase system. preliminary studies with resting cells of strain rw1 in a model fly ash system showed the complete removal of dibenzofuran (df) and 81% of dibenzo-p-dioxin (dd). incubation of real fly ash collected from municipal waste incinerators with strain rw1 for 15 days resulted in a 75.5% reduction in toxic pcdds. wh ...	2005	16256169
cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil.	atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. the species composition of the culture was determined by pcr-dgge. the bacterial species included agrobacterium tumefaciens, caulobacter crescentus, pseudomonas putida, sphingomonas yaniokuyae, nocardia sp., rhizobium ...	2005	16329946
physicochemical properties and biological activities of deae-derivatized sphingomonas gellan.	physicochemical characteristics and biological activities of sphingomonas gellan (s-gellan) were investigated. the s-gellan weight fractions of glc and glcua were 0.45 and 0.25, respectively, and the molar ratio of glc:rha:glcua was approximately 4:2:3. the s-gellan was chemically derivatized with diethylaminoethyl chloride-hcl (deae-hcl), and the resulting modified s-gellan contained both positive and negative charges. the elemental and ir analyses were conducted to confirm the successful incor ...	2005	16076099
formation of catechols via removal of acid side chains from ibuprofen and related aromatic acids.	although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria. sphingomonas sp. strain ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. a slight preference toward the r enantiomer was observed, though both ibuprofen enantiomers were metabolized. a yellow color, indicative of meta-cleavage, accumulated t ...	2005	16204529
enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases lina1 and lina2 from the soil bacterium sphingomonas paucimobilis b90a.	sphingomonas paucimobilis b90a contains two variants, lina1 and lina2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (r. kumari, s. subudhi, m. suar, g. dhingra, v. raina, c. dogra, s. lal, j. r. van der meer, c. holliger, and r. lal, appl. environ. microbiol. 68:6021-6028, 2002). on the amino acid level, lina1 and lina2 were 88% identical to each other, and lina2 was 100% identical to lina of s. paucimobilis ut26. incubation of chir ...	2005	16332842
effect of slow desorption on the kinetics of biodegradation of polycyclic aromatic hydrocarbons.	the bioavailability to bacteria of 14c-labeled polycyclic aromatic hydrocarbons (pahs) sorbed onto lake sediments was assessed using a mathematical model and three experimental series. the experiments were performed under similar conditions and included: (1) abiotic desorption of pahs from sediments by tenax extraction, (2) mineralization of dissolved pahs with no sediment present, and (3) mineralization of pahs sorbed onto sediments. results obtained from the first two series were used to obtai ...	2005	16323776
molecular identification of sphingomonas sp. a1 alginate lyase (a1-iv') as a member of novel polysaccharide lyase family 15 and implications in alginate lyase evolution.	sphingomonas sp. a1 (strain a1) produces three endotypes (a1-i [65 kda], a1-ii [25 kda], and a1-iii [40 kda]) and an exotype (a1-iv [86 kda]) alginate lyases in cytoplasm. these four enzymes cooperatively depolymerize alginate into constituent monosaccharides. in addition to the genes for these lyases, novel genes encoding hypothetical proteins homologous with a1-iv were found in the genomes of many bacteria including strain a1. one such protein, a1-iv' (90 kda) of strain a1, was overexpressed i ...	2005	16233753
sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate.	a gram-negative bacterium, yim 003t, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. the organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on isp2 medium and its optimum growth ph was 7.0-7.5. the major respiratory lipoquinone was ubiquinone q-10. the phosphate-containing lipids detected in strain yim 003t were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sph ...	2005	16280497
nonionic surfactant sorption onto the bacterial cell surface: a multi-interaction isotherm.	the adsorption of linear polyoxyethylene (poe) alcohol surfactants of the form cxey onto the surface of a sphingomonas sp. has been examined. for this study, the alkyl chain length (x) was fixed at 12 and the poe chain length (y) was varied, with y = 4, 7, 9, 10, and 23 ethylene oxide units. langmuirian isotherms were observed for c12e4 and c12e23, and more complex isotherms were observed for the three intermediate poe chain length surfactants, with c12e7 and c12e9 exhibiting strong s-shaped iso ...	2005	16285812
non-specific biodegradation of the organophosphorus pesticides, cadusafos and ethoprophos, by two bacterial isolates.	an enrichment culture technique was used for the isolation of microorganisms responsible for the enhanced biodegradation of the nematicide cadusafos in soils from a potato monoculture area in northern greece. mineral salts medium supplemented with nitrogen (msmn), where cadusafos (10 mg l(-1)) was the sole carbon source, and soil extract medium (sem) were used for the isolation of cadusafos-degrading bacteria. two pure bacterial cultures, named cadi and cadii, were isolated and subsequently char ...	2005	16329956
application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow.	here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. the internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. high-resolution digital time-lapse imaging was em ...	2005	16332867
toxic effect of biosurfactant addition on the biodegradation of phenanthrene.	the effect of the biosurfactant rhamnolipid on phenanthrene biodegradation and cell growth of phenanthrene degraders was investigated. to compare the effect of rhamnolipid addition, two bacterial strains, 3y and 4-3, which were isolated from a diesel-contaminated site in korea, were selected. without the biosurfactant, large amounts of phenanthrene were degraded with both strains at neutral ph, with higher rates of phenanthrene degradation when the cell growth was higher. upon the addition of 24 ...	2005	16398112
proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in sphingomonas sp. a1: alginate-binding flagellin on the cell surface.	a nonmotile gram-negative bacterium, sphingomonas sp. a1, directly incorporates macromolecules such as alginate through a "super-channel" consisting of a pit formed on the cell surface, alginate-binding proteins in the periplasm, and an atp-binding cassette transporter in the inner membrane. here, we demonstrate the proteomics-based identification of cell-surface proteins involved in the formation of the pit and/or import of alginate. cell-surface proteins were prepared from the outer membrane r ...	2005	16229468
[screening methods for detection of metallo-beta-lactamase producing gram negative rods].	modified hodge test and a method using a disk with imipenem plus 1000 mg of edta were used to determine the presence of metallo-beta-lactamase producing gram-negative rods among 166 clinical isolates from hospitals in iaşi and galaţi. of 9 imipenem resistant strains found, only one pseudomonas aeruginosa gave positive results with both tests and other two p. aeruginosa clinical isolates gave negative results with both tests. the rest of the strains (2 p. aeruginosa, 2 acinetobacter baumanii, 1 s ...	2005	16607806
[construction of multifunctional genetically engineered pesticides-degrading bacteria by homologous recombination].	construction of multifunctional pesticides-degrading genetically engineered microorganisms (gems) is increasing important in the bioremediation of various pesticides contaminants in environment. however, construction of genetically stable gems without any exogenous antibiotic resistance is thought to be one of the bottlenecks in gems construction. in this article, homologous recombination vectors with the recipient's 16s rdna as homologous recombination directing sequence (hrds) and sacb gene as ...	2005	16468341
['in vitro' activity of different antimicrobial agents on gram-negative nonfermentative bacilli, excluding pseudomonas aeruginosa and acinetobacter spp].	gram-negative nonfermentative bacilli (nfb) are widely spread in the environment. besides of difficulties for identification, they often have a marked multiresistance to antimicrobial agents, including those active against pseudomonas aeruginosa. the objective of this study was to evaluate the 'in vitro' activity of different antimicrobial agents on 177 gram-negative nonfermentative bacilli isolates (excluding pseudomonas aeruginosa and acinetobacter spp.) isolated from clinical specimens. minim ...	2005	15991478
isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene.	the goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (pahs) to pah-degrading microbes. micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model pah. enrichments from pah-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. in contrast, only three strains of burkholderia spp. and one ...	2005	16000791
catabolic role of a three-component salicylate oxygenase from sphingomonas yanoikuyae b1 in polycyclic aromatic hydrocarbon degradation.	sphingomonas yanoikuyae b1 possesses several different multicomponent oxygenases involved in metabolizing aromatic compounds. six different pairs of genes encoding large and small subunits of oxygenase iron-sulfur protein components have previously been identified in a gene cluster involved in the degradation of both monocyclic and polycyclic aromatic hydrocarbons. insertional inactivation of one of the oxygenase large subunit genes, bpha1c, results in a mutant strain unable to grow on naphthale ...	2005	15649397
identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, sphingomonas paucimobilis ut26.	tn5-derived mutants of the gamma-hexachlorocyclohexane-degrading bacterium sphingomonas paucimobilis ut26 were genetically characterized, and an endogenous insertion sequence (is) which belongs to the is1380 family was identified. the is, named issp1, existed as multi copies in ut26, and its transposition appeared to be activated during the process of tn5-mutagenesis. it was found that transposon mutagenesis can cause endogenous mutations.	2005	15665490
a tetrahydrofolate-dependent o-demethylase, ligm, is crucial for catabolism of vanillate and syringate in sphingomonas paucimobilis syk-6.	vanillate and syringate are converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively, by o-demethylases in sphingomonas paucimobilis syk-6. pca is further degraded via the pca 4,5-cleavage pathway, while 3mga is degraded through multiple pathways in which pca 4,5-dioxygenase (ligab), 3mga 3,4-dioxygenase (desz), and an unidentified 3mga o-demethylase and gallate dioxygenase are participants. for this study, we isolated a 4.7-kb smai fragment that conferred on escherichia c ...	2005	15743951
quantitative analysis of substrate specificity of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26.	haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. the haloalkane dehalogenase linb, isolated from sphingomonas paucimobilis ut26, is a broad-specificity enzyme. fifty-five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the linb enzyme. the compounds for testing were systematically selected using a statistical experimental design. steady-state kinetic constants k(m) and k(cat) were determined for 25 substr ...	2005	15736949