Publications

characterization of the ybdt gene product of bacillus subtilis: novel fatty acid beta-hydroxylating cytochrome p450.	we have characterized the gene encoding fatty acid alpha-hydroxylase, a cytochrome p450 (p450) enzyme, from sphingomonas paucimobilis. a database homology search indicated that the deduced amino acid sequence of this gene product was 44% identical to that of the ybdt gene product that is a 48 kda protein of unknown function from bacillus subtilis. in this study, we cloned the ybdt gene and characterized this gene product using a recombinant enzyme to clarify function of the ybdt gene product. th ...	1999	10529095
selective and continuous degradation of carbazole contained in petroleum oil by resting cells of sphingomonas sp. cdh-7.	microbial degradation of carbazole (ca), a model of hard-removal heterocyclic nitrogen compounds contained in petroleum oil, was examined using sphingomonas sp. cdh-7 isolated from a soil sample by screening for ca-assimilating microorganisms. cdh-7 used ca as a sole source of carbon and nitrogen, and metabolized ca to ammonia via anthranilic acid as an intermediate product. when cdh-7 was cultivated in the medium containing ca at the concentration of 500 mg/l (2.99 mm), ca was completely degrad ...	1999	10540744
cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis.	sphingomonas (formerly pseudomonas) paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch), a halogenated organic insecticide, as a sole source of carbon and energy. in a previous study, we showed that gamma-hch is degraded to chlorohydroquinone (chq) and then to hydroquinone (hq), although the rate of reaction from chq to hq was slow (k. miyauchi, s. k. suh, y. nagata, and m. takagi, j. bacteriol. 180:1354-1359, 1998). in this study, we cloned and characterized a gene, designated li ...	1999	10542173
construction and characterization of histidine-tagged haloalkane dehalogenase (linb) of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, sphingomonas paucimobilis ut26.	the linb gene product (linb), which is involved in the degradation of gamma-hexachlorocyclohexane in sphingomonas paucimobilis ut26, is a member of haloalkane dehalogenases with a broad range of substrate specificity. elucidation of the factors determining its substrate specificity is of interest. aiming to facilitate purification of recombinant linb protein for site-directed mutagenesis analysis, a 6-histidyl tail was added to the c-terminus of linb. the his-tagged linb was specifically bound w ...	1999	10545279
isrm10: a new insertion sequence of sinorhizobium meliloti: nucleotide sequence and geographic distribution.	in this study the description of a new insertion sequence of sinorhizobium meliloti, isrm10, is reported. isrm10 was found in the intergenic region between nodj and nodq of a natural isolated strain. isrm10 was 1047 bp long and showed the typical features of the iss belonging to the is630-tc1/is3 superfamily. in particular the isrm10 nucleotide sequence showed the highest homology (62%) with a sphingomonas aromaticivorans is. isrm10 was present in 32% of the analyzed s. meliloti strains while it ...	1999	10564804
enhanced biodegradation of phenanthrene by a marine bacterium in presence of a synthetic surfactant.	the biodegradation of phenanthrene by the marine strain sphingomonas sp. 2mpii (dsmz 11572) was enhanced by the solubilizating properties of the nonionic surfactant tween 80. after 197 h of incubation, 85 +/- 4% of the initial amount of phenanthrene (0.4 g l-1) was biodegraded in presence of tween 80 (0.5 g l-1) as opposed to 52 +/- 5% without this synthetic surfactant. these results confirm that the activity of the strain 2mpii is limited by the bioavailability of the polycyclic aromatic hydroc ...	1999	10583752
analysis of the reaction mechanism and substrate specificity of haloalkane dehalogenases by sequential and structural comparisons.	haloalkane dehalogenases catalyse environmentally important dehalogenation reactions. these microbial enzymes represent objects of interest for protein engineering studies, attempting to improve their catalytic efficiency or broaden their substrate specificity towards environmental pollutants. this paper presents the results of a comparative study of haloalkane dehalogenases originating from different organisms. protein sequences and the models of tertiary structures of haloalkane dehalogenases ...	1999	10585505
characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (pcpa) of sphingomonas chlorophenolica atcc 39723.	pentachlorophenol (pcp) is a general biocide and a major environmental pollutant. the initial steps of pcp degradation by sphingomonas chlorophenolica atcc 39723 have been studied and characterized. two enzymes are responsible for converting pcp to 2, 6-dichloro-p-hydroquinone (2,6-dich) which is a common metabolic intermediate of the biodegradation of polychlorinated phenols. 2, 6-dich is degraded by pcpa from strain atcc 39723, but the reaction end product has been misidentified as 6-chlorohyd ...	1999	10600501
genetic and biochemical characterization of a 2-pyrone-4, 6-dicarboxylic acid hydrolase involved in the protocatechuate 4, 5-cleavage pathway of sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on a wide variety of dimeric lignin compounds with guaiacyl moieties, which are converted into protocatechuate by the actions of lignin degradation enzymes in this strain. protocatechuate is a key metabolite in the syk-6 degradation of lignin compounds with guaiacyl moieties, and it is thought that it degrades to pyruvate and oxaloacetate via the protocatechuate 4,5-cleavage pathway. in a 10.5-kb ecori fragment carrying the protocatechuate 4,5-diox ...	1999	9864312
chlorine inactivation of sphingomonas cells attached to goethite particles in drinking water.	bacteria in drinking water, attached or not attached to goethite particles, were disinfected with chlorine. no additional protection was provided to the bacteria by their attachment to particles, and the limited efficiency of inactivation by chlorine was attributed to the presence of bacterial aggregates in both types of suspension.	1999	9872809
isolation of a bacterial strain able to degrade branched nonylphenol.	conventional enrichment of microorganisms on branched nonylphenol (np) as only carbon and energy source yielded mixed cultures able to grow on the organic compound. however, plating yielded no single colonies capable, alone or in combination with other isolates, of degrading the np in liquid culture. therefore, a special approach was used, referred to as "serial dilution-plate resuspension," to reduce culture complexity. in this way, one isolate, ttnp3, tentatively identified as a sphingomonas s ...	1999	9925611
complement activation by bacterial surface glycolipids: a study with planar bilayer membranes.	planar asymmetric glycolipid/phospholipid bilayer membranes were used as a reconstitution model of the lipid matrix of the outer membrane of gram-negative bacteria to study complement (c) activation by various bacterial surface glycolipids with the aim of defining the c activation pathway. as glycolipids the lipopolysaccharides of salmonella enterica serovar minnesota r mutant strains r595 (re lps) and r4 (rd2 lps), pentaacyl lipid a from the lps of the escherichia coli re mutant f515, and glyco ...	1999	9929374
polyphasic classification of 0.2 microm filterable bacteria from the western mediterranean sea	the 0.2 microm filtration of sea water samples from the mediterranean sea (bay of calvi, corsica), collected from 10 m and 35 m depth led to the isolation of several gram-negative bacterial strains able to grow on full-strength media as well as on diluted media. the analysis of the 16s rrna gene sequences and estimation of the phylogenetic relationships of these facultative oligotrophic bacteria indicated that they grouped into two phylogenetic branches. the strains re10f/2, re10f/5 (10 m depth ...	1999	10794152
enzymatic and genetic bases on assimilation, depolymerization, and transport of heteropolysaccharides in bacteria.	when microorganisms utilize macromolecules for their growth, they commonly produce extracellular depolymerization enzymes and then incorporate the depolymerized low-molecular-weight products. assimilation of heteropolysaccharides (gellan and xanthan) by bacillus sp. gl1 depends on this generally accepted mechanism. on the other hand, sphingomonas sp. a1 represents an unexplored specific and interesting system for macromolecule assimilation. in the presence of heteropolysaccharide (alginate), the ...	1999	16232439
application of a floc-forming genetically engineered microorganism to a sequencing batch reactor for phenolic wastewater treatment.	for enhancing the survival of genetically engineered microorganisms (gems) in activated sludge processes, the use of a floc-forming bacterium as the host for a recombinant plasmid was proposed. the floc-forming and phenol-degrading gem sphingomonas paucimobilis 551 (ps10-45) was cultured to demonstrate this proposal. although the maximum growth rate of the host strain s. paucimobilis 551 was low and the recombinant plasmid ps10-45 was unstable in the host, the resultant gem s. paucimobilis 551 ( ...	1999	16232579
biodegradation of dibenzothiophene and 4,6-dimethyldibenzothiophene by sphingomonas paucimobilis strain tzs-7.	strain tzs-7, tentatively identified as sphingomonas paucimobilis, was isolated from crude oil for its ability to degrade dibenzothiophene (dbt) and 4,6-dimethyldibenzothiophene (4,6-dmdbt). this strain did not utilize dbt or 4,6-dmdbt as the sole source of sulfur. however, the degradative activity was induced by various aromatic compounds, including dbt, fluorene, anthracene, naphthalene and toluene. three products formed from 4,6-dmdbt degradation were detected and two of these were proposed t ...	1999	16232614
preferential occurrence of diazotrophic endophytes, azoarcus spp., in wild rice species and land races of oryza sativa in comparison with modern races.	several diazotrophic species of azoarcus spp. occur as endophytes in the pioneer plant kallar grass. the purpose of this study was to screen asian wild rice and cultivated oryza sativa varieties for natural association with these endophytes. populations of culturable diazotrophs in surface-sterilized roots were characterized by 16s rdna sequence analysis, and azoarcus species were identified by genomic fingerprints. a. indigens and azoarcus sp. group c were detected only rarely, whereas azoarcus ...	2000	11220300
chemotaxonomic and phylogenetic analyses of sphingomonas strains isolated from ears of plants in the family gramineae and a proposal of sphingomonas roseoflava sp. nov.	chemotaxonomic and phylogenetic characteristics of sphingomonas strains isolated from plants of the family gramineae were investigated. all strains contained the monosaccharide (glucuronic acid) type of glycosphingolipid (gsl-1). most were found also to contain the oligosaccharide-type glycosphingolipids. fatty acid and sphingosine profiles of the isolates were identical, although the ratio of the contents varies among the isolates. they all contained ubiquinone q-10, and the g1c contents were f ...	2000	12483599
multimicrobial sensor using microstructured three-dimensional electrodes based on silicon technology.	two microbial strains with different substrate spectra were immobilized separately within a single biosensor chip featuring four individually addressable platinum electrodes. these were sputtered onto the inner surface of four isolated pyramidal cavities ("containments") micromachined on a silicon wafer. the biosensor chip was integrated into a flow-through system to measure the oxygen consumption of the immobilized microorganisms in the presence of assimilable analytes. as a model system, a yea ...	2000	10815960
comparison of biotin production by recombinant sphingomonas sp. under various agitation conditions.	biotin production by fermentation of recombinant sphingomonas sp./psp304 was investigated. a complex medium containing 60g/l of glycerol and 30g/l of yeast extract was suitable for biotin production. biotin was produced in the late logarithmic or stationary phase after glycerol starvation. the optimum ph value for biotin production was 7.0. when the dissolved oxygen concentration (do) was controlled at a constant level, the biotin concentration produced after 120h was significantly lower than th ...	2000	10817818
recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol.	tetrachlorohydroquinone dehalogenase catalyzes the replacement of chlorine atoms on tetrachlorohydroquinone and trichlorohydroquinone with hydrogen atoms during the biodegradation of pentachlorophenol by sphingomonas chlorophenolica. the sequence of the active site region of tetrachlorohydroquinone dehalogenase is very similar to those of the corresponding regions of maleylacetoacetate isomerases, enzymes that catalyze the glutathione-dependent isomerization of a cis double bond in maleylacetoac ...	2000	10820000
description of sphingomonas xenophaga sp. nov. for strains bn6t and n,n which degrade xenobiotic aromatic compounds.	the taxonomic position of two bacterial strains, bn6t and n,n, with the ability to degrade xenobiotic aromatic compounds (naphthalenesulfonates or n,n-dimethylaniline) was investigated. the 165 rrna gene sequence, the g+c content of the dna (62-63 mol%) and the detection of ubiquinone q-10, 2-hydroxymyristic acid and the sphingoglycolipid present clearly placed the two strains into the genus sphingomonas. both strains are representatives of one species according to the level of dna relatedness ( ...	2000	10826785
aerobic denitrifiers isolated from diverse natural and managed ecosystems.	twenty-eight bacterial strains were isolated from an ecosystem adapted to fluctuating oxic-anoxic conditions. this ecosystem comprised a mixture of different natural and wastewater treatment environments. among the 28 strains isolated, 10 exhibited aerobic denitrifying activity, i.e., co-respiration of oxygen and nitrate and simultaneous production of nitrite by 4 of them and of nitrogen gas by the remaining 6. comparisons between the 16s rdna sequences of the 10 strains showed that 3 of them we ...	2000	10833227
overexpression in escherichia coli, purification, and characterization of sphingomonas sp. a1 alginate lyases.	a bacterium sphingomonas sp. a1 produces three kinds of alginate lyases [a1-i (66 kda), a1-ii (25 kda), and a1-iii (40 kda)] from a single precursor, through posttranslational processing. overexpression systems for these alginate lyases were constructed in escherichia coli cells by controlling of the lyase genes under t7 promoter and terminator. expression levels of a1-i, a1-ii, and a1-iii in e. coli cells were 3.50, 3.04, and 2.13 ku/liter of culture, respectively, and were over 10-fold higher ...	2000	10833394
evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach.	the pathway for degradation of the xenobiotic pesticide pentachlorophenol in sphingomonas chlorophenolica probably evolved in the past few decades by the recruitment of enzymes from two other catabolic pathways. the first and third enzymes in the pathway, pentachlorophenol hydroxylase and 2,6-dichlorohydroquinone dioxygenase, may have originated from enzymes in a pathway for degradation of a naturally occurring chlorinated phenol. the second enzyme, a reductive dehalogenase, may have evolved fro ...	2000	10838562
physiological and genetic comparison of two aromatic hydrocarbon-degrading sphingomonas strains.	sphingomonas yanoikuyae strain b1 is able to degrade a wider range of aromatic hydrocarbons than s. paucimobilis strain tne12 can degrade. various culture techniques were used to corroborate that b1 used m-xylene, biphenyl, toluene, naphthalene, and phenanthrene as sole carbon and energy sources. in contrast, tne12 could not mineralize m-xylene, biphenyl, toluene, or naphthalene. however, fluoranthene served as carbon and energy source for tne12 but not b1. southern blots were performed using th ...	2000	10850662
fatty acid-specific, regiospecific, and stereospecific hydroxylation by cytochrome p450 (cyp152b1) from sphingomonas paucimobilis: substrate structure required for alpha-hydroxylation.	fatty acid alpha-hydroxylase from sphingomonas paucimobilis is an unusual cytochrome p450 enzyme that hydroxylates the alpha-carbon of fatty acids in the presence of h2o2. herein, we describe our investigation concerning the utilization of various substrates and the optical configuration of the alpha-hydroxyl product using a recombinant form of this enzyme. this enzyme can metabolize saturated fatty acids with carbon chain lengths of more than 10. the km value for pentadecanoic acid (c15) was th ...	2000	10858020
carbofuran degradation mediated by three related plasmid systems.	two carbofuran-metabolizing sphingomonas strains, ta and cd, were isolated from soils with differing histories of exposure to carbofuran. these strains were compared with a previously described strain, sphingomonas sp. cfo6, with regard to growth rate, formation of metabolites, and plasmid content and structure. extensive regions of similarity were observed between the three different plasmid systems as evidenced by cross hybridization. in addition, all three systems harbor is1412, an insertion ...	2000	10858578
a novel bacterial atp-binding cassette transporter system that allows uptake of macromolecules.	a gram-negative bacterium, sphingomonas sp. strain a1, isolated as a producer of alginate lyase, has a characteristic cell envelope structure and forms a mouth-like pit on its surface. the pit is produced only when the cells have to incorporate and assimilate alginate. an alginate uptake-deficient mutant was derived from cells of strain a1. one open reading frame, algs (1,089 bp), exhibiting homology to the bacterial atp-binding domain of an abc transporter, was cloned as a fragment complementin ...	2000	10869078
monitoring by laser-flow-cytometry of the polycyclic aromatic hydrocarbon-degrading sphingomonas sp. strain 107 during biotreatment of a contaminated soil.	a flow cytometric method (fcm) was used to detect and accurately enumerate a polycyclic aromatic hydrocarbon-degrading bacterial strain, sphingomonas sp. 107, inoculated into a soil sample artificially contaminated with pyrene. to compare the fcm method with colony forming unit (cfu) assays, a rifampicin-resistant sphingomonas sp. 107 was obtained which could be distinguished from the indigenous microflora, since there was no organism resistant to rifampicin in the soil that could transform indo ...	2000	10872079
riboprints as a tool for rapid preliminary identification of sphingomonads.	fourtythree strains of the genus sphingomonas and close relatives were subjected to riboprint analyses generated after digestion of genomic dna with the restriction enzyme ecori and hybridization with e. coli rrnb operon. the majority of strains were characterized by a complex banding pattern in the riboprints. high degrees of similarities in the riboprints were only observed among strains of the same species such as s. yanoikuyae, s. aromaticivorans, s. subarctica and s. chlorophenolica. strain ...	2000	10879985
ability of casamino acids to support gellan production by sphingomonas paucimobilis atcc 31461.	the ability of casamino acids and vitamin-assay casamino acids to support gellan production by sphingomonas paucimobilis atcc 31461 was examined in a medium containing glucose or corn syrup as the carbon source relative to yeast extract supplementation. when glucose or corn syrup served as the carbon source, the presence of yeast extract in the growth medium stimulated gellan production by strain atcc 31461 on casamino acids. using vitamin-assay casamino acids as the nitrogen source, the additio ...	2000	10885499
cloning and expression of genes encoding meta-cleavage enzymes from 4,6-dimethyldibenzothiophene-degrading sphingomonas strain tzs-7.	sphingomonas strain tzs-7 was reported as the first strain to have the ability to degrade 4,6-dimethyldibenzothiophene (4,6-dmdbt) by the ring-destructive pathway. two genes for meta-cleavage dioxygenases were cloned from strain tzs-7. expression of each gene showed that one enzyme was specific for 2,3-dihydroxybiphenyl while another was more specific for catechol. the genes for the two enzymes were named dmdc and cata. the analysis of deduced amino acid sequences indicates that cata falls into ...	2000	10899588
isolation and sequence analysis of repa from the incurable 90 mda plasmid of azospirillum brasilense.	an open reading frame encoding a protein of 312 amino acids was identified in an essential region of the 90 mda plasmid of azospirillum brasilense. the putative protein shows similarity with repa proteins of plasmids of sphingomonas aromacitovorans, rhodotermus marinus, chlorobium limicola and bifidobacterium asteroides and with the repa protein of the broad host range plasmid psa. a putative helix-turn-helix motif was identified in the central part of the a. brasilense repa protein. analysis of ...	2000	10902916
identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product.	a genomic region involved in tetralin biodegradation was recently identified in sphingomonas strain tfa. we have cloned and sequenced from this region a gene designated thnc, which codes for an extradiol dioxygenase required for tetralin utilization. comparison to similar sequences allowed us to define a subfamily of 1, 2-dihydroxynaphthalene extradiol dioxygenases, which comprises two clearly different groups, and to show that thnc clusters within group 2 of this subfamily. 1,2-dihydroxy-5,6,7, ...	2000	10633115
analysis of bacterial dna in skin and muscle of the tyrolean iceman offers new insight into the mummification process.	about 80 sequences (16s ribosomal rna gene) of bacterial dna in samples of skin and muscle taken directly from the tyrolean iceman (3350-3100 years b.c.) or recovered during the 1992 archaeological expedition at the alpine site were analyzed to obtain clues to the natural mummification process that allowed the corpse of the neolithic shepherd/hunter to be preserved for more than 5,000 years. the investigation was made more complex by the fact that the surface of the mummy had been swabbed with p ...	2000	10640948
culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs.	recent investigations of oil reservoirs in a variety of locales have indicated that these habitats may harbor active thermophilic prokaryotic assemblages. in this study, we used both molecular and culture-based methods to characterize prokaryotic consortia associated with high-temperature, sulfur-rich oil reservoirs in california. enrichment cultures designed for anaerobic thermophiles, both autotrophic and heterotrophic, were successful at temperatures ranging from 60 to 90 degrees c. heterotro ...	2000	10653739
crystallization and preliminary x-ray crystallographic analysis of alginate lyase a1-ii from sphingomonas species a1.	alginate lyase a1-ii of sphingomonas species a1 was purified and crystallized using the hanging drop vapor-diffusion method in 0.1 m tris-hcl buffer containing 43% saturated ammonium sulfate, 8% polyethylene glycol 4000 and 0.2 m li(2)so(4) at ph 8.5 and 20 degrees c. the crystals are tetragonal and belong to the space group p4(3)2(1)2 or p4(1)2(1)2 with unit cell dimensions of a=b=144.07 and c=296.38 a. the diffraction data up to 2.8 a were collected by a synchrotron radiation source at spring- ...	2000	10669804
evaluation of autoscan-w/a and the vitek gni+ automicrobic system for identification of non-glucose-fermenting gram-negative bacilli.	the autoscan-w/a (w/a; dade behring microscan inc., west sacramento, calif.) and vitek automicrobic system (vitek ams; biomérieux vitek systems, inc., hazelwood, mo.) are both fully automated microbiology systems. we evaluated the accuracy of these two systems in identifying nonglucose-fermenting gram-negative bacilli. we used the w/a with conventional-panel neg combo type 12 and vitek gni+ identification systems. a total of 301 isolates from 25 different species were tested. of these, 299 isola ...	2000	10699007
structural analysis of two glycosphingolipids from the lipopolysaccharide-lacking bacterium sphingomonas capsulata.	two glycosphingolipids, gsl-1 and gsl-3, were isolated from sphingomonas capsulata and studied by methylation analysis, laser desorption mass spectrometry, and 1h and 13c nmr spectroscopy, including two-dimensional 1h,1h cosy and heteronuclear 13c,1h cosy experiments. gsl-1 and gsl-3 differ in their carbohydrate part, their structures being alpha-d-glcpa-(1-->1)-cer and alpha-d-galp-(1-->6)-alpha-d-glcpn-(1-->4)-alpha-d-glcpa(1-- >1)cer, respectively. variations occur in the ceramide of gsl-1 an ...	2000	10712617
complete nucleotide sequence of a plant tumor-inducing ti plasmid.	crown gall tumor disease in dicot plants is caused by agrobacterium tumefaciens harboring a giant tumor-inducing (ti) plasmid. here, for the first time among agrobacterial plasmids, the nucleotide sequence of a typical nopaline-type ti plasmid (pti-sakura) was determined completely. in total, 195 open reading frames (orfs) were estimated in the 206479 bp long sequence. 20 genes for conjugation, three for replication, 22 for pathogenesis and 37 for genetic colonization of host plants were found w ...	2000	10721727
detection of groel in activated sludge: a model for detection of system stress.	groel is a ubiquitous constitutively synthesized protein that is also stress inducible. activated sludge, which is a standard biological process used in wastewater treatment systems, is made up of a diverse microbial consortium. the synthesis of groel in activated sludge was significantly induced after heat (42 degrees c) shock. the increased level of groel expression was shown to be due to de novo protein synthesis. we have demonstrated a method which shows that stress proteins can be detected ...	2000	10728556
presence of two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases in naphthalenesulfonate-assimilating sphingomonas paucimobilis ta-2: comparison of some properties.	two trans-o-hydroxybenzylidenepyruvate hydratase-aldolases named thbp ha a and thbp ha b were purified from a cell-free extract of naphthalenesulfonate-assimilating sphingomonas paucimobilis (formerly pseudomonas sp.) ta-2 to an electrophoretically homogeneous state by successive column chromatographies on deae-cellulose, deae-toyopearl 650m, sephacryl s-100, hydroxyapatite, and mono q. these enzymes were similar to each other in molecular mass (ca. 37 kda on sds-page, ca. 110 kda on ultracentri ...	2000	10731665
use of oligotrophic bacteria for the biological monitoring of heavy metals.	oligotrophic bacteria exhibited active growth even in nutritionally deficient medium made with nutrient broth that had been diluted with distilled water, 1 : 10 000. the oligotrophic bacteria, sphingomonas paucimobilis kps01 and burkholderia cepacia kpc01 and kpc02 were found to be highly susceptible to heavy metals and to be potentially useful as sensors for the assessment of toxicity. the susceptibility of the bacteria to metals was measured by incubating the bacteria with metals of varying co ...	2000	10735254
a second [2fe-2s] ferredoxin from sphingomonas sp. strain rw1 can function as an electron donor for the dioxin dioxygenase.	the first step in the degradation of dibenzofuran and dibenzo-p-dioxin by sphingomonas sp. strain rw1 is carried out by dioxin dioxygenase (dxna1a2), a ring-dihydroxylating enzyme. an open reading frame (fdx3) that could potentially specify a new ferredoxin has been identified downstream of dxna1a2, a two-cistron gene (j. armengaud, b. happe, and k. n. timmis, j. bacteriol. 180:3954-3966, 1998). in the present study, we report a biochemical analysis of fdx3 produced in escherichia coli. this thi ...	2000	10735867
phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method.	aerobically grown enrichment cultures derived from hydrocarbon-contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. the bacterial species composition of these cultures was investigated by pcr of the 16s rdna gene using multiple primer combinations. near full-length 16s rdna clone libraries were generated and screened by restriction analysis prior to ...	2000	10739339
the function of cytoplasmic flavin reductases in the reduction of azo dyes by bacteria.	a flavin reductase, which is naturally part of the ribonucleotide reductase complex of escherichia coli, acted in cell extracts of recombinant e. coli strains under aerobic and anaerobic conditions as an "azo reductase." the transfer of the recombinant plasmid, which resulted in the constitutive expression of high levels of activity of the flavin reductase, increased the reduction rate for different industrially relevant sulfonated azo dyes in vitro almost 100-fold. the flavin reductase gene (fr ...	2000	10742223
formation of the metabolic intermediate 2,4,4-trimethyl-2-pentanol during incubation of a sphingomonas sp. strain with the xeno-estrogenic octylphenol.	degradation of branched octylphenol was studied in a bacterial culture of a sphingomonas sp. strain. octylphenol is considered to be the most stable degradation intermediate formed from the corresponding nonionic octylphenol polyethoxylates surfactants during biological wastewater treatment. since octylphenol can exert estrogenic effects in wildlife, a detailed study of its biodegradation is warranted. the aerobic microbiological transformation of octylphenol was examined with and without the ad ...	2000	11194969
microbial degradation of poly(aspartic acid) by two isolated strains of pedobacter sp. and sphingomonas sp.	microbial degradation of thermally synthesized poly(aspartic acid) (paa) was investigated. a paa-p1 sample (mn, 7500; mw, 20,000; number of branched units/100 monomer units, 3.1) was completely degraded in natural river water within 15 days at 25 degrees c. a new paa-degrading bacterium (strain kp-2: jcm10638) was isolated together with sphingomonas sp. kt-1 (jcm10459) from river water, and identified as a member of pedobacter. a pedobacter isolate was capable of degrading high-molecular-weight ...	2000	11710094
interpenetrating network formation in gellan--agarose gel composites.	thermal, mechanical, turbidity, and microscope evidence is provided which strongly suggests molecular interpenetrating network (ipn) formation by mixtures of the bacterial and seaweed polysaccharides gellan and agarose. there is no evidence for synergistic coupling of the networks, and simple phase separation (demixing) can definitely be ruled out. some changes in the gellan gelling behavior are suggested, however, by the increased gellan effective concentrations implicit in cure curve data. the ...	2000	11710203
horizontal transfer of an exopolymer complex from one bacterial species to another.	alasan, the exocellular polymeric emulsifier produced by acinetobacter radioresistens ka53 was shown to bind to the surface of sphingomonas paucimobilis epa505 and acinetobacter calcoaceticus rag-1. the presence of alasan on the surface of s. paucimobilis epa505 and a. calcoaceticus rag-1 caused a decrease in their cell-surface hydrophobicities. binding was proportional to the concentration of recipient cells and input alasan. at the highest concentration of a. calcoaceticus rag-1 (4 x 10(9) ml( ...	2000	11234924
an evaluation of terminal-restriction fragment length polymorphism (t-rflp) analysis for the study of microbial community structure and dynamics.	a systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (t-rflp) analysis for the study of microbial community structure has been undertaken. the reproducibility and robustness of the method has been assessed using environmental dna samples isolated directly from pcb-polluted or pristine soil, and subsequent polymerase chain reaction (pcr) amplification of total community 16s rdna. an initial investigation to assess the variability both within and ...	2000	11243261
evolution of bacterial diversity during enrichment of pcp-degrading activated soils.	the microbiota of completely mixed soil slurry was acclimated with pentachlorophenol (pcp) or with a wood preservative mixture (wpm) containing several pollutants such as pcp and petroleum hydrocarbons. the impact of these compounds on the bacterial diversity was studied by using molecular tools. pcr amplifications of the 16s ribosomal rna gene sequences (rdna) were carried out with total dna extracted from soil slurry samples taken at different time points during the enrichment process of the p ...	2000	12035093
catabolic and genetic diversity of degradative bacteria from fuel-hydrocarbon contaminated aquifers.	a bstractsubsurface sediments were recovered from two aquifers contaminated with petroleum hydrocarbons in order to isolate and characterize indigenous microorganisms capable of biodegrading fuel-related compounds. these sediments had been previously studied using catabolic gene probes providing putative demonstration of significant biodegradation potential. based on 16s rdna sequence analysis, the isolates were phylogenetically similar to common soil microorganisms, including members of the gen ...	2000	12035098
molecular identification of oligoalginate lyase of sphingomonas sp. strain a1 as one of the enzymes required for complete depolymerization of alginate.	a bacterium, sphingomonas sp. strain a1, can incorporate alginate into cells through a novel abc (atp-binding cassette) transporter system specific to the macromolecule. the transported alginate is depolymerized to di- and trisaccharides by three kinds of cytoplasmic alginate lyases (a1-i [66 kda], a1-ii [25 kda], and a1-iii [40 kda]) generated from a single precursor through posttranslational autoprocessing. the resultant alginate oligosaccharides were degraded to monosaccharides by cytoplasmic ...	2000	10913091
evaluation of fluorescently labeled lectins for noninvasive localization of extracellular polymeric substances in sphingomonas biofilms.	three strains of sphingomonas were grown as biofilms and tested for binding of five fluorescently labeled lectins (con a-type iv-tritc or -cy5, pha-e-tritc, pna-tritc, uea 1-tritc, and wga-texas red). only cona and wga were significantly bound by the biofilms. binding of the five lectins to artificial biofilms made of the commercially available sphingomonas extracellular polysaccharides was similar to binding to living biofilms. staining of the living and artificial biofilms by cona might be exp ...	2000	10919811
unique heme environment at the putative distal region of hydrogen peroxide-dependent fatty acid alpha-hydroxylase from sphingomonas paucimobilis (peroxygenase p450(spalpha).	fatty acid alpha-hydroxylase from sphingomonas paucimobilis is a hydrogen peroxide-dependent cytochrome p450 (p450) enzyme (p450(spalpha)). in this study, heme-ligand exchange reactions of p450(spalpha) were investigated using the optical spectroscopic method and compared with those of various p450s. alkylamines (c >/= 5) induced changes in the spectrum of ferric p450(spalpha) to one typical of a nitrogenous ligand-bound low-spin form of ferric p450, although their affinities were lower than tho ...	2000	10920253
construction of mutants of sphingomonas paucimobilis defective in terminal mannose in the glycosphingolipid.	mutants of sphingomonaspaucimobilis defective in a part of the carbohydrate moiety of the glycosphingolipid (gsl) were constructed by transposon (tn5)-insertional mutagenesis. defective mutants were selected by elisa using the antibody recognizing the tetrasaccharide-type gsl (gsl-4a) of s. paucimobilis. eight defective mutants were selected from about 8,000 kanamycin-resistant strains, and seven of them were found to lack the terminal mannose of gsl-4a. the chemical structure of the mutant gsl ...	2000	10923808
enhanced attachment of bradyrhizobium japonicum to soybean through reduced root colonization of internally seedborne microorganisms.	internally seedborne microorganisms are those surviving common surface sterilization procedures. such microbes often colonize the radicle surface of a germinating soybean (glycine max) seed, introducing an undefined parameter into studies on attachment and infection by bradyrhizobium japonicum. bacterial isolates from surface-sterilized soybean seed, cv. williams 82 and cv. maverick, used in our studies, were identified as agrobacterium radiobacter, aeromonas sp., bacillus spp., chryseomonas lut ...	2000	10932352
preparation of (s)-n-substituted 4-hydroxy-pyrrolidin-2-ones by regio- and stereoselective hydroxylation with sphingomonas sp. hxn-200.	[reaction: see text] enantiopure (s)-n-substituted 4-hydroxy-pyrrolidin-2-ones have been prepared for the first time by regio- and stereoselective hydroxylation of the corresponding pyrrolidin-2-ones by use of a biocatalyst. hydroxylation of 6 and 8 with sphingomonas sp. hxn-200 afforded 68% of (s)-7 in >99.9% ee and 46% of (s)-9 in 92% ee, respectively. simple crystallization increased the ee of (s)-9 to 99. 9% in 82% yield.	2000	11101461
isolation of bacteria from toxic dinoflagellate alexandrium minutum and their effects on algae toxicity.	attempts were made to isolate the bacteria from toxic dinoflagellate alexandrium minutum t1 and to study the effect of these bacteria on the growth and toxicity of a. minutum t1. it was found that intracellular bacterial species including pasteurella haemolytica, pseudomonas vesicularis, and sphingomonas sp., and extracellular bacterial species including pasteurolla pneumotropica, morganella wisconsensis, flavobacterium oryzihabitans, pseudomonas pseudomallei, and sphingomonas sp. all of them we ...	2000	11126517
identification of four structural genes and two putative promoters necessary for utilization of naphthalene, phenanthrene, fluoranthene by sphingomonas paucimobilis var. epa505.	sphingomonas paucimobilis var. epa505 utilizes fluoranthene (fla), naphthalene (nap), and phenanthrene (phe) as sole carbon sources for energy and growth. a genetic library of epa505 was constructed using mini-tn5 promoter reporter genes encoding for tetracycline resistance (tc(p-)) or luminescence (luxab(p-)). out of 2250 tn5 mutants, ten were deficient in utilization of fla, nap, and/or phe as sole carbon sources. three classes of tn5 mutants were defined: classi (nap(-)phe(-)fla(-)), classii ...	2000	11137301
a novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of sphingomonas yanoikuyae.	a novel sphingoglycolipid was isolated from sphingomonas yanoikuyae, and its structure was identified as a galacturonosyl-beta (1-->1)-ceramide. this was a characteristic sphingoglycolipid present in s. yanoikuyae and certain other species of sphingomonas, such as sphingomonas mali, sphingomonas terrae, and sphingomonas macrogoltabidus, but not in the type species of sphingomonas, sphingomonas paucimobilis.	2000	10762275
isolation of adherent polycyclic aromatic hydrocarbon (pah)-degrading bacteria using pah-sorbing carriers.	two different procedures were compared to isolate polycyclic aromatic hydrocarbon (pah)-utilizing bacteria from pah-contaminated soil and sludge samples, i.e., (i) shaken enrichment cultures in liquid mineral medium in which pahs were supplied as crystals and (ii) a new method in which pah degraders were enriched on and recovered from hydrophobic membranes containing sorbed pahs. both techniques were successful, but selected from the same source different bacterial strains able to grow on pahs a ...	2000	10788347
products from the incomplete metabolism of pyrene by polycyclic aromatic hydrocarbon-degrading bacteria.	pyrene is a regulated pollutant at sites contaminated with polycyclic aromatic hydrocarbons (pah). it is mineralized by some bacteria but is also transformed to nonmineral products by a variety of other pah-degrading bacteria. we examined the formation of such products by four bacterial strains and identified and further characterized the most apparently significant of these metabolites. pseudomonas stutzeri strain p16 and bacillus cereus strain p21 transformed pyrene primarily to cis-4,5-dihydr ...	2000	10788360
physiological responses to starvation in the marine oligotrophic ultramicrobacterium sphingomonas sp. strain rb2256.	sphingomonas sp. strain rb2256 is representative of the ultramicrobacteria that proliferate in oligotrophic marine waters. while this class of bacteria is well adapted for growth with low concentrations of nutrients, their ability to respond to complete nutrient deprivation has not previously been investigated. in this study, we examined two-dimensional protein profiles for logarithmic and stationary-phase cells and found that protein spot intensity was regulated by up to 70-fold. a total of 72 ...	2000	10788378
coexistence of two different o demethylation systems in lignin metabolism by sphingomonas paucimobilis syk-6: cloning and sequencing of the lignin biphenyl-specific o-demethylase (ligx) gene.	sphingomonas paucimobilis syk-6 can grow on several dimeric model compounds of lignin as a carbon and energy source. it has o demethylation systems on three kinds of substrates: 5, 5'-dehydrodivanillic acid (ddva), syringate, and vanillate. we previously reported the cloning of a gene involved in the tetrahydrofolate-dependent o demethylation of syringate and vanillate. in the study reported here, we cloned the gene responsible for ddva o demethylation. using nitrosoguanidine mutagenesis, a muta ...	2000	10788391
identification of the pgmg gene, encoding a bifunctional protein with phosphoglucomutase and phosphomannomutase activities, in the gellan gum-producing strain sphingomonas paucimobilis atcc 31461.	the pgmg gene of sphingomonas paucimobilis atcc 31461, the industrial gellan gum-producing strain, was cloned and sequenced. it encodes a 50,059-da polypeptide that has phosphoglucomutase (pgm) and phosphomannomutase (pmm) activities and is 37 to 59% identical to other bifunctional proteins with pgm and pmm activities from gram-negative species, including pseudomonas aeruginosa algc. purified pgmg protein showed a marked preference for glucose-1-phosphate (g1p); the catalytic efficiency was abou ...	2000	10788412
biocatalytic preparation of a chiral synthon for a vasopeptidase inhibitor: enzymatic conversion of n(2)-	[4s-(4i,7i,10aj)]1-octahydro-5-oxo-4-[phenylmethoxy)carbonyl]amino]-7h-pyrido-[2,1-b] [1,3]thiazepine-7-carboxylic acid methyl ester (bms-199541-01) is a key chiral intermediate for the synthesis of omapatrilat (bms-186716), a new vasopeptidease inhibitor under development. by using a selective enrichment culture technique we have isolated a strain of sphingomonas paucimobilis sc 16113, which contains a novel l-lysine epsilon-aminotransferase. this enzyme catalyzed the oxidation of the epsilon-a ...	2000	10938417
polyphasic assignment of an aromatic-degrading pseudomonas sp., strain dj77, in the genus sphingomonas as sphingomonas chungbukensis sp. nov.	pseudomonas sp. strain dj77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. phylogenetic analysis based on 16s rdna sequences indicated that the strain belonged to the genus sphingomonas and formed a monophyletic clade with the type strains of sphingomonas chlorophenolica, sphingomonas herbicidovorans and sphingomonas yanoikuyae with sequence similarity values of 98.1, 96.1 and 95.6%, respectively. genomic relatedness based on dna-dna ...	2000	10939671
distribution of alkb genes within n-alkane-degrading bacteria.	fifty-four bacterial strains belonging to 37 species were tested for their ability to assimilate short chain and/or medium chain liquid n-alkanes. a gene probe derived from the alkb gene of pseudomonas oleovorans atcc 29347 was utilized in hybridization experiments. results of southern hybridization of pcr-amplificates were compared with those of colony hybridization and dot blot hybridization. strongest signals were received only from gram-negative bacteria growing solely with short n-alkanes ( ...	2000	10971768
[osteomyelitis caused by sphingomonas paucimobilis].		2000	10974775
proposal of sphingomonadaceae fam. nov., consisting of sphingomonas yabuuchi et al. 1990, erythrobacter shiba and shimidu 1982, erythromicrobium yurkov et al. 1994, porphyrobacter fuerst et al. 1993, zymomonas kluyver and van niel 1936, and sandaracinobacter yurkov et al. 1997, with the type genus sphingomonas yabuuchi et al. 1990.	based on the results of phylogenetic analysis of the 16s rdna sequences and the presence of n-2'-hydroxymyristoyl dihydrosphingosine 1-glucuronic acid (sgl-1) and 2-hydroxymyristic acid (non-hydroxymyristic acid in zymomonas) in cellular lipids, a new family, sphingomonadaceae, for group 4 of the alpha-subclass of the class proteobacteria is herein proposed and a description of the family is given. the family consists of six genera, sphingomonas, erythrobacter, erythromicrobium, porphyrobacter, ...	2000	10981829
identification of a serine hydrolase which cleaves the alicyclic ring of tetralin.	a gene designated thnd, which is required for biodegradation of the organic solvent tetralin by sphingomonas macrogoltabidus strain tfa, has been identified. sequence comparison analysis indicated that thnd codes for a carbon-carbon bond serine hydrolase showing highest similarity to hydrolases involved in biodegradation of biphenyl. an insertion mutant defective in thnd accumulates the ring fission product which results from the extradiol cleavage of the aromatic ring of dihydroxytetralin. the ...	2000	10986248
regioselectivity and enantioselectivity of naphthalene dioxygenase during arene cis-dihydroxylation: control by phenylalanine 352 in the alpha subunit.	the naphthalene dioxygenase (ndo) system catalyzes the first step in the degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the enzyme has a broad substrate range and catalyzes several types of reactions including cis-dihydroxylation, monooxygenation, and desaturation. substitution of valine or leucine at phe-352 near the active site iron in the alpha subunit of ndo altered the stereochemistry of naphthalene cis-dihydrodiol formed from naphthalene and also changed the region of ox ...	2000	10986254
identification of novel metabolites in the degradation of phenanthrene by sphingomonas sp. strain p2.	sphingomonas sp. strain p2, which is capable of utilizing phenanthrene as a sole carbon and energy source, was isolated from petroleum-contaminated soil in thailand. gas chromatography-mass spectrometry and (1)h and (13)c nuclear magnetic resonance analyses revealed two novel metabolites from the phenanthrene degradation pathway. one was identified as 5,6-benzocoumarin, which was derived by dioxygenation at the 1- and 2-positions of phenanthrene, and the other was determined to be 1,5-dihydroxy- ...	2000	11004408
enhanced degradation of hexachlorocyclohexane isomers by sphingomonas paucimobilis.	hexachlorocyclohexane (hch) has been banned for use in technologically advanced countries; however, it is still in use in tropical countries like india. earlier we reported the degradation of hch isomers by sphingomonas paucimobilis within 12 days of incubation. here we report the role of different factors that could enhance the degradation rate of hch isomers. we found that an increase in the cell number from 10(2) to 10(8) cells/ml resulted in an increased degradation rate of hch isomers viz. ...	2000	11014865
alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.	alginate lyases, characterized as either mannuronate (ec 4.2.2.3) or guluronate lyases (ec 4.2.2.11), catalyze the degradation of alginate, a complex copolymer of alpha-l-guluronate and its c5 epimer beta-d-mannuronate. lyases have been isolated from a wide range of organisms, including algae, marine invertebrates, and marine and terrestrial microorganisms. this review catalogs the major characteristics of these lyases, the methods for analyzing these enzymes, as well as their biological roles. ...	2000	11018131
gellan gum.	for decades microbial exopolysaccharides have been invaluable ingredients in the food industry, as well as having many attractive pharmaceutical and chemical applications. gellan gum is a comparatively new gum elaborated by the gram-negative bacterium sphingomonas paucimobilis. although its physico-chemical properties have been well characterized, the ecology and physiology of sphingomonas, and the factors influencing the fermentation process for production of this gum have received much less at ...	2000	11039329
microbial degradation of phenanthrene by addition of a sophorolipid mixture.	the influence of sophorolipids on microbial degradation of poorly soluble phenanthrene in liquid and soil suspension culture was evaluated in the work presented. experiments were carried out in two parts. in the first part, important basic physico-chemical characteristics of the biosurfactant and the pollutant used were determined. the critical micelle concentration (cmc) and the solubilization ratio of the biosurfactant were found to be in a good range compared with synthetic surfactants. also, ...	2000	11051416
characterization of sphingomonas isolates from finnish and swedish drinking water distribution systems.	sphingomonas species were commonly isolated from biofilms in drinking water distribution systems in finland (three water meters) and sweden (five water taps in different buildings). the sphingomonas isolates (n = 38) were characterized by chemotaxonomic, physiological and phylogenetic methods. fifteen isolates were designated to species sphingomonas aromaticivorans, seven isolates to s. subterranea, two isolates to s. xenophaga and one isolate to s. stygia. thirteen isolates represented one or m ...	2000	11054174
lipid composition and taxonomy of [pseudomonas] echinoides: transfer to the genus sphingomonas.	lipid components of [pseudomonas] echinoides ncimb 9420 have been studied as an aid to taxonomic relocation of the organism. non-polar lipids include the carotenoid nostoxanthin and the ubiquinone q-10. the major fatty acids are cis-vaccenic acid [18:1(11c)], hexadecanoic acid (16:0) and 2-hydroxy-tetradecanoic acid (2-oh-14:0), but 11-methyloctadec-11-enoic acid[11-me-18:1(11)] is a significant minor component. the preponderant phospholipids are phosphatidylethanolamine and phosphatidylglycerol ...	2000	11065379
genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in sphingomonas paucimobilis syk-6.	protocatechuate (pca) is the key intermediate metabolite in the lignin degradation pathway of sphingomonas paucimobilis syk-6 and is metabolized to pyruvate and oxaloacetate via the pca 4,5-cleavage pathway. we characterized the 4-carboxy-2-hydroxymuconate-6-semialdehyde (chms) dehydrogenase gene (ligc). chms is the 4,5-cleavage product of pca and is converted into 2-pyrone-4,6-dicarboxylate (pdc) by ligc. we found that ligc was located 295 bp downstream of ligb, which encodes the large subunit ...	2000	11073908
crystal structure of the haloalkane dehalogenase from sphingomonas paucimobilis ut26.	the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. the enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. here, we present the 1.58 a crystal structure of linb and the 2.0 a structure of linb with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. the enzyme belongs to the alpha/beta hydro ...	2000	11087355
the 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in sphingomonas paucimobilis syk-6.	sphingomonas paucimobilis syk-6 is able to grow on various dimeric lignin compounds, which are converted to vanillate and syringate by the actions of unique lignin degradation enzymes in this strain. vanillate and syringate are degraded by the o-demethylase and converted into protocatechuate (pca) and 3-o-methylgallate (3mga), respectively. pca is further degraded via the pca 4,5-cleavage pathway, while the results suggested that 3mga is degraded through another pathway in which pca 4,5-dioxygen ...	2000	11092855
evidence for a role of rpoe in stressed and unstressed cells of marine vibrio angustum strain s14.	we report the cloning, sequencing, and characterization of the rpoe homolog in vibrio angustum s14. the rpoe gene encodes a protein with a predicted molecular mass of 19.4 kda and has been demonstrated to be present as a single-copy gene by southern blot analysis. the deduced amino acid sequence of rpoe is most similar to that of the rpoe homolog of sphingomonas aromaticivorans, sigma(24), displaying sequence similarity and identity of 63 and 43%, respectively. northern blot analysis demonstrate ...	2000	11092857
apparent contradiction: psychrotolerant bacteria from hydrocarbon-contaminated arctic tundra soils that degrade diterpenoids synthesized by trees.	resin acids are tricyclic terpenoids occurring naturally in trees. we investigated the occurrence of resin acid-degrading bacteria on the arctic tundra near the northern coast of ellesmere island (82 degrees n, 62 degrees w). according to most-probable-number assays, resin acid degraders were abundant (10(3) to 10(4) propagules/g of soil) in hydrocarbon-contaminated soils, but they were undetectable (<3 propagules/g of soil) in pristine soils from the nearby tundra. plate counts indicated that t ...	2000	11097882
profile of a nonylphenol-degrading microflora and its potential for bioremedial applications.	nonylphenol (np) is an important intermediate in the production of various commercial and industrial materials, but is also known as a ubiquitous pollutant in urban aquatic environments. we recently studied the np-degrading activities of microflora in several aquatic environments, and found a notable degrading activity for wastewater from a sewage treatment plant in tokyo. this result led us to isolate np-degrading microbes and identify biodegradation products. using conventional plate culture t ...	2000	11098132
reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase lina.	gamma-hexachlorocyclohexane dehydrochlorinase (lina) catalyzes the initial steps in the biotransformation of the important insecticide gamma-hexachlorocyclohexane (gamma-hch) by the soil bacterium sphingomonas paucimobilis ut26. stereochemical analysis of the reaction products formed during conversion of gamma-hch by lina was investigated by gc-ms, nmr, cd, and molecular modeling. the nmr spectra of 1,3,4,5,6-pentachlorocyclohexene (pcch) produced from gamma-hch using either enzymatic dehydrochl ...	2001	11099497
alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates.	we analyzed the composition of aggregate (lake snow)-associated bacterial communities in lake constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rrna-targeted oligonucleotide probes of various specificity. in addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. generally, between 40 and m ...	2001	11157226
biochemical characterization of broad-specificity enzymes using multivariate experimental design and a colorimetric microplate assay: characterization of the haloalkane dehalogenase mutants.	the ph indicator dye-based colorimetric method and multivariate experimental design were used for the systematic biochemical characterization of the broad-specificity enzymes haloalkane dehalogenases. halogenated compounds for characterization of the enzymes were selected using principal component analysis. the substrates were characterised by 24 physico-chemical and structural descriptors. thirty-four substrates were selected for testing out of 194 halogenated compounds. relative activities det ...	2001	11165344
new broad-host-range promoter probe vectors based on the plasmid rk2 replicon.	broad-host-range plasmid rk2-based promoter probe vectors with a known nucleotide sequence were constructed. in the absence of an upstream promoter, the expression of two tested reporter genes (luc and lacz) in escherichia coli was virtually zero, while insertion of the ptrc promoter resulted in strong inducer-dependent expression. the lacz-based vectors were mobilized into pseudomonas fluorescens st, pseudomonas putida kt2442, sphingomonas spp. and burkholderia spp. lb400, and expression analys ...	2001	11167001
a simple and easy method for the monitoring of environmental pollutants using oligotrophic bacteria.	sphingomonas paucimobilis kps01, an oligotrophic bacterium isolated from soil, may be a useful tool for monitoring heavy metals. previous methods relying on counting of viable cells require a relatively long time and some skill; we have developed a method based on optical density (o.d.) measurements which is significantly faster and does not require skilled personnel. the results of the o.d. and viable count methods were consistent; both methods detected heavy metals at concentrations ranging fr ...	2001	11169034
growth of a bacterial consortium on triclosan.	triclosan is a polychlorinated hydroxy diphenylether that has been widely used as an antimicrobial compound. an enrichment using triclosan as a sole source of carbon and energy yielded a consortium of bacteria capable of growing on this compound. the dichloro ring was partially mineralized, resulting in the conversion of approximately 35% of the [(14)c]triclosan to [(14)c]co(2). use of molecular fingerprinting techniques and 16s rdna cloning and sequencing aided in the identification and eventua ...	2001	11451514
phosphorus-31 nuclear magnetic resonance study of the effect of pentachlorophenol (pcp) on the physiologies of pcp-degrading microorganisms.	free and agarose-encapsulated pentachlorophenol (pcp)-degrading sphingomonas sp. isolates ug25 and ug30 were compared to sphingomonas chlorophenolica atcc 39723 with respect to the ability to degrade pcp. pretreatment of the ug25 and ug30 strains with 50 microg of pcp per ml enabled the cells to subsequently degrade higher levels of this environmental pollutant. similar treatment of atcc 39723 cells had no effect on the level of pcp degraded by this strain. phosphorus-31 nuclear magnetic resonan ...	2001	11472931
proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.	phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ...	2001	11491340
sphingomonas aquatilis sp. nov., sphingomonas koreensis sp. nov., and sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water.	the taxonomic status of four strains from several mineral water sources in taejon, korea, was examined. the dna base compositions of these strains ranged from 62 to 66 mol %. all of the strains contained sphingolipids and ubiquinone 10 as the main respiratory quinone. the cellular fatty acids of these strains included octadecenoic acid, hexadecanoic acid and 2-hydroxymyristic acid, without 3-hydroxy fatty acids. on the basis of morphological, physiological and chemotaxonomic characteristics, tog ...	2001	11491350
microbial reduction of alpha-chloroketone to alpha-chlorohydrin.	microbial reduction of alpha-chloroketone to alpha-chlorohydrin was studied as one of the approaches for construction of the chiral center of the corresponding epoxide. about 100 microorganisms covering many species of candida, pichia, hansenula, geotrichum, rhodococcus and aureobasidium were screened to reduce the alpha-chloroketone stereospecifically. many strains provided the r-alpha-chlorohydrin with 100% enantiomeric excess (ee), e.g., candida sonorensis sc 16117, geotrichum candidum sc 546 ...	2001	11494099
biodegradation of polycyclic aromatic hydrocarbons by sphingomonas strains isolated from the terrestrial subsurface.	several strains of sphingomonas isolated from deep atlantic coastal plain aquifers at the us department of energy savannah river site (srs) near aiken, sc were shown to degrade a variety of aromatic hydrocarbons in a liquid culture medium. sphingomonas aromaticivorans strain b0695 was the most versatile of the five strains examined. this strain was able to degrade acenaphthene, anthracene, phenanthrene, 2,3-benzofluorene, 2-methylnaphthalene, 2,3-dimethylnaphthalene, and fluoranthene in the pres ...	2001	11494104
effects of nonionic surfactants on the uv/visible absorption of bacterial cells.	nonionic surfactants are used in a number of different microbiological applications, including solubilization of cell membranes, washing bacterial cultures prior to experimentation, and enhancing biodegradation of low-solubility compounds. an important consideration in these applications is the potential for the surfactant to alter the cell membrane. one potential means to monitor the impact of surfactants on the bacterial cell membrane is through monitoring the absorbance spectrum of the bacter ...	2001	11494214