Publications

use of a two-phase partitioning bioreactor for degrading polycyclic aromatic hydrocarbons by a sphingomonas sp.	a two-phase partitioning bioreactor (tppb) utilizing the bacterium sphingomonas aromaticivorans b0695 was used to degrade four low molecular weight (lmw) polycyclic aromatic hydrocarbons (pahs). the tppb concept is based on the use of a biocompatible, immiscible organic solvent in which high concentrations of recalcitrant substrates are dissolved. these substances partition into the cell-containing aqueous phase at rates determined by the metabolic activity of the cells. experiments showed that ...	2002	12111172
cadmium biosorption by sphingomonas paucimobilis biomass.	among microorganisms isolated in bangkok, the gram-negative bacterium sphingomonas paucimobilis exhibited the greatest cadmium tolerance. it was able to survive in the medium containing cadmium as high as 200 mg/l. however, concentrations of cadmium at 25-200 mg/l inhibited its growth. the biosorption properties for cadmium of this bacterial biomass and the effects of environmental factors (i.e., biosorbent type, initial ph and biosorbent concentration) on the cadmium biosorption were explored. ...	2002	12146636
organization and regulation of pentachlorophenol-degrading genes in sphingobium chlorophenolicum atcc 39723.	the first three enzymes of the pentachlorophenol (pcp) degradation pathway in sphingobium chlorophenolicum (formerly sphingomonas chlorophenolica) atcc 39723 have been characterized, and the corresponding genes, pcpa, pcpb, and pcpc, have been individually cloned and sequenced. to search for new genes involved in pcp degradation and map the physical locations of the pcp genes, a 24-kb fragment containing pcpa and pcpc was completely sequenced. a putative lysr-type transcriptional regulator gene, ...	2002	12169590
characterization of sphingomonas sp. ant 17, an aromatic hydrocarbon-degrading bacterium isolated from antarctic soil.	sphingomonas sp. strain ant 17 was isolated from fuel-contaminated soil collected at scott base, ross island, antarctica. we anticipated that ant 17 would be a good model organism for studying cold climate bioremediation, and therefore determined its biodegradation capabilities and tolerance of potentially growth-limiting environmental conditions. sphingomonas sp. ant 17 degrades the aromatic fraction of several different crude oils, jet fuel, and diesel fuel at low temperatures and without nutr ...	2002	11984628
sphingopyxis witflariensis sp. nov., isolated from activated sludge.	classification of strain w-50(t), which was isolated from a wastewater treatment plant, was investigated by a polyphasic approach. cells of strain w-50(t) were gram-negative, strictly aerobic, oxidase-positive and yellow-pigmented. ubiquinone q-10 was the main respiratory lipoquinone system and polar lipid fingerprints were characterized by the presence of a sphingoglycolipid, suggesting that strain w-50(t) belongs to the alpha-4 subclass of the proteobacteria. sequencing and comparative analyse ...	2002	12508864
sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow spanish melon fruits.	a polyphasic taxonomic study was performed on the phytopathogenic bacterial strains dapp-pg 224(t) and dapp-pg 228, which cause brown spot on yellow spanish melon (cucumis melo var. inodorus) fruits. based on the presence of glucuronosyl ceramide (sgl-1) in cellular lipids, the results of fatty acid analysis and 16s rdna sequence comparison, the strains had been identified as belonging to the genus sphingomonas and as phylogenetically related to sphingomonas mali, sphingomonas pruni and sphingom ...	2002	12508872
linking of microorganisms to phenanthrene metabolism in soil by analysis of (13)c-labeled cell lipids.	phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [(14)c]phenanthrene, by most-probable-number (mpn) counting, by 16s-23s spacer dna analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [(13)c]phenanthrene-derived carbon into sterols and polar lipid fatty acids (plfas). an unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (pahs), ...	2002	12450834
characterization of tetrachlorohydroquinone reductive dehalogenase from sphingomonas sp. ug30.	tetrachlorohydroquinone reductive dehalogenase (pcpc) is the second of three enzymes that catalyze the initial degradation of pentachlorophenol in sphingomonas sp. ug30 and several other bacterial strains. the ug30 pcpc shares a high degree (94%) of primary sequence identity with the well-studied pcpc from sphingobium chlorophenolicum atcc 39723. significant differences, however, were observed between the two pcpc enzymes in some of their functional and kinetic properties. the temperature optimu ...	2002	12459186
a super-channel in bacteria: macromolecule uptake and depolymerization systems of sphingomonas sp. a1 with a special cell surface structure.		2002	12520874
bacterial growth and biofilm production on pyrene.	enrichment cultures inoculated with arctic soil yielded a biofilm that grew on pyrene and phenanthrene. in a 60-day period, the biofilm degraded 20 microg ml(-1) pyrene or 39 microg ml(-1) phenanthrene. single colonized pyrene crystals (approximately 1.5x0.75x0.35 mm) yielded 10(11) culturable heterotrophs and 10(5) biofilm propagules. analysis of ribosomal intergenic spacers identified six phylotypes in a clone library from the pyrene biofilm. analysis of 16s rrna gene sequences indicated that ...	2002	19709207
influence of phenanthrene and fluoranthene on the degradation of fluorene and glucose by sphingomonas sp. strain lb126 in chemostat cultures.	abstract since bacteria degrading polycyclic aromatic hydrocarbon compounds (pahs) in polluted soils are generally exposed to mixtures of pahs, we examined the influence of simple pah mixtures on the degradation activity of sphingomonas sp. strain lb126. fluorene serves as sole carbon and energy source for the strain lb126 and phenanthrene and fluoranthene are cometabolically degraded by this species. chemostat cultures of the strain lb126 were used to study a potential inhibiting effect of phen ...	2003	19719587
degradation of polyvinyl alcohol by sphingomonas sp. sa3 and its symbiote.	a total of 800 samples was taken from taegu province, korea, where many textile factories provide a source of polyvinyl alcohol (pva) waste. these samples were screened for pva-degrading bacteria. a new strain, sa3, was discovered which formed yellow colonies and used pva as the sole carbon and energy source. strain sa3 was identified as a sphingomonas sp., based on the partial nucleotide sequence analysis of 16s ribosomal rna, the presence of 2-hydroxymyristic acid (14:o 2-oh) and sphingolipids ...	2003	12545389
cloning and sequence analysis of the ces10 gene encoding a sphingomonas paucimobilis esterase.	the ces10 gene of the gellan gum-producing strain sphingomonas paucimobilis atcc 31461 was cloned and sequenced. multi-sequence alignment of the deduced protein indicated that ces10 belongs to the serine hydrolase family with a potential catalytic triad comprising ser(153) (within the g-x-s-x-g consensus sequence), his(75) and asp(125). the mixed block results obtained following pattern search and the low identities detected in a blast analysis indicate that ces10 is significantly different from ...	2003	12764567
biodegradation of selected uv-irradiated and non-irradiated polycyclic aromatic hydrocarbons (pahs).	biodegradation of uv-irradiated anthracene, pyrene, benz[a]anthracene, and dibenz[a,h]anthracene was compared to that of the non-irradiated samples, individually and in synthetic mixtures with enrichment cultures. combined treatment was repeated for individual anthracene and for the pah mixture with sphingomonas sp. strain epa 505 and sphingomonas yanoikuyae. enrichment culture studies were performed on the pah mixtures in the presence of the main photoproduct of anthracene, pure 9,10-anthracene ...	2003	12948055
catalytic mechanism of the maloalkane dehalogenase linb from sphingomonas paucimobilis ut26.	haloalkane dehalogenases are bacterial enzymes capable of carbon-halogen bond cleavage in halogenated compounds. to obtain insights into the mechanism of the haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb), we studied the steady-state and presteady-state kinetics of the conversion of the substrates 1-chlorohexane, chlorocyclohexane, and bromocyclohexane. the results lead to a proposal of a minimal kinetic mechanism consisting of three main steps: (i) substrate binding, (ii) cl ...	2003	12952988
preferential surfactant utilization by a pah-degrading strain: effects on micellar solubilization phenomena.	biodegradable nonionic tween series surfactants were employed to assess the effects of synthetic surfactants on the bioavailability of a target polycyclic aromatic hydrocarbon (pah), phenanthrene, in soil/sediment-free micellar solutions. dosages of surfactants in excess of their respective critical micelle concentrations (cmcs) dramatically enhanced solubilization of phenanthrene, but the micellar-solubilized phenanthrene was neither directly nor readily bioavailable to the pah-degrading strain ...	2003	12953868
biochemical and molecular characterization of poly(aspartic acid) hydrolase-2 from sphingomonas sp. kt-1.	poly(aspartic acid) (paa) hydrolase-2 was purified from crude soluble cellular extracts of sphingomonas sp. kt-1 (jcm10459) and characterized to elucidate the mechanism of alpha,beta-poly(d,l-aspartic acid) (tpaa) biodegradation. the molecular mass of paa hydrolase-2 was 42 kda, and the isoelectric point was 9.6. the optimum values of ph and temperature for the hydrolysis of alpha-di(l-aspartic acid) by paa hydrolase-2 were 7.0 and 55 degrees c, respectively. the effect of inhibitors on the hydr ...	2003	12959596
argimicins b and c, new anti-cyanobacterial compounds produced by sphingomonas sp. m-17.		2003	14513910
modification of activity and specificity of haloalkane dehalogenase from sphingomonas paucimobilis ut26 by engineering of its entrance tunnel.	structural comparison of three different haloalkane dehalogenases suggested that substrate specificity of these bacterial enzymes could be significantly influenced by the size and shape of their entrance tunnels. the surface residue leucine 177 positioned at the tunnel opening of the haloalkane dehalogenase from sphingomonas paucimobilis ut26 was selected for modification based on structural and phylogenetic analysis; the residue partially blocks the entrance tunnel, and it is the most variable ...	2003	14525993
enantioselective trans dihydroxylation of nonactivated c-c double bonds of aliphatic heterocycles with sphingomonas sp. hxn-200.	the bacterial strain sphingomonas sp. hxn-200 was used to catalyze the trans dihydroxylation ofn-substituted 1,2,5,6-tetrahydropyridines 1 and 3-pyrrolines 4 giving the corresponding 3,4-dihydroxypiperidines 3 and 3,4-dihydroxypyrrolidines 6, respectively, with high enantioselectivity and high activity. the trans dihydroxylation was sequentially catalyzed by a monooxygenase and an epoxide hydrolase in the strain with epoxide as intermediate. while both epoxidation and hydrolysis steps contribute ...	2003	14575492
sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment.	a nonylphenol-degrading bacterial strain (yt(t)) was isolated previously from a river sediment sample obtained in ami-machi, ibaraki, japan, and identified as a sphingomonas species. in this study, the taxonomic relationship between strain yt(t), a recently described nonylphenol-degrading strain, sphingomonas cloacae, and sphingobium yanoikuyae, which is phylogenetically related, was examined. their phenotypic characteristics were compared and levels of dna-dna relatedness between these strains ...	2003	14657143
detection and sequencing of the microcystin lr-degrading gene, mlra, from new bacteria isolated from japanese lakes.	mlra is the only microcystin-degrading gene detected in sphingomonas sp. mj-pv. the gene has an extremely rare nucleotide sequence and homologous genes have not yet been discovered in the dna database. we discovered the existence of a gene homologous to mlra in new microcystin-degrading bacteria, md-1 and y2. these strains possessed mlra homologues, and the identities of the genes of md-1 and y2 with the corresponding mj-pv exceeded 98% and 84%, respectively. on the other hand, the mlra gene was ...	2003	14680710
identification and distribution of insertion sequences of paracoccus solventivorans.	three novel insertion sequences (iss) (ispso1, ispso2, and ispso3) of the soil bacterium paracoccus solventivorans dsm 11592 were identified by transposition into entrapment vector pmec1. ispso1 (1,400 bp) carries one large open reading frame (orf) encoding a putative basic protein (with a dde motif conserved among transposases [tnps] of elements belonging to the is256 family) with the highest levels of similarity with the hypothetical tnps of rhodospirillum rubrum and sphingopyxis macrogoltabid ...	2003	14660342
site-directed mutagenesis of an extradiol dioxygenase involved in tetralin biodegradation identifies residues important for activity or substrate specificity.	the sequence of the extradiol dioxygenase thnc, involved in tetralin biodegradation, was aligned with other extradiol dioxygenases involved in biodegradation of polycyclic compounds, and a three-dimensional model of thnc, based on the structure of the previously crystallized 2,3-dihydroxybiphenyl dioxygenase from burkholderia fungorum lb400, was built. in order to assess the functional importance of some non-active-site residues whose relevance could not be established by structural information, ...	2003	12777496
sphingomonas aurantiaca sp. nov., sphingomonas aerolata sp. nov. and sphingomonas faeni sp. nov., air- and dustborne and antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus sphingomonas.	seven psychrotolerant, gram-negative bacterial strains, five dust- and airborne isolates (ma101b(t), ma306a, ma405/90, ma-olki(t) and nw12(t)) and two from the antarctic (ant 20 and m3c203b-b), were subjected to a polyphasic characterization to determine their taxonomic position. high 16s rdna sequences similarities (99.3-100.0 %) demonstrated that they were closely related to each other. phylogenetic evaluation of their 16s rdna sequences revealed that they are members of the genus sphingomonas ...	2003	13130003
monitoring the coral disease, plague type ii, on coral reefs in st. john, u.s. virgin islands.	in july 1997, conspicuous white patches of necrotic tissue and bare skeleton began to appear on scleractinian corals in several bays around st. john, us virgin islands. analysis of diseased coral tissue from five different species confirmed the presence of a sphingomonas-like bacterium, the pathogen for plague type ii. to date, 14 species of hard corals have been affected by plague type ii around st. john. this disease was monitored at haulover and tektite reefs at depths of 7-12 meters. the stu ...	2003	15264553
differential growth response of colony-forming alpha- and gamma-proteobacteria in dilution culture and nutrient addition experiments from lake kinneret (israel), the eastern mediterranean sea, and the gulf of eilat.	even though it is widely accepted that bacterioplankton growth in lakes and marine ecosystems is determined by the trophic status of the systems, knowledge of the relationship between nutrient concentrations and growth of particular bacterial species is almost nonexistent. to address this question, we performed a series of culture experiments with water from lake kinneret (israel), the eastern mediterranean sea, and the gulf of eilat (northern red sea). in the initial water samples, the proporti ...	2003	12513996
degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils.	the potential for biodegradation of polycyclic aromatic hydrocarbons (pahs)at low temperature and under anaerobic conditions is not well understood, but such biodegradation would be very useful for remediation of polluted sites. biodegradation of a mixture of 11 different pahs with two to five aromatic rings, each at a concentration of 10 micro g/ml, was studied in enrichment cultures inoculated with samples of four northern soils. under aerobic conditions, low temperature severely limited pah b ...	2003	12514005
xylene monooxygenase, a membrane-spanning non-heme diiron enzyme that hydroxylates hydrocarbons via a substrate radical intermediate.	the non-heme diiron enzyme xylene monooxygenase (xylm) has been shown to hydroxylate hydrocarbons via a hydrogen abstraction-carbon radical recombination mechanism (oxygen rebound). using the radical clock bicyclo[4.1.0]heptane (norcarane) in a whole-cell assay, and observing the ratio of rearranged 3-(hydroxymethyl)cyclohexene and unrearranged 2-norcaranol products, the lifetime of the substrate radical was determined to be approximately 0.2 ns. the wild-type organism pseudomonas putida mt-2 an ...	2003	12811621
intersubunit interaction and catalytic activity of catechol 2,3-dioxygenases.	catechol 2,3-dioxygenases (c23os; ec 1.3.11.2) form a large protein family that is divided into several subgroups. amino acid sequences of c23os belonging to subgroup i.2.a and those belonging to i.2.b are found to be approx. 50% identical. when the central parts of the c23o sequences belonging to i.2.b were fused with the n-terminal and c-terminal sequences of i.2.a c23o, the hybrid enzymes were not active. to understand why these hybrid c23os were inactive, hybrids between xyle(p) (c23o found ...	2003	12519074
roles of the enantioselective glutathione s-transferases in cleavage of beta-aryl ether.	cleavage of the beta-aryl ether linkage is the most important process in lignin degradation. here we characterize the three tandemly located glutathione s-transferase (gst) genes, ligf, lige, and ligg, from low-molecular-weight lignin-degrading sphingomonas paucimobilis syk-6, and we describe the actual roles of these genes in the beta-aryl ether cleavage. based on the identification of the reaction product by electrospray ionization-mass spectrometry, a model compound of beta-aryl ether, alpha- ...	2003	12618439
identification and functional characterization of sphingomonas macrogolitabida strain tfa genes involved in the first two steps of the tetralin catabolic pathway.	five genes involved in the two initial steps of the tetralin biodegradation pathway of sphingomonas macrogolitabida strain tfa have been characterized. thna1a2 and thna3a4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. thna1, thna2, and thna3 were essential for tetralin ring-hydroxylating dioxygenase activity. thnb was identified as a dehydrogenase required for tetralin biodegradation.	2003	12618469
a common structure of substrate shared by lignostilbenedioxygenase isozymes from sphingomonas paucimobilis tmy1009.	a common structure of substrates of lignostilbenedioxygenases was investigated using synthesized stilbenes. cell-free extracts of sphingomonas paucimobilis tmy1009 degraded only trans-4-hydroxystilbene and trans-4-hydroxy-3-methoxystilbene. other stilbenes that had no 4-hydroxyl group and had a cis structure were not substrates for lignostilbenedioxygenases. these results indicate that a 4-hydroxyl group and trans-structure is necessary for the common structure for substrates of lignostilbenedio ...	2003	12843670
life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of sphingopyxis alaskensis (formerly sphingomonas alaskensis).	the oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. an important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. this goal has been recognized not only for its relevance in defining the dyn ...	2003	12632213
fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs.	in this work we isolated a culturable endophytic aerobic heterotrophic bacterial community from the stem and root tissues of elm trees (ulmus spp.) and analyzed its fluctuations. a total of 724 bacterial isolates were collected at different times (april, june, september and december) from two elm trees, one infected with elm yellows phytoplasmas, and one which was healthy-looking. the isolates were grouped into 82 haplotypes, identified by means of amplified ribosomal dna restriction analysis (a ...	2003	12648725
implication of two glutathione s-transferases in the optimal metabolism of m-toluate by sphingomonas yanoikuyae b1.	a putative glutathione s-transferase (gst) gene (bphk) was identified in the meta-cleavage operon for the degradation of m-toluate by sphingomonas yanoikuyae b1. disruption of bphk resulted in the loss of gst activity against 1-chloro-2,4-dinitrobenzene and a much increased lag time of the mutant strain mb3 (bphk::km) following subculture into m-toluate medium. in contrast, an increased lag time was not observed when mb3 was grown on biphenyl or m-xylene and mb3 showed normal growth on m-toluate ...	2003	12906359
saccharin as a sole source of carbon and energy for sphingomonas xenophaga skn.	a bacterium, strain skn, that was able to utilize saccharin as the sole source of carbon and energy for aerobic growth, was enriched and isolated from communal sewage. the isolate was identified as a strain of sphingomonas xenophaga. saccharin was quantitatively converted to cell material, sulfate, ammonium and, presumably, co(2). the specific rate of saccharin-dependent oxygen uptake during growth reached a maximum before the culture entered the stationary phase and then fell to undetectable le ...	2003	12610724
characterization of the ugpg gene encoding a udp-glucose pyrophosphorylase from the gellan gum producer sphingomonas paucimobilis atcc 31461.	the ugpggene, which codes for a udp-glucose pyrophosphorylase (ugp) (or glucose-1-phosphate uridylyltransferase; ec 2.7.7.9) in sphingomonas paucimobilis atcc 31461, was cloned and sequenced. this industrial strain produces the exopolysaccharide gellan, a new commercial gelling agent, and the ugpg gene may convert glucose-1-phosphate into udp-glucose in the gellan biosynthetic pathway. the ugpg gene is capable of restoring the capacity of an escherichia coli galu mutant to grow on galactose by f ...	2003	12655408
shifts in diversity and microscale distribution of the adapted bacterial phenotypes due to hg(ii) spiking in soil.	in a previous experiment [ranjard et al. (2000) fems microbiol ecol 31:107-115], the spatial heterogeneity of a mercury impact on soil bacterial community was revealed by an increase of mercury-resistant (hgr) bacterial numbers in the outer fraction and the sand fractions when compared to those in the silt fractions. the objectives of the present study were (i) to investigate whether mercury exposure affects the diversity and the distribution within the various fractions of the hgr populations a ...	2003	12658524
dimethylphthalate hydrolysis by specific microbial esterase.	two bacterial strains: arthrobacter sp. and sphingomonas paucimobilis were isolated from soil by enrichment cultures using dimethylphthalate (dmp) or monomethylphthalate (mmp) as sole carbon source, respectively. dmp was rapidly transformed by an arthrobacter sp. culture with formation of mmp and phthalic acid (pa) which is further degraded. this strain was unable to hydrolyse mmp. a mechanism of degradation of dmp was proposed with two ways: dmp-->pa and dmp-->mmp. the s. paucimobilis strain hy ...	2003	12668024
spatial and temporal analysis of the microbial community in slow sand filters used for treating horticultural irrigation water.	an experimental slow sand filter (ssf) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, phytophthora cryptogea. passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. to monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the atp content was measu ...	2003	12676691
ice from an ice machine is a potential source of bacterial contamination for hpc products -- implications for cell-processing facilities.		2003	12944241
wide geographic distribution of bacteriophages that lyse the same indigenous freshwater isolate (sphingomonas sp. strain b18).	an indigenous freshwater bacterium (sphingomonas sp. strain b18) from lake plubetasee (schleswig-holstein, germany) was used to isolate 44 phages from 13 very different freshwater and brackish habitats in distant geographic areas. this bacterial strain was very sensitive to a broad spectrum of phages from different aquatic environments. phages isolated from geographically distant aquatic habitats, but also those from the same sample, were diverse with respect to morphology and restriction patter ...	2003	12676728
the unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (pahs).	many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (pahs) and related compounds. these sphingomonads such as sphingobium yanoikuyae strain b1, novosphingobium aromaticivorans strain f199, and sphingobium sp. strain p2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology ...	2003	12682862
synergistic relationships in algal-bacterial microcosms for the treatment of aromatic pollutants.	the potential of algal-bacterial microcosms was studied for the biodegradation of salicylate, phenol and phenanthrene. the isolation and characterization of aerobic bacterial strains capable of mineralizing each pollutant were first conducted. ralstonia basilensis was isolated for salicylate degradation, acinetobacter haemolyticus for phenol and pseudomonas migulae and sphingomonas yanoikuyae for phenanthrene. the green alga chlorella sorokiniana was then cultivated in the presence of the pollut ...	2003	12688473
elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by sphingomonas sp. lb126.	the metabolic pathway of the pah fluorene and the cometabolic pathway of the pahs phenanthrene, fluoranthene, anthracene and dibenzothiophene in sphingomonas sp. lb126 were examined. to our knowledge this is the first study on the cometabolic degradation of the three-ring pahs phenanthrene, anthracene and the four-ring pah fluoranthene by a fluorene-utilizing species. metabolism of fluorene was shown to proceed via the 9-fluorenone pathway to form o-phthalic acid and protocatechuic acid. the com ...	2003	12706509
characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from burkholderia cepacia dbo1.	anthranilate (2-aminobenzoate) is an important intermediate in tryptophan metabolism. in order to investigate the degradation of tryptophan through anthranilate by burkholderia cepacia, several plasposon mutations were constructed of strain dbo1 and one mutant with the plasposon insertion in the anthranilate dioxygenase (antdo) genes was chosen for further study. the gene sequence obtained from flanking dna of the plasposon insertion site revealed unexpected information. b. cepacia dbo1 antdo (d ...	2003	13129960
sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of sphingomonas alaskensis to sphingopyxis alaskensis comb. nov.	the taxonomic position of a chlorophenol-degrading bacterium, strain s37t, was investigated. the 16s rdna sequence indicated that this strain belongs to the genus sphingopyxis, exhibiting high sequence similarity to the 16s rdna sequences of sphingomonas alaskensis lmg 18877t (98.8%), sphingopyxis macrogoltabida lmg 17324t (98.2%), sphingopyxis terrae ifo 15098t (95%) and sphingomonas adhaesiva gifu 11458t (92%). these strains (except sphingopyxis terrae ifo 15098t, which was not investigated) a ...	2003	12710615
action mechanism of a selective anti-cyanobacterial compound, argimicin a.	argimicin a is a potent anti-cyanobacterial compound produced by one of algae-lysing bacteria, sphingomonas sp. m-17. since the compound seemed to exhibit selective activities against cyanobacteria and such selectivity were considered to be quite rare, the mode of action of argimicin a was investigated. argimicin a showed a unique delayed action, i.e., the cyanobacterial cell division continued until at least 36 hours treatment even though the decrement of oxygen evolution has been observed at 2 ...	2003	12715875
microbial degradation of high and low molecular weight polyaromatic hydrocarbons in a two-phase partitioning bioreactor by two strains of sphingomonas sp.	a mixture of six polyaromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene, pyrene, chyrysene and benzo[a]pyrene), varying in size from 2 to 5 rings, was dissolved in dodecane, and used as the delivery phase of a partitioning bioreactor. two species of sphingomonas were then used individually, and as a consortium, to determine which of the pahs were degraded. only low molecular weight pahs (naphthalene, phenanthrene and fluoranthene) were degraded by the individual strains, but the cons ...	2003	14514047
isolation and taxonomic and catabolic characterization of a 3,6-dimethylphenanthrene-utilizing strain of sphingomonas sp.	a bacterial strain capable of utilizing 3,6-dimethylphenanthrene (3,6-dmp) as its sole source of carbon and energy was isolated from a creosote-contaminated soil. the isolate was identified as a strain of sphingomonas sp. and was designated strain js1. utilization of 3,6-dmp was demonstrated by an increase in bacterial biomass concomitant with a decrease in 3,6-dmp in a liquid mineral medium with this compound as its sole source of carbon and energy. strain js1 showed a high specificity in the u ...	2003	12718400
an exotype alginate lyase in sphingomonas sp. a1: overexpression in escherichia coli, purification, and characterization of alginate lyase iv (a1-iv).	sphingomonas sp. a1 (strain a1) cells contain three kinds of endotype alginate lyases [a1-i, a1-ii, and a1-iii], all of which are formed from a common precursor through posttranslational processing. in addition to these lyases, another type of lyase (a1-iv) that acts on oligoalginates exists in the bacterium. a1-iv was overexpressed in escherichia coli cells through control of its gene under the t7 promoter. the expression level of the enzyme in e. coli cells was 8.6u/l-culture, which was about ...	2003	12729723
sediment microbes of deep-sea bioherms on the northwest shelf of australia.	the northwest shelf of australia is a region with known petroleum reserves. recent geological investigations have revealed carbonate knolls postulated to be of biological origin. sediment microbial populations at three sites on the northwest shelf, pee shoal, mermaid reef, and scott reef, were investigated for the presence of hydrocarbon-degrading bacteria. from two sampling trips, 246 bacterial strains were purified, and 182 of these strains displayed preferential growth on hydrocarbon-selectiv ...	2003	12739077
a genetic system for the rapid isolation of aromatic-ring-hydroxylating dioxygenase activities.	aromatic-ring-hydroxylating dioxygenases (arhdos) are key enzymes in the aerobic bacterial metabolism of aromatic compounds. they are of biotechnological importance as they function as biocatalysts in the stereospecific synthesis of chiral synthons and the degradation of aromatic pollutants. this report describes the development and validation of a system for the rapid isolation and characterization of specific arhdo activities. the system is based on the identification of arhdo gene segments th ...	2003	12777487
highly enantioselective hydrolysis of alicyclic meso-epoxides with a bacterial epoxide hydrolase from sphingomonas sp. hxn-200: simple syntheses of alicyclic vicinal trans-diols.	hydrolysis of n-benzyloxycarbonyl-3,4-epoxy-pyrrolidine and cyclohexene oxide with the epoxide hydrolase of sphingomonas sp. hxn-200, respectively, gave the corresponding vicinal trans-diols in high ee and yield, representing the first example of enantioselective hydrolysis of a meso-epoxide with a bacterial epoxide hydrolase.	2003	12744319
efficient degradation of 2,4,6-trichlorophenol requires a set of catabolic genes related to tcp genes from ralstonia eutropha jmp134(pjp4).	2,4,6-trichlorophenol (2,4,6-tcp) is a hazardous pollutant. several aerobic bacteria are known to degrade this compound. one of these, ralstonia eutropha jmp134(pjp4), a well-known, versatile chloroaromatic compound degrader, is able to grow in 2,4,6-tcp by converting it to 2,6-dichlorohydroquinone, 6-chlorohydroxyquinol, 2-chloromaleylacetate, maleylacetate, and beta-ketoadipate. three enzyme activities encoded by tcp genes, 2,4,6-tcp monooxygenase (tcpa), 6-chlorohydroxyquinol 1,2-dioxygenase ...	2003	14660355
microbial diversity of biofilms in dental unit water systems.	we investigated the microbial diversity of biofilms found in dental unit water systems (duws) by three methods. the first was microscopic examination by scanning electron microscopy (sem), acridine orange staining, and fluorescent in situ hybridization (fish). most bacteria present in the biofilm were viable. fish detected the beta and gamma, but not the alpha, subclasses of proteobacteria: in the second method, 55 cultivated biofilm isolates were identified with the biolog system, fatty acid an ...	2003	12788744
combination of microautoradiography and fluorescence in situ hybridization for identification of microorganisms degrading xenobiotic contaminants.	one of the central topics in environmental bioremediation research is to identify microorganisms that are capable of degrading the contaminants of interest. here we report application of combined microautoradiography (mar) and fluorescence in situ hybridization (fish). the method has previously been used in a number of systems; however, here we demonstrate its feasibility in studying the degradation of xenobiotic compounds. with a model system (coculture of pseudomonas putida b2 and sphingomonas ...	2003	14713022
microbial consortia that degrade 2,4-dnt by interspecies metabolism: isolation and characterisation.	two consortia, isolated by selective enrichment from a soil sample of a nitroaromatic-contaminated site, degraded 2,4-dnt as their sole nitrogen source without accumulating one or more detectable intermediates. though originating from the same sample, the optimised consortia had no common members, indicating that selective enrichment resulted in different end points. consortium 1 and consortium 2 contained four and six bacterial species respectively, but both had two members that were able to co ...	2003	12801097
microbial contamination of dialysate and its prevention in haemodialysis units.	at the haemodialysis centres of nine hospitals in japan, microbial contamination of treated water (reverse osmosis method), acid and bicarbonate concentrates, and dialysate was investigated. among these fluids used in haemodialysis, the dialysate was most frequently contaminated and had the highest concentration of bacteria. of 40 dialysate samples analysed, 42.5% showed a bacterial count of more than 2000cfu/ml, which was above the association for the advancement of medical instrumentation (aam ...	2003	12818584
rhizoremediation of dioxin-like compounds by a recombinant rhizobium tropici strain expressing carbazole 1,9a-dioxygenase constitutively.	a recombinant rhizobium strain, pbk3-is, that constitutively expressed the oxygenase component of carbazole 1,9a-dioxygenase from sphingomonas sp. strain ka1, was constructed. in the water-cultured siratro rhizospheres inoculated with strain pbk3-is, 48% of the dibenzofuran was removed within 3 days (initial substrate, 25 microg). similar results were obtained in soil-cultured siratro rhizospheres using sterile vermiculite. when non-sterile field soils were used instead of sterile vermiculite, t ...	2003	12834297
biodegradation of nonylphenol in a continuous packed-bed bioreactor.	a packed bed bioreactor, with 170 ml glass bead carriers and 130 ml medium, was tested for the removal of the endocrine disrupter, nonylphenol, with a sphingomonas sp. the bioreactor was first continuously fed with medium saturated with nonylphenol in an attempt to simulate groundwater pollution. at best, nonylphenol was degraded by 99.5% at a feeding rate of 69 ml h(-1) and a removal rate of 4.3 mg nonylphenol day(-1), resulting in a 7.5-fold decrease in effluent toxicity according to the micro ...	2003	12889825
simultaneous and rapid monitoring of biomass and biopolymer production by sphingomonas paucimobilis using fourier transform-near infrared spectroscopy.	the application of fourier transform near infrared spectroscopy (ft-nirs) to near real-time monitoring of polysaccharide and biomass concentration was investigated using a gellan-producing strain of sphingomonas paucimobilis grown in a stirred tank reactor. successful models for both biomass and gellan were constructed despite the physichochemical complexity of the viscous process fluid. modelling of biomass proved more challenging than for gellan, partly because of the low range of biomass conc ...	2003	12889834
a novel antarctic microbial endolithic community within gypsum crusts.	a novel endolithic microbial habitat is described from a climatically extreme site at two step cliffs, alexander island, antarctic peninsula (71 degrees 54's, 68 degrees 13'w). small endolithic colonies (<3 mm in diameter) are found within the translucent gypsum crust that forms on the surface of sandstone boulders. gypsum crusts are found on ice-free rocks throughout the antarctic and therefore offer potential colonization sites at more inhospitable locations, including sites at higher latitude ...	2003	12823188
potential of a new biotreatment: sphingomonas cloacae s-3t degrades nonylphenol in industrial wastewater.	sphingomonas cloacae s-3(t), a nonylphenol (np)-degrading bacterium, was evaluated for its utility in the remediation of np-contaminated wastewater. in flask-scale experiments, s-3(t) cells immobilized on porous polypropylene carriers (beads) efficiently degraded np to concentrations routinely measured in aquatic environments [a few parts per billion (ppb), or micrograms per liter). therefore, we constructed and evaluated a laboratory-scale wastewater treatment system with a 3-l carrier-filled c ...	2003	12915961
mineralization of soil-aged isoproturon and isoproturon metabolites by sphingomonas sp. strain srs2.	the aim of the study was to determine the effect of aging of the herbicide isoproturon and its metabolites monodesmethyl-isoproturon and 4-isopropyl-aniline in agricultural soil on their availability to the degrading bacterium sphingomonas sp. strain srs2. the 14c-ring-labeled isoproturon, monodesmethyl-isoproturon, and 4-isopropyl-aniline were added to sterilized soil and stored for 1, 49, 71, or 131 d before inoculation with strain srs2. the availability of the compounds was estimated from the ...	2003	12931879
haloalkane dehalogenase linb from sphingomonas paucimobilis ut26: x-ray crystallographic studies of dehalogenation of brominated substrates.	the haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. complete crystal structures of haloalkane dehalogenase from sphingomonas paucimobilis ut26 (linb), and complexes of linb with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 a resolution x-ray diffraction data. published structures of n ...	2003	12939138
formyltetrahydrofolate synthetase sequences from salt marsh plant roots reveal a diversity of acetogenic bacteria and other bacterial functional groups.	sixty-two partial formyltetrahydrofolate synthetase (fthfs) structural gene sequences were recovered from roots of salt marsh plants, including spartina alterniflora, salicornia virginica, and juncus roemerianus. only s. alterniflora roots yielded sequences grouping with fthfs sequences from known acetogens. most other fthfs or fthfs-like sequences grouped with those from sulfate-reducing bacteria. several sequences that grouped with sphingomonas paucimobilis ligh were also recovered.	2003	12514064
genetic analysis and characterization of poly(aspartic acid) hydrolase-1 from sphingomonas sp. kt-1.	sphingomonas sp. kt-1 hydrolyzes poly(aspartic acid) (paa) containing alpha- and beta-amide units and has at least two different types of paa hydrolases. the paa hydrolase-1 hydrolyzes selectively beta-beta amide units in paa. molecular cloning of paa hydrolase-1 from sphingomonas sp. kt-1 has been carried out to characterize its gene products. genetic analysis shows that the deduced amino acid sequence of paa hydrolase-1 has a similarity with those of the catalytic domain of poly(3-hydroxybutyr ...	2003	12523851
bacterial serine palmitoyltransferase: a water-soluble homodimeric prototype of the eukaryotic enzyme.	serine palmitoyltransferase (spt, ec 2.3.1.50) is a key enzyme in sphingolipid biosynthesis and catalyzes the decarboxylative condensation of l-serine and palmitoyl coenzyme a (coa) to 3-ketodihydrosphingosine (kds). we found that the gram-negative obligatory aerobic bacteria sphingomonas paucimobilis ey2395(t) have significant spt activity, and purified spt to homogeneity. unlike eukaryotic enzymes, this enzyme was a water-soluble homodimeric protein. we isolated the spt gene encoding 420 amino ...	2003	12686119
in-field spatial variability in the degradation of the phenyl-urea herbicide isoproturon is the result of interactions between degradative sphingomonas spp. and soil ph.	substantial spatial variability in the degradation rate of the phenyl-urea herbicide isoproturon (ipu) [3-(4-isopropylphenyl)-1,1-dimethylurea] has been shown to occur within agricultural fields, with implications for the longevity of the compound in the soil, and its movement to ground- and surface water. the microbial mechanisms underlying such spatial variability in degradation rate were investigated at deep slade field in warwickshire, united kingdom. most-probable-number analysis showed tha ...	2003	12571001
characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in sphingomonas paucimobilis syk-6.	the protocatechuate (pca) 4,5-cleavage pathway is the essential metabolic route for degradation of low-molecular-weight products derived from lignin by sphingomonas paucimobilis syk-6. in the 10.5-kb ecori fragment carrying the genes for pca 4,5-dioxygenase (ligab), 2-pyrone-4,6-dicarboxylate hydrolase (ligi), 4-oxalomesaconate hydratase (ligj), and a part of 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase (ligc), we found the ligk gene, which encodes 4-carboxy-4-hydroxy-2-oxoadipate (c ...	2003	12486039
crystal structure of algq2, a macromolecule (alginate)-binding protein of sphingomonas sp. a1, complexed with an alginate tetrasaccharide at 1.6-a resolution.	sphingomonas sp. a1 possesses a high molecular weight (hmw) alginate uptake system composed of a novel pit formed on the cell surface and a pit-dependent atp-binding cassette (abc) transporter in the inner membrane. the transportation of hmw alginate from the pit to the abc transporter is mediated by the periplasmic hmw alginate-binding proteins algq1 and algq2. we determined the crystal structure of algq2 complexed with an alginate tetrasaccharide using an alginate-free (apo) form as a search m ...	2003	12486124
reconstruction of mycobacterial dehalogenase rv2579 by cumulative mutagenesis of haloalkane dehalogenase linb.	the homology model of protein rv2579 from mycobacterium tuberculosis h37rv was compared with the crystal structure of haloalkane dehalogenase linb from sphingomonas paucimobilis ut26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in linb and rv2579. to characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of linb. the sixfold mutant, ...	2003	12676719
sphingomonas paucimobilis beta-glucosidase bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1.	the sphingomonas paucimobilis beta-glucosidase bgl1 is encoded by the bgl1 gene, associated with an 1308 bp open reading frame. the deduced protein has a potential signal peptide of 24 amino acids in the n-terminal region, and experimental evidence is consistent with the processing and export of the bgl1 protein through the inner membrane to the periplasmic space. a his(6)-tagged 44.3 kda protein was over-produced in the cytosol of escherichia coli from a recombinant plasmid, which contained the ...	2003	12444924
a two-species test of the hypothesis that spatial isolation influences microbial diversity in soil.	the hypothesis that spatial isolation is a key determinant of microbial community structure in soils was evaluated by examining the competitive dynamics of two species growing on a single resource in a uniform sand matrix under varied moisture content. one species dominated the community under highly connected, saturated treatments, suggesting that these conditions allow competitive interactions to structure the community. as moisture content decreased, however, the less competitive species beca ...	2003	12415419
[identification, cloning and sequencing of gst gene of bacterium degrading poly-aromatic hydrocarbons].	a bacterium (designated strain zx4) able to degrade poly aromatic hydrocarbons was isolated from oil-contaminated soil. based on analysis of the 16s rdna sequence, whole cell fatty acid, and biolog-gn, the strain was identified as sphingomonas paucimobilis. the detection of gst (glutathione s-transferase) indicated that the gst from the strain had the activity of conjugating with cdnb and it maybe relate with degradation of pahs. the pcr product of gst gene from the strain confirmed its presence ...	2003	16276887
biodegradation of methyl tertiary butyl ether (mtbe) by a bacterial enrichment consortia and its monoculture isolates.	methyl tertiary butyl ether (mtbe), an important gasoline additive, is a recalcitrant compound posing serious environmental health problems. in this study, mtbe-degrading bacteria were enriched from five environmental samples. enrichments from stewart lake sediments and an mtbe contaminated soil displayed the highest rate of mtbe removal; 29.6 and 27.8% respectively, in 28 days. a total of 12 bacterial monocultures isolated from enrichment cultures were screened for mtbe degradation in liquid cu ...	2003	12906382
screening of bifidobacterium strains isolated from human faeces for antagonistic activities against potentially bacterial pathogens.	as probiotic bacteria, strains belonging to the genus bifidobacterium colonise the gastro-intestinal tract of humans and animals at the time of birth, and they are found in young as well as in adult individuals in great numbers. moreover, they can interact with the development of enteric infections by the production of antimicrobial metabolites. in this work 281 strains of bifidobacteria were anaerobically isolated from human faecal samples, supplied by volunteers of different ages (youngs, adul ...	2003	12906392
[bacterial systems of sugar transport].		2003	15176119
[isolation and characteristics of pahs-degrading strains].	the predominant indigenous microbial population and the strain zl5 pahs-degrading were obtained by selective enrichment culture from liaohe viscous oil-contaminated field. the sequence analysis of 16s rdna showed that strain zl5 belonged to sphingomonas sp. the microbial population and the strain could degrade phenanthrene well. 95.28% and 69.24% of phenanthrene in the medium were degraded in 120 hrs. however, the degradation of pyrene by the microbial population or by the strain was low. the de ...	2003	14986388
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
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
rapid screening and dereplication of bacterial isolates from marine sponges of the sula ridge by intact-cell-maldi-tof mass spectrometry (icm-ms).	rapid grouping of bacterial isolates is critical in comprehensive microbial studies of environmental samples or screening programmes e.g. in unknown marine environments where large numbers of strains have to be isolated on different growth media. sets of bacteria have been cultured from the marine sponges isops phlegraei, haliclona sp. 1, phakellia ventilabrum and plakortis sp. growing at a depth of about 300 m on the sula ridge close to the norwegian coast. we employed intact-cell maldi-tof (ic ...	2004	15614563
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
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
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
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
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
plant-assisted degradation of phenanthrene as assessed by solid-phase microextraction (spme).	the soil bacterium sphingomonas yanoikuyae was isolated from a petroleum-contaminated soil and grown on mineral salts agar overlaid with the polycyclic aromatic hydrocarbon phenanthrene. the effect of white mustard, sinapis alba, on phenanthrene degradation by s. yanoikuyae in artificially contaminated redi-earth-sand was examined. solid-phase-microextraction (spme) gas chromatography-flame ionization detection (gc-fid) was used to quantify the concentration of phenanthrene in the gas phase of m ...	2004	15554477
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
isolation and characterization of a novel sphingomonad capable of growth with chrysene as sole carbon and energy source.	a bacterial strain able to grow in pure culture with chrysene as sole added carbon and energy source was isolated from pah-contaminated soil after successive enrichment cultures in a biphasic growth medium. initially, growth occurred in the form of a biofilm at the interface between the aqueous and non-aqueous liquid phases. however, after a certain time, a transition occurred in the enrichment cultures, with growth occurring in suspension and a concomitant increase in the rate of chrysene degra ...	2004	15598525
aerobic degradation of polychlorinated biphenyls.	the microbial degradation of polychlorinated biphenyls (pcbs) has been extensively studied in recent years. the genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been de ...	2004	15614564
three-block bi-focal pls (3bif-pls) and its application in qsar.	when x and y are multivariate, the two-block partial least squares (pls) method is often used. in this paper, we outline an extension addressing a special case of the three-block (x/y/z) problem, where z sits "under" y. we have called this approach three-block bi-focal pls (3bif-pls). it views the x/y relationship as the dominant problem, and seeks to use the additional information in z in order to improve the interpretation of the y-part of the x/y association. two data sets are used to illustr ...	2004	15669704
two unusual chlorocatechol catabolic gene clusters in sphingomonas sp. tfd44.	the genes responsible for the degradation of 2,4-dichlorophenoxyacetate (2,4-d) by alpha-proteobacteria have previously been difficult to detect by using gene probes or polymerase chain reaction (pcr) primers. pcr products of the chlorocatechol 1,2-dioxygenase gene, tfdc, now allowed cloning of two chlorocatechol gene clusters from the sphingomonas sp. strain tfd44. sequence characterization showed that the first cluster, tfdd,rfce, comprises all the genes necessary for the conversion of 3,5-dic ...	2004	15688254
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
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
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
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
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