Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| the degradation of alpha-quaternary nonylphenol isomers by sphingomonas sp. strain ttnp3 involves a type ii ipso-substitution mechanism. | the degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (np)] was tested with resting cells of sphingomonas sp. strain ttnp3. concomitantly to the degradation of np, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. two other radiolabeled isomers of np, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. in parallel experiments, the 4(2', ... | 2006 | 16091931 |
| 16s rdna phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading sphingomonas strains. | hexachlorocyclohexane (hch) is a highly recalcitrant pesticide that persists in soils. three novel hch-degrading strains (ds2, ds2-2 and ds3-1) were isolated after enrichment from hch-contaminated soil from germany. these strains efficiently degraded the alpha-, gamma- and delta-isomers of hch, while strain ds3-1 also degraded beta-hch. based on 16s rdna analysis, strain ds3-1 was closely related to sphingomonas taejonensis, while strains ds2 and ds2-2 were closely related to sphingomonas flava ... | 2005 | 16104856 |
| ecochemical studies of interrelationships between epiphytic bacteria and host plants via secondary metabolites. | the plant surface, which is representative of the phylloplane and rhizoplane, is a characteristic habitat for microorganisms. in this review, the ecological roles of phytoepiphytic bacteria will be described. the phylloplane and rhizoplane, which are adjacent to the atmosphere and soil sphere respectively, accumulate topically and/or selectively release secondary metabolites that are specific to the plant genera and species which reside within these regions. some epiphytes have abilities to deca ... | 2005 | 16116269 |
| a second 5-carboxyvanillate decarboxylase gene, ligw2, is important for lignin-related biphenyl catabolism in sphingomonas paucimobilis syk-6. | a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (ddva), is degraded to 5-carboxyvanillate (5cva) by the enzyme reactions catalyzed by ddva o-demethylase (ligx), meta-cleavage oxygenase (ligz), and meta-cleavage compound hydrolase (ligy) in sphingomonas paucimobilis syk-6. 5cva is then transformed to vanillate by a nonoxidative 5cva decarboxylase and is further degraded through the protocatechuate 4,5-cleavage pathway. a 5cva decarboxylase gene, ligw, was isolated from syk-6 (x. peng, ... | 2005 | 16151081 |
| recovery of microbially mediated processes in soil augmented with a pentachlorophenol-mineralizing bacterium. | specific physiological groups can be used to evaluate the recovery of soil microbial communities following disturbance. in this study, soil was contaminated with pentachlorophenol (pcp) to assess the resiliency of microorganisms responsible for carbon and nitrogen cycling. methane fluxes were monitored in soil microcosms to evaluate the effects of contamination and augmentation on microbial populations involved in carbon cycling. the addition of a pcp-mineralizing bacterium, sphingomonas chlorop ... | 2005 | 16152961 |
| hexachlorocyclohexane-degrading bacterial strains sphingomonas paucimobilis b90a, ut26 and sp+, having similar lin genes, represent three distinct species, sphingobium indicum sp. nov., sphingobium japonicum sp. nov. and sphingobium francense sp. nov., and reclassification of [sphingomonas] chungbukensis as sphingobium chungbukense comb. nov. | three strains of sphingomonas paucimobilis, b90a, ut26 and sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. phylogenetic analysis based on 16s rrna gene sequences indicated that these strains do not fall in a clade that includes the type strain, sphingomonas paucimobilis atcc 29837(t), but form a coherent cluster with [sphingomonas] chungbukensis imsnu 11152(t) followed by sphingobium chlorophenolicum atcc 33790(t). the three strains showed low dn ... | 2005 | 16166696 |
| formation of catechols via removal of acid side chains from ibuprofen and related aromatic acids. | although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria. sphingomonas sp. strain ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. a slight preference toward the r enantiomer was observed, though both ibuprofen enantiomers were metabolized. a yellow color, indicative of meta-cleavage, accumulated t ... | 2005 | 16204529 |
| expression of glycosylated haloalkane dehalogenase linb in pichia pastoris. | heterologous expression of the bacterial enzyme haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 in methylotrophic yeast pichia pastoris is reported. the haloalkane dehalogenase gene linb was subcloned into the ppiczalphaa vector and integrated into the genome of p. pastoris. the recombinant linb secreted from the yeast was purified to homogeneity and biochemically characterized. the deglycosylation experiment and mass spectrometry measurements showed that the recombinant linb ex ... | 2006 | 16216524 |
| [metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]. | 2005 | 16218450 | |
| proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in sphingomonas sp. a1: alginate-binding flagellin on the cell surface. | a nonmotile gram-negative bacterium, sphingomonas sp. a1, directly incorporates macromolecules such as alginate through a "super-channel" consisting of a pit formed on the cell surface, alginate-binding proteins in the periplasm, and an atp-binding cassette transporter in the inner membrane. here, we demonstrate the proteomics-based identification of cell-surface proteins involved in the formation of the pit and/or import of alginate. cell-surface proteins were prepared from the outer membrane r ... | 2005 | 16229468 |
| diversity of n-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere. | in gram-negative bacteria, quorum-sensing (qs) communication is mostly mediated by n-acyl homoserine lactones (n-ahsl). the diversity of bacterial populations that produce or inactivate the n-ahsl signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (rflp) analysis of amplified 16s dna and dna sequencing. such analysis indicated the occurrence of n-ahsl-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to pro ... | 2005 | 16232294 |
| 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 |
| super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules. | cells of sphingomonas sp. a1 directly incorporate a macromolecule, alginate, into the cytoplasm through a biosystem, super-channel, consisting of a pit on the cell surface, alginate-binding proteins in the periplasm, and an atp-binding cassette transporter in the inner membrane. the alginate is finally depolymerized into constituent monosaccharides by polysaccharide lyases present in the cytoplasm. the fundamental frame of the biosystem for alginate transport, and the functions of the pit, bindi ... | 2004 | 16233728 |
| molecular identification of sphingomonas sp. a1 alginate lyase (a1-iv') as a member of novel polysaccharide lyase family 15 and implications in alginate lyase evolution. | sphingomonas sp. a1 (strain a1) produces three endotypes (a1-i [65 kda], a1-ii [25 kda], and a1-iii [40 kda]) and an exotype (a1-iv [86 kda]) alginate lyases in cytoplasm. these four enzymes cooperatively depolymerize alginate into constituent monosaccharides. in addition to the genes for these lyases, novel genes encoding hypothetical proteins homologous with a1-iv were found in the genomes of many bacteria including strain a1. one such protein, a1-iv' (90 kda) of strain a1, was overexpressed i ... | 2005 | 16233753 |
| characterization of floating activity of indigenous diesel-assimilating bacterial isolates. | six diesel-degrading bacterial strains were isolated from oil-polluted sites located in central taiwan. the floating activity of the isolates in an oil-supplemented liquid medium was monitored. cell-surface hydrophobicity as well as cell-free and cell-residue emulsification activities were also investigated. three isolates, identified as gordonia alkanivorans cc-jg 39, rhodococcus erythropolis cc-bc 04, and r. erythropolis cc-bc 11, were found to float and grow near the diesel layer on the surfa ... | 2005 | 16233818 |
| biofilm formation characteristics of bacterial isolates retrieved from a reverse osmosis membrane. | high-quality water purification systems using reverse osmosis (ro) membrane separation have faced a major challenge related to biofilm formation on the membrane surface, or biofouling. to understand this issue, the biofilm formation characteristics of four bacterial isolates previously retrieved from an ro membrane treating potable water were investigated. biofilm formation of all four isolates occurred to different extents in microtiter plates and could be related to one or more cell properties ... | 2005 | 16245826 |
| biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1. | the ability of sphingomonas wittichii strain rw1 to remove polychlorinated dibenzo-p-dioxins (pcdds) from fly ash was investigated. all experiments were carried out in a slurry-phase system. preliminary studies with resting cells of strain rw1 in a model fly ash system showed the complete removal of dibenzofuran (df) and 81% of dibenzo-p-dioxin (dd). incubation of real fly ash collected from municipal waste incinerators with strain rw1 for 15 days resulted in a 75.5% reduction in toxic pcdds. wh ... | 2005 | 16256169 |
| bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. | bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. the dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (pah) degraders, and the total petroleum hydrocarbon (tph) and pah concentrations were monitored during the bioremediation process. tph and pahs were significantly degraded in all treatments (72 to 79% and 83 to 87%, ... | 2005 | 16269736 |
| microbial conversion of major ginsenoside rb(1) to pharmaceutically active minor ginsenoside rd. | more than seventy strains of aerobic bacteria showing beta-glucosidase activity were isolated from a ginseng field, using a newly designed esculin-r2a agar, and identified by their 16s rrna gene sequences. of these microorganisms, twelve strains could convert the major ginsenoside, rb(1), to the pharmaceutically active minor ginsenoside rd. three strains, burkholderia pyrrocinia gp16, bacillus megaterium gp27 and sphingomonas echinoides gp50, were phylogenetically studied, and observed to be mos ... | 2005 | 16273039 |
| [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 |
| sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate. | a gram-negative bacterium, yim 003t, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. the organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on isp2 medium and its optimum growth ph was 7.0-7.5. the major respiratory lipoquinone was ubiquinone q-10. the phosphate-containing lipids detected in strain yim 003t were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sph ... | 2005 | 16280497 |
| description of two novel species, sphingomonas abaci sp. nov. and sphingomonas panni sp. nov. | two gram-negative, rod-shaped, non-spore-forming bacterial strains designated c42t and c52t were isolated in the medical clinic for small animals and ungulates at the university for veterinary medicine vienna, austria. on the basis of 16s rrna gene sequence similarity, both strains were shown to belong to the genus sphingomonas. strain c42t showed the greatest levels of sequence similarity with sphingomonas melonis dsm 14444t and sphingomonas aquatilis kctc 2881t (both 97.7 %). strain c52t showe ... | 2005 | 16280528 |
| nonionic surfactant sorption onto the bacterial cell surface: a multi-interaction isotherm. | the adsorption of linear polyoxyethylene (poe) alcohol surfactants of the form cxey onto the surface of a sphingomonas sp. has been examined. for this study, the alkyl chain length (x) was fixed at 12 and the poe chain length (y) was varied, with y = 4, 7, 9, 10, and 23 ethylene oxide units. langmuirian isotherms were observed for c12e4 and c12e23, and more complex isotherms were observed for the three intermediate poe chain length surfactants, with c12e7 and c12e9 exhibiting strong s-shaped iso ... | 2005 | 16285812 |
| isolation of pah-degrading bacteria from mangrove sediments and their biodegradation potential. | surface sediment samples were collected from seven mangrove swamps in hong kong sar with different degrees of contamination. the total concentrations of 16 pahs in these sediments ranged from 169.41 to 1058.37 ng g(-1) with the highest concentration found in ma wan and the lowest in kei ling ha lo wai mangrove swamp. in each swamp, three bacterial consortia were enriched from sediments using phenanthrene (phe) as the sole carbon and energy source, and individual bacterial colony showing phe degr ... | 2005 | 16291206 |
| characterization of four rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols. | four genes were isolated and characterized for alcohol dehydrogenases (adhs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading rhodococcus opacus tkn14 and the other three from n-alkane-degrading rhodococcus erythropolis pr4. various aromatic alcohols were bioconverted to their corresponding carboxylic acids using escherichia coli cells expressing each of the four adh genes together with an aromatic aldehyde dehydro ... | 2006 | 16292529 |
| characterization of the novel hch-degrading strain, microbacterium sp. itrc1. | a gram-positive microbacterium sp. strain, itrc1, that was able to degrade the persistent and toxic hexachlorocyclohexane (hch) isomers was isolated and characterized. the itrc1 strain has the capacity to degrade all four major isomers of hch present in both liquid cultures and aged contaminated soil. dna fragments corresponding to the two initial genes involved in gamma-hch degradative pathway, encoding enzymes for gamma-pentachlorocyclohexene hydrolytic dehalogenase (linb) and a 2,5-dichloro-2 ... | 2006 | 16315057 |
| efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function. | sphingomonas paucimobilis syk-6, which can degrade various low molecular weight compounds derived from plant polyphenols such as lignin, lignan, and tannin, metabolizes these substances via 2-pyrone-4,6-dicarboxylic acid (pdc). we focused on this metabolic intermediate as a potential raw material for novel, bio-based polymers. we cloned the ligab and ligc genes of syk-6, which respectively encode protocatechuate 4,5-dioxygenase and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase, into a ... | 2006 | 16322989 |
| effect of slow desorption on the kinetics of biodegradation of polycyclic aromatic hydrocarbons. | the bioavailability to bacteria of 14c-labeled polycyclic aromatic hydrocarbons (pahs) sorbed onto lake sediments was assessed using a mathematical model and three experimental series. the experiments were performed under similar conditions and included: (1) abiotic desorption of pahs from sediments by tenax extraction, (2) mineralization of dissolved pahs with no sediment present, and (3) mineralization of pahs sorbed onto sediments. results obtained from the first two series were used to obtai ... | 2005 | 16323776 |
| symbiotic association in chlorella culture. | chlorella sorokiniana iam c-212 has long been maintained in slant culture as a mixed strain, representing an associated natural microbial consortium. in this study, the consortium was separated and five nonalgal constituents, a fungal strain (cssf-1), and four bacterial strains (cssb-1, cssb-2, cssb-3, and cssb-4) were isolated and identified. 16s rdna sequence analysis revealed that strains cssb-1, cssb-2, cssb-3, and cssb-4 were close to ralstonia pickettii (99.8% identity), sphingomonas sp. d ... | 2005 | 16329867 |
| identification of culturable bacteria present in haemodialysis water and fluid. | water used to prepare haemodialysis fluid is not sterile, and its microbiological control is important for the prevention of haemodialysis-associated illness. bacterial populations inhabiting a distribution system for haemodialysis water were studied over an 18-month period. 203 planktonic bacteria isolated on r2a medium were identified by restriction analysis and sequencing of 16s rrna gene. a diverse bacterial community was detected, containing predominantly gram-negative members of the alphap ... | 2004 | 16329897 |
| hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica. | a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ... | 2004 | 16329936 |
| cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. | atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. the species composition of the culture was determined by pcr-dgge. the bacterial species included agrobacterium tumefaciens, caulobacter crescentus, pseudomonas putida, sphingomonas yaniokuyae, nocardia sp., rhizobium ... | 2005 | 16329946 |
| non-specific biodegradation of the organophosphorus pesticides, cadusafos and ethoprophos, by two bacterial isolates. | an enrichment culture technique was used for the isolation of microorganisms responsible for the enhanced biodegradation of the nematicide cadusafos in soils from a potato monoculture area in northern greece. mineral salts medium supplemented with nitrogen (msmn), where cadusafos (10 mg l(-1)) was the sole carbon source, and soil extract medium (sem) were used for the isolation of cadusafos-degrading bacteria. two pure bacterial cultures, named cadi and cadii, were isolated and subsequently char ... | 2005 | 16329956 |
| purification of cytochrome p450 and ferredoxin, involved in bisphenol a degradation, from sphingomonas sp. strain ao1. | in a previous study (m. sasaki, j. maki, k. oshiman, y. matsumura, and t. tsuchido, biodegradation 16:449-459, 2005), the cytochrome p450 monooxygenase system was shown to be involved in bisphenol a (bpa) degradation by sphingomonas sp. strain ao1. in the present investigation, we purified the components of this monooxygenase, cytochrome p450 (p450bisd), ferredoxin (fd(bisd)), and ferredoxin reductase (red(bisd)). we demonstrated that p450bisd and fd(bisd) are homodimeric proteins with molecular ... | 2005 | 16332782 |
| enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases lina1 and lina2 from the soil bacterium sphingomonas paucimobilis b90a. | sphingomonas paucimobilis b90a contains two variants, lina1 and lina2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (r. kumari, s. subudhi, m. suar, g. dhingra, v. raina, c. dogra, s. lal, j. r. van der meer, c. holliger, and r. lal, appl. environ. microbiol. 68:6021-6028, 2002). on the amino acid level, lina1 and lina2 were 88% identical to each other, and lina2 was 100% identical to lina of s. paucimobilis ut26. incubation of chir ... | 2005 | 16332842 |
| application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow. | here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. the internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. high-resolution digital time-lapse imaging was em ... | 2005 | 16332867 |
| culture-dependent and -independent approaches establish the complexity of a pah-degrading microbial consortium. | a microbial consortium (am) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (pah) mixture of three- and four-ringed pahs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (dgge), and the screening of 16s and 18s rrna gene clone libraries. eleven different sequences by culture-dependent techniques and seven by both dgge and clone libraries wer ... | 2005 | 16333329 |
| [isolation and characterization of a hch degradation sphingomanas sp. stain bhc-a]. | an aerobic bacterium was isolated successfully from a long-term contaminated upland field, which was named bhc-a. the bacterium can utilize hexachlorocycloexane as a sole carbon source and decompose this substance rapidly and completely. according to its physiological & biochemical characters and the homology analysis of its 16s rdna sequence, this strain was identified as sphingomonas sp. stain bhc-a canmineralize not only alpha, gamma and delta-hch rapidly, but also 5 mg/l beta-hch in 12h comp ... | 2005 | 16342765 |
| distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from spain. | hexachlorocyclohexane (hch)-degrading bacteria are believed to mediate natural attenuation of hch contamination and have potential for active bioremediation processes. this study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of hch contamination, from four sites in spain. hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. hexachlorocyclohexane-degrading populations we ... | 2006 | 16343322 |
| composition of microbial communities in hexachlorocyclohexane (hch) contaminated soils from spain revealed with a habitat-specific microarray. | microarray technology was used to characterize and compare hexachlorocyclohexane (hch) contaminated soils from spain. a library of 2,290 hypervariable 16s rrna gene sequences was prepared with serial analysis of ribosomal sequence tags (sarst) from a composite of contaminated and uncontaminated soils. by designing hybridization probes specific to the 100 most abundant ribosomal sequence tags (rsts) in the composite library, the rst array was designed to be habitat-specific and predicted to monit ... | 2006 | 16343328 |
| identification of hydrocarbon-degrading bacteria in soil by reverse sample genome probing. | bacteria with limited genomic cross-hybridization were isolated from soil contaminated with c5+, a mixture of hydrocarbons, and identified by partial 16s rrna sequencing. filters containing denatured genomic dnas were used in a reverse sample genome probe (rsgp) procedure for analysis of the effect of an easily degradable compound (toluene) and a highly recalcitrant compound (dicyclopentadiene [dcpd]) on community composition. hybridization with labeled total-community dna isolated from soil exp ... | 1998 | 16349504 |
| survey of environmental biocontamination on board the international space station. | the international space station (iss) is an orbital living and working environment extending from the original zarya control module built in 1998. the expected life span of the completed station is around 10 years and during this period it will be constantly manned. it is inevitable that the iss will also be home to an unknown number of microorganisms. this survey reports on microbiological contamination in potable water, air, and on surfaces inside the iss. the viable counts in potable water di ... | 2006 | 16364606 |
| influence of growth phase on the phospholipidic fatty acid composition of two marine bacterial strains in pure and mixed cultures. | this in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. these two strains, namely corynebacterium sp. and sphingomonas sp. 2mpii, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). the incubations were stopped at different times corresponding to point of lag ... | 2006 | 16380233 |
| biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p- dioxin by sphingomonas wittichii strain rw1. | sphingomonas wittichii rw1 is able to catabolize 1,2,3,4-tetrachlorodibenzo-p-dioxin (h. b. hong, y. s. chang, i. h. nam, p. fortnagel, and s. schmidt, appl. environ. microbiol. 68:2584-2588, 2002). here we demonstrate the aerobic bacterial catabolism of the ubiquitous toxic diaryl ether pollutant 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by this strain. the products of this biotransformation were identified as tetrachlorocatechol and 2-methoxy-3,4,5,6-tetrachlorophenol by comparing mass spectra re ... | 2006 | 16391032 |
| slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane. | this study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (gamma-hexachlorocyclohexane [gamma-hch]). slow-release inoculation of sphingomonas sp. gamma 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. the capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluate ... | 2006 | 16391099 |
| toxic effect of biosurfactant addition on the biodegradation of phenanthrene. | the effect of the biosurfactant rhamnolipid on phenanthrene biodegradation and cell growth of phenanthrene degraders was investigated. to compare the effect of rhamnolipid addition, two bacterial strains, 3y and 4-3, which were isolated from a diesel-contaminated site in korea, were selected. without the biosurfactant, large amounts of phenanthrene were degraded with both strains at neutral ph, with higher rates of phenanthrene degradation when the cell growth was higher. upon the addition of 24 ... | 2005 | 16398112 |
| sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. | three strains of bacteria that degrade the cyanobacterial hepatotoxin microcystin, y2t, mdb2 and mdb3, were isolated from a eutrophic lake, lake suwa, and the tenryu river, japan, and characterized. these strains were aerobic and chemo-organotrophic and their cells were gram-negative, non-spore-forming rods, motile by means of single polar flagella. yellow-pigmented colonies were formed on nutrient agar media. the strains assimilated only citrate among the organic compounds tested as carbon sour ... | 2006 | 16403871 |
| engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. | sphingomonas sp. a1 possesses specialized membrane structures termed 'superchannels' that enable the direct incorporation of macromolecules into the cell. we have engineered two related sphingomonads, the dioxin-degrading s. wittichii rw1 and the polypropylene glycol-degrading s. subarctica ifo 16058(t), to incorporate this superchannel into their cell membranes. in both cases the bioremediation capability of the organisms was substantially increased pointing at the potential of this approach as ... | 2006 | 16415854 |
| [rare bacteria species found in wounds of tsunami patients. predominance of gram-negative rods, increased antibiotic resistance]. | microbiological cultures from 229 patients seeking medical advise in stockholm after the tsunami catastrophe december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative rods were the most common findings from wound cultures. common human pathogens as escherichia coli, proteus species, klebsiella spp, and pseudomonas aeruginosa were isolated. however, more rare species of gram-negative rods were also isolated, e.g. myroides ... | 2005 | 16416946 |
| effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture. | the degradation of polycyclic aromatic hydrocarbons (pahs) by an undefined culture obtained from a pah-polluted soil and the same culture bioaugmented with three pah-degrading strains was studied in carbon-limited chemostat cultures. the pahs were degraded efficiently by the soil culture and bioaugmentation did not significantly improve the pah degrading performance. the presence of pahs did, however, influence the bacterial composition of the bioaugmented and non-bioaugmented soil cultures, res ... | 2006 | 16420621 |
| confirmation of the anomeric structure of galacturonic acid in the galacturonosyl-ceramide of sphingomonas yanoikuyae. | the anomeric structure of glycosphingolipids significantly influences their activity to stimulate natural killer t cells. in this study the chemical structure of the galacturonosyl-ceramide in sphingomonas yanoikuyae, designated gsl-1'sy, was re-examined to prove the anomeric structure of the dgalacturonic acid (gala) in the lipid, which was reported as beta-configuration by naka et al., but was suggested as alpha-configuration in our preliminary study. gsl-1'sy was purified from the bacterial c ... | 2006 | 16428876 |
| effects of nonionic surfactants on the cell surface hydrophobicity and apparent hamaker constant of a sphingomonas sp. | nonionic surfactants of the form cxey were studied for their ability to alter the cell surface hydrophobicity and apparent hamaker constants of a sphingomonas sp. through contact angle measurements on hydrated and dried bacterial lawns, it was found that the cell surface hydrophobicity changed systematically with both the alkyl (x) and polyoxyethylene (y) chain lengths. while differences in contact angles were observed between hydrated and dried lawns, they could not be attributed to the mere pr ... | 2006 | 16433351 |
| suspected ventilator-associated pneumonia in cardiac patients admitted to the coronary care unit. | to determine the incidence, risk factors, associated pathogens, and outcome of ventilator-associated pneumonia (vap) in patients admitted to a coronary care unit (ccu). | 2006 | 16438476 |
| a novel automated waterline cleaning system that facilitates effective and consistent control of microbial biofilm contamination of dental chair unit waterlines: a one-year study. | microbial contamination of dental chair unit (dcu) output water caused by biofilm growth in dental unit waterlines (duws) is a universal problem and a potentially significant source of cross-infection. the microbial quality of output water from a planmeca compact i dcu equipped with the novel water management system (wms), an integrated and automated duw cleaning system, was investigated over a 12-month period with the hydrogen peroxide- and silver ion-containing disinfectants planosil and plano ... | 2006 | 16442201 |
| sequence and analysis of the 46.6-kb plasmid pa1 from sphingomonas sp. a1 that corresponds to the typical incp-1beta plasmid backbone without any accessory gene. | sphingomonas sp. a1 (strain a1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system--"super-channel." here, we report the complete dna sequence and genetic organization of plasmid pa1 from strain a1. nucleotide sequence analysis revealed that pa1 comprises 46,557 bp encoding 49 open reading frames (orfs) with 65% g+c content and abundant gccg/cggc motifs. many predicted pa1 orfs showed high similarity to pa81 orfs; pa81 is supposedly a self- ... | 2006 | 16445980 |
| bioaugmentation of bromoamine acid degradation with sphingomonas xenophaga qyy and dna fingerprint analysis of augmented systems. | one high-effective bromoamine acid (1-amino-4-bromoanthraquinone-2-sulfonic acid, baa) degrading strain was isolated previously with the ability to use baa as sole source of carbon and nitrogen. it was identified as sphingomonas xenophaga qyy by 16s rdna sequence analysis and physio-biochemical tests. in this study, bioaugmentation of baa degradation with suspended and immobilized cells of strain qyy was investigated. the optimal degradation conditions were as follows: temperature 30 degrees c, ... | 2006 | 16453174 |
| [construction of multifunctional genetically engineered pesticides-degrading bacteria by homologous recombination]. | construction of multifunctional pesticides-degrading genetically engineered microorganisms (gems) is increasing important in the bioremediation of various pesticides contaminants in environment. however, construction of genetically stable gems without any exogenous antibiotic resistance is thought to be one of the bottlenecks in gems construction. in this article, homologous recombination vectors with the recipient's 16s rdna as homologous recombination directing sequence (hrds) and sacb gene as ... | 2005 | 16468341 |
| surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacz-based phenotypes. | the ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a dna clone into a selectable/scorable phenotype. we established this strategy with a system to expose the activity of dehydrochlorinases acting upon gamma-hexachlorocyclohexane (gamma-hch or lindane). to this end, the effector-binding protein, xylr, was evolved by gene shuffling plus mutagenic polymerase chain reacti ... | 2006 | 16478460 |
| glycolipid activation of invariant t cell receptor+ nk t cells is sufficient to induce airway hyperreactivity independent of conventional cd4+ t cells. | asthma is an inflammatory lung disease, in which conventional cd4+ t cells producing il-4/il-13 appear to play an obligatory pathogenic role. here we show, in a mouse model of asthma, that activation of pulmonary il-4/il-13 producing invariant tcr+ cd1d-restricted natural killer t (nkt) cells is sufficient for the development of airway hyperreactivity (ahr), a cardinal feature of asthma, in the absence of conventional cd4+ t cells and adaptive immunity. respiratory administration of glycolipid a ... | 2006 | 16478801 |
| degradation of microcystin-rr by sphingomonas sp. cba4 isolated from san roque reservoir (córdoba - argentina). | we report the aerobic biodegradation of microcystin-rr (mc-rr) by a bacterial strain isolated from san roque reservoir (córdoba - argentina). this bacterium was identified as sphingomonas sp. (cba4) on the basis of 16s rdna sequencing. the isolated strain was capable of degrading completely mc-rr (200 mug l(-1)) within 36 h. we have found evidence that mc-rr biodegradation pathway by this sphingomonas sp. strain would start by demethylating mc-rr, affording an intermediate product, which is fina ... | 2006 | 16485086 |
| distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in sphingobium japonicum ut26. | sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 utilizes the important insecticide gamma-hexachlorocyclohexane as a sole source of carbon and energy. in previous studies, we isolated and characterized six structural genes (lina to linf) and one regulatory gene (linr) of ut26 for the degradation of gamma-hexachlorocyclohexane to beta-ketoadipate. our analysis in this study indicated that the ut26 genome consists of three large circular replicons of 3.6 mb, 670 kb, and 185 kb. the ... | 2006 | 16487327 |
| identifying the bacterial community on the surface of intralox belting in a meat boning room by culture-dependent and culture-independent 16s rdna sequence analysis. | we examined the bacterial community present on an intralox conveyor belt system in an operating lamb boning room by sequencing the 16s ribosomal dna (rdna) of bacteria extracted in the presence or absence of cultivation. rflp patterns for 16s rdna clone library and cultures were generated using haeiii and mspi restriction endonucleases. 16s rdna amplicons produced 8 distinct rflp pattern groups. rflp groups i-iv were represented in the clone library and rflp groups i and v-viii were represented ... | 2006 | 16488497 |
| comparison of mineralization of solid-sorbed phenanthrene by polycyclic aromatic hydrocarbon (pah)-degrading mycobacterium spp. and sphingomonas spp. | the mineralization of 14c-phenanthrene, sorbed to porous synthetic amberlite sorbents, i.e., irc50, xad7-hp, and xad2, by three phenanthrene-degrading mycobacterium soil isolates, i.e., strains vm552, vm531, and vm451 and three phenanthrene-degrading sphingomonas soil isolates, i.e., strains lh162, epa505 and lh227, was compared. in p-buffer and in the presence of irc50, for all strains the maximum rate of mineralization of 14c-phenanthrene was significantly higher (1.1-1.9 ng ml(-1) h(-1)) than ... | 2006 | 16496139 |
| microbial contamination of nebulization solution and its measures. | we evaluated the microbial contamination of nebulization solutions in medication cups from a total of 76 ultrasonic nebulizers in use in 10 hospitals. in addition, an interview survey was given to nurses to evaluate the disinfection methods of these ultrasonic nebulizers. of a total of 76 nebulization solution samples, 11 (14.5%) were contaminated with 10-10(2) colony-forming units (cfu)/ml and 9 (11.8%) with 10(3)-10(5) cfu/ml. the major contaminants were glucose non-fermentative bacilli such a ... | 2006 | 16508154 |
| crystallization and preliminary x-ray analysis of alginate lyases a1-ii and a1-ii' from sphingomonas sp. a1. | alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-l-guluronate and beta-d-mannuronate, through a beta-elimination reaction. the alginate lyases a1-ii (25 kda) and a1-ii' (25 kda) from sphingomonas sp. a1, which belong to polysaccharide lyase family pl-7, exhibit 68% homology in primary structure but have different substrate specificities. to determine clearly the structural basis for substrate recognition in the depolymerization mechanism by alginate lyases, both ... | 2005 | 16511020 |
| proposal to reclassify [sphingomonas] xenophaga stolz et al. 2000 and [sphingomonas] taejonensis lee et al. 2001 as sphingobium xenophagum comb. nov. and sphingopyxis taejonensis comb. nov., respectively. | the sphingomonad group contains bacterial isolates that are quite diverse in terms of their phylogenetic, ecological and physiological properties. thus, the genus sphingomonas was divided into four distinct genera, sphingomonas sensu stricto, sphingobium, novosphingobium and sphingopyxis on the basis of 16s rrna gene sequence phylogenetic analysis, signature nucleotides, fatty acid profiles and polyamine patterns and this classification is currently widely accepted. in this study, a complete ana ... | 2006 | 16514047 |
| bioremediation of hydrocarbon-contaminated polar soils. | bioremediation is increasingly viewed as an appropriate remediation technology for hydrocarbon-contaminated polar soils. as for all soils, the successful application of bioremediation depends on appropriate biodegradative microbes and environmental conditions in situ. laboratory studies have confirmed that hydrocarbon-degrading bacteria typically assigned to the genera rhodococcus, sphingomonas or pseudomonas are present in contaminated polar soils. however, as indicated by the persistence of sp ... | 2006 | 16514512 |
| molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica. | the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ... | 2007 | 16517136 |
| effect of sphingobium yanoikuyae b1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly pah-contaminated soils. | sphingobium yanoikuyae b1 is able to degrade a range of polycyclic aromatic hydrocarbons (pahs) and as a sphingomonad belongs to one of the dominant genera found in pah-contaminated soils. we examined the ecological effect that soil inoculation with s. yanoikuyae b1 has on the native bacterial community in three different soils: aged pah-contaminated soil from an industrial site, compost freshly contaminated with pahs and un-contaminated compost. survival of s. yanoikuyae b1 was dependent on the ... | 2006 | 16524654 |
| bioavailability of sorbed 3-chlorodibenzofuran. | one of the main factors impeding the bioremediation of polluted soils, sediments, and aquifers is the low bioavailability of chemicals which are sorbed by organic matter. to obtain more insight into the factors that control the degradation of sorbed compounds, we used a defined model system in which 3-chlorodibenzofuran (3cdf) was the organic contaminant, porous teflon granules were the sorbent, and sphingomonas sp. strain hh19k was the test organism. the sorption of 3cdf to teflon reached equil ... | 1995 | 16534908 |
| studies on a viscous, gel-forming exopolysaccharide from sphingomonas paucimobilis gs1. | a new strain, sphingomonas paucimobilis gs1, accumulated 6.5 g of a highly viscous exopolysaccharide per liter, using sucrose as a substrate. the anionic heteropolysaccharide contained the following, in grams per gram: glucose, 0.7; galacturonic acid, 0.11; glucuronic acid, 0.07; and acetate, 0.12. the viscosity of the exopolysaccharide (4.0 g/liter; 4,200 cp) was 5.5 times that of xanthan gum and was stable over a wide ph and temperature range as well as in the presence of nacl. deacetylated po ... | 1995 | 16534966 |
| metabolism of hydroxydibenzofurans, methoxydibenzofurans, acetoxydibenzofurans, and nitrodibenzofurans by sphingomonas sp. strain hh69. | the metabolism of 11 substituted dibenzofurans by the dibenzofuran-degrading sphingomonas sp. strain hh69 was investigated. strain hh69 utilizes 2-, 3-, and 4-acetoxydibenzofuran as well as 2-, 3-, and 4-hydroxydibenzofuran as sole sources of carbon and energy. the degradation of acetoxydibenzofurans is initiated by hydrolysis of the ester bonds, yielding the corresponding hydroxydibenzofurans and acetate. strain hh69 grew on 2-methoxydibenzofuran only after it was adapted to the utilization of ... | 1995 | 16535067 |
| degradation of chlorinated dibenzofurans and dibenzo-p-dioxins by sphingomonas sp. strain rw1. | the ability of the dibenzofuran- and dibenzo-p-dioxin-mineralizing bacterium sphingomonas sp. strain rw1 (r.-m. wittich, h. wilkes, v. sinnwell, w. francke, and p. fortnagel, appl. environ. microbiol. 58:1005-1010, 1992) to oxidize chlorinated derivatives of dibenzofuran and dibenzo-p-dioxin was analyzed. strain rw1 degraded several mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins, but it did not degrade more highly chlorinated congeners. most mono- and dichlorinated dibenzofurans and ... | 1996 | 16535225 |
| responses to stress and nutrient availability by the marine ultramicrobacterium sphingomonas sp. strain rb2256. | sphingomonas sp. strain rb2256 was isolated from resurrection bay in alaska and possibly represents the dominant bacterial species in some oligotrophic marine environments. strain rb2256 has a high-affinity nutrient uptake system when growing under nutrient-limiting conditions, and growing cells are very small (<0.08 (mu)m(sup3)). these characteristics indicate that rb2256 is highly evolved for withstanding nutrient limitations and grazing pressure by heterotrophic nanoflagellates. in this study ... | 1996 | 16535292 |
| accelerated mineralization of pentachlorophenol in soil upon inoculation with mycobacterium chlorophenolicum pcp1 and sphingomonas chlorophenolica ra2. | mineralization of pentachlorophenol (pcp) was studied in nonsterile soil from a pcp-contaminated site upon inoculation with two pcp-degrading bacterial strains. at spiked [(sup14)c]pcp concentrations of 30 and 100 mg/kg, the effects of organism type, different inoculation techniques, including structural amendment with sawdust and cell attachment to polyurethane (pu), as well as the effect of different inoculum sizes of 10(sup4) to 10(sup8) cells per g (dry weight) of soil were compared with pcp ... | 1996 | 16535458 |
| bacterial metabolism of chlorinated dehydroabietic acids occurring in pulp and paper mill effluents. | chlorinated dehydroabietic acids are formed during the chlorine bleaching of wood pulp and are very toxic to fish. thus, destruction of these compounds is an important function of biological treatment systems for pulp and paper mill effluents. in this study, 12 strains of diverse, aerobic resin acid-degrading bacteria were screened for the ability to grow on chlorinated dehydroabietic acids as sole organic substrates. all seven strains of the class proteobacteria able to use dehydroabietic acid ... | 1997 | 16535663 |
| mineralization of 4-chlorodibenzofuran by a consortium consisting of sphingomonas sp. strain rw1 and burkholderia sp. strain jws. | the dibenzofuran-degrading bacterium sphingomonas sp. strain rw1 (r.-m. wittich, h. wilkes, v. sinnwell, w. francke, and p. fortnagel, appl. environ. microbiol. 58:1005-1010, 1992) attacks 4-chlorodibenzofuran on the unsubstituted aromatic ring via distal dioxygenation adjacent to the ether bridge to produce 3(prm1)-chloro-2,2(prm1),3-trihydroxybiphenyl, which was identified by nuclear magnetic resonance spectroscopy and mass spectrometry. the compound is subsequently meta cleaved, and the respe ... | 1997 | 16535686 |
| localization of the enzyme system involved in anaerobic reduction of azo dyes by sphingomonas sp. strain bn6 and effect of artificial redox mediators on the rate of azo dye reduction. | the effect of different artificial redox mediators on the anaerobic reduction of azo dyes by sphingomonas sp. strain bn6 or activated sludge was investigated. reduction rates were greatly enhanced in the presence of sulfonated anthraquinones. for strain bn6, the presence of both cytoplasmic and membrane-bound azo reductase activities was shown. | 1997 | 16535698 |
| design of natural killer t cell activators: structure and function of a microbial glycosphingolipid bound to mouse cd1d. | natural killer t (nkt) cells provide an innate-type immune response upon t cell receptor interaction with cd1d-presented antigens. we demonstrate through equilibrium tetramer binding and antigen presentation assays with valpha14i-positive nkt cell hybridomas that the sphingomonas glycolipid alpha-galacturonosyl ceramide (gala-gsl) is a nkt cell agonist that is significantly weaker than alpha-galactosylceramide (alpha-galcer), the most potent known nkt agonist. for gala-gsl, a shorter fatty acyl ... | 2006 | 16537470 |
| a biosystem for alginate metabolism in agrobacterium tumefaciens strain c58: molecular identification of atu3025 as an exotype family pl-15 alginate lyase. | the gram-negative bacterium sphingomonas sp. strain a1 (strain a1) has a peculiar biosystem to directly import and depolymerize a macromolecule, alginate, which is encoded by a cluster of genes on the genome. we identified five clustered orfs homologous to some genes of the strain a1 cluster in the genome of agrobacterium tumefaciens strain c58 (strain c58). these orfs are atu3021, atu3022, atu3023, and atu3024, encoding a putative sugar abc transporter system and atu3025, which encodes a putati ... | 2006 | 16545947 |
| plasmid-encoded gamma-hexachlorocyclohexane degradation genes and insertion sequences in sphingobium francense (ex-sphingomonas paucimobilis sp+). | the lin genes encode the gamma-hexachlorocyclohexane (gamma-hch or lindane) catabolic pathway in lindane-degrading strains. the location and stability of these genes have been explored in the lindane-degrading sphingobium francense strain sp+, and in two non-lindane-degrading mutants (sp1- and sp2-). the lin genes, lina, linb, line and linx were localized by hybridization on three of the six plasmids of the s. francense strain sp+ showing dispersal within the genome. the linc gene was detected b ... | 2006 | 16553860 |
| degradation of microcystins using immobilized microorganism isolated in an eutrophic lake. | the final purpose of our series of studies is to establish a biological removal method of cyanobacteria and their toxic products using immobilized microorganisms that can lyse cyanobacteria and decompose microcystins. to establish the biological removal method in non-point areas and water purification plants, as the first step, we explored bacteria active against the cyanobacterial hepatotoxin microcystin in the present study. eleven active bacteria were isolated from samples taken from lakes ts ... | 2006 | 16563465 |
| aerobic degradation of diethyl phthalate by sphingomonas sp. | an aerobic diethyl phthalate (dep) degrading bacterium, dep-ad1, was isolated from activated sludge. based on its 16s rdna sequence, this isolate was identified belonging to sphingomonas genus with 99% similarity to sphingomonas sp. strain c28242 and 98% similarity to s. capsulate. the specific degradation rate of dep was concentration dependent with a maximum of 14 mg-dep/(lh). results of degradation tests showed that dep-ad1 could also degrade monoethyl phthalate (mep), dimethyl phthalate (dmp ... | 2007 | 16563747 |
| characterization of psychrotolerant heterotrophic bacteria from finnish lapland. | a total of 331 aerobic heterotrophic bacterial strains were isolated from various ecosystems of finnish lapland (68-69 degrees n) including forest soil, arctic alpine-tundra soil, stream water, lake and mire sediments, lichen and snow algae. whole cell fatty acid and 16s rrna gene sequence analysis and microscopy indicated that the isolates were dominated by gram-negative bacteria, while only 20 gram-positive strains were isolated. based on 16s rrna gene sequences the isolates were members of al ... | 2006 | 16564959 |
| autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons. | autecological properties that are thought to be important for polycyclic aromatic hydrocarbon (pah)-degradation by bacteria in contaminated soils include the ability to utilize a broad range of carbon sources, efficient biofilm formation, cell-surface hydrophobicity, surfactant production, motility, and chemotaxis. sphingomonas species are common pah-degraders, and a selection of pah-degrading sphingomonad strains isolated from contaminated soils was therefore characterized in terms of these pro ... | 2006 | 16568318 |
| replicability of dominant bacterial populations after long-term surfactant-enrichment in lab-scale activated sludge. | bacterial communities were examined in replicate lab-scale activated sludge reactors after a period of several months of enrichment with non-ionic nonylphenol ethoxylate (npe) surfactants. four sequential batch reactors were fed with synthetic sewage, two of which received additionally npe. small subunit rdna-derived denaturing gel gradient electrophoresis (dgge) profiles and 16s rdna clone libraries were dominated by clones of gammaproteobacteria class. sequences of the other codominant rdna ph ... | 2006 | 16584474 |
| sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family sphingomonadaceae in the alpha-4 subgroup of the proteobacteria. | strain t5-04t, a gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in south korea and characterized in order to determine its taxonomic position. 16s rrna gene sequence analysis revealed that strain t5-04t belongs to the alpha-4 subgroup of the proteobacteria, and the highest degrees of sequence similarity determined were to sphingomonas asaccharolytica ifo 10564t (97.5 %), sphingomonas koreensis jss26t (97.1 %), sphingomonas mali ifo 15500t (96.7 ... | 2006 | 16585680 |
| sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of oryza sativa. | three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. the nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifh gene detection. the three strains were found to be very closely related, with 99.9 % 16s rrna gene sequence similarity and greater than 70 % dna-dna hybridization values, suggesting that the three strains represent a single species. 16s rrna gene sequence analysis indicated that the strain ... | 2006 | 16585711 |
| diverse bacteria associated with root nodules of spontaneous legumes in tunisia and first report for nifh-like gene within the genera microbacterium and starkeya. | we characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of tunisia by 16s rdna polymerase chain reaction (pcr)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page), 16s rdna and 16s-23s rdna internal transcribed spacer sequencing. phylogenetically, these isolates belong to the branches containing the genera inquilinus, bosea, rhodopseudomonas, para ... | 2006 | 16598639 |
| cloning, expression, and characterization of a self-sufficient cytochrome p450 monooxygenase from rhodococcus ruber dsm 44319. | a new member of class iv of cytochrome p450 monooxygenases was identified in rhodococcus ruber strain dsm 44319. as the genome of r. ruber has not been sequenced, a p450-like gene fragment was amplified using degenerated primers. the flanking regions of the p450-like dna fragment were identified by directional genome walking using polymerase chain reaction. the primary protein structure suggests a natural self-sufficient fusion protein consisting of ferredoxin, flavin-containing reductase, and p ... | 2006 | 16607529 |
| [screening methods for detection of metallo-beta-lactamase producing gram negative rods]. | modified hodge test and a method using a disk with imipenem plus 1000 mg of edta were used to determine the presence of metallo-beta-lactamase producing gram-negative rods among 166 clinical isolates from hospitals in iaşi and galaţi. of 9 imipenem resistant strains found, only one pseudomonas aeruginosa gave positive results with both tests and other two p. aeruginosa clinical isolates gave negative results with both tests. the rest of the strains (2 p. aeruginosa, 2 acinetobacter baumanii, 1 s ... | 2005 | 16607806 |
| comment on "biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1" by i.-h. nam, y.-m. kim, b.-h. kim, k. murugesan, and y.-s. chang. | 2006 | 16620903 | |
| [contamination with sphingomonas paucimobilis: about seven cases isolated in conservation and transport mediums of corneal grafts]. | from september to december 2004, contaminations were found in fifteen conservation and transport mediums of corneal grafts at the tissue bank of brest, including seven by sphingomonas paucimobilis. the pulsed-field gel electrophoresis made it possible to establish the genotypic profiles of each strain and to compare them. similarities were found between certain strains of the contaminated mediums and those of the thermostated double boiler of the tissue bank. the link between the contamination a ... | 2007 | 16631318 |
| growth inhibition by metabolites of gamma-hexachlorocyclohexane in sphingobium japonicum ut26. | the growth of a gamma-hexachlorocyclohexane (gamma-hch)-degrading bacterium sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 in rich medium was inhibited by gamma-hch. this growth inhibition was not observed in a mutant that lacked the initial or second step enzymatic activity for gamma-hch degradation, suggesting that metabolites of gamma-hch are toxic to ut26. two metabolites of gamma-hch, 2,5-dichlorophenol (2,5-dcp) and 2,5-dichlorohydroquinone (2,5-dchq), showed a direct toxi ... | 2006 | 16636477 |
| plasmid pcar3 contains multiple gene sets involved in the conversion of carbazole to anthranilate. | the carbazole degradative car-i gene cluster (caraaibaibbiciaci) of sphingomonas sp. strain ka1 is located on the 254-kb circular plasmid pcar3. carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (cardo; caraaiaci), meta-cleavage enzyme (carbaibbi), and hydrolase (carci). cardo is a three-component dioxygenase, and caraai and caraci are its terminal oxygenase and ferredoxin components. the car-i gene cluster lacks the gene encoding the ferredoxin reductase component ... | 2006 | 16672458 |
| characterization of novel carbazole catabolism genes from gram-positive carbazole degrader nocardioides aromaticivorans ic177. | nocardioides aromaticivorans ic177 is a gram-positive carbazole degrader. the genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. the car genes were clustered into the caraacbabbacad and cardfe gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme a, respectively. th ... | 2006 | 16672473 |
| modeling for gellan gum production by sphingomonas paucimobilis atcc 31461 in a simplified medium. | gellan gum production was carried out by sphingomonas paucimobilis atcc 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. the results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter(-1). as for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rot ... | 2006 | 16672479 |
| population dynamics within a microbial consortium during growth on diesel fuel in saline environments. | the diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near comodoro rivadavia in patagonia (argentina) were investigated. community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% nacl were monitored by single-strand conformation polymorphism community fingerprinting of the pcr-amplified v4-v5 region of the 16s rrna genes. information obtained by this qualitative approach was extended by ... | 2006 | 16672500 |