| proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. | phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ... | 2001 | 11491340 |
| emendation of the genus sphingomonas yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, sphingobium, novosphingobium and sphingopyxis, in conjunction with blastomonas ursincola. | the 16s rdna sequence similarities between the type strains of sphingomonas paucimobilis and 32 other sphingomonas species range from 90.2 to 99.6%. it might be possible to divide the genus into several new genera according to a dendrogram drawn from 16s rdna sequence similarity. however, the phenotypic and biochemical information needed to define clusters of strains representing distinct genera within this group of organisms was not previously available. although the cellular lipids of type str ... | 2002 | 12361250 |
| 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 |
| 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 |
| poly-beta-hydroxyalkanoates consumption during degradation of 2,4,6-trichlorophenol by sphingopyxis chilensis s37. | to analyse the possible effect of poly-beta-hydroxyalkanoate (pha) consumption on 2,4,6-trichlorophenol (2,4,6-tcp) degradation during starvation by sphingopyxis chilensis s37 strain, which stores phas and degrades 2,4,6-tcp. | 2003 | 12680945 |
| 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 |
| aerobic secondary utilization of a non-growth and inhibitory substrate 2,4,6-trichlorophenol by sphingopyxis chilensis s37 and sphingopyxis-like strain s32. | this paper reports 2,4,6-trichlorophenol (246tcp) degradation by sphingopyxis chilensis s37 and sphingopyxis chilensis-like strain s32, which were unable to use 246tcp as the sole carbon and energy source. in r2a broth, the strains degraded 246tcp up to 0.5 mm. results with mixtures of different 246tcp and glucose concentrations in mineral salt media demonstrated dependence on glucose to allow bacterial growth and degradation of 246tcp. strain s32 degraded halophenol up to 0.2 mm when 5.33 mm gl ... | 2003 | 12948056 |
| 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 |
| cross-species identification of proteins from proteome profiles of the marine oligotrophic ultramicrobacterium, sphingopyxis alaskensis. | sphingopyxis (formerly sphingomonas) alaskensis is a model bacterium for studying adaptation to oligotrophy (nutrient-limitation). it has a unique physiology which is fundamentally different to that of the well studied bacteria such as escherichia coli. to begin to identify the genes involved in its physiological responses to nutrient-limited growth and starvation, we developed high resolution two-dimensional electrophoresis (2-de) methods and determined the identity of 12 proteins from a total ... | 2004 | 15174144 |
| novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. | a gram-negative, yellow-pigmented, halophilic bacterial strain us6-1t, which degrades high-molecular-mass polycyclic aromatic hydrocarbons of two to five rings, was isolated from muddy sediment of ulsan bay, republic of korea. the 16s rrna gene of the isolate showed high sequence similarity to novosphingobium subarcticum (96.23 %) and sphingopyxis alaskensis (96.18 %); however, the isolate formed a distinct phyletic line within the genus novosphingobium. dna-dna relatedness between us6-1t and th ... | 2004 | 15388699 |
| streptomycin as a selective agent to facilitate recovery and isolation of introduced and indigenous sphingomonas from environmental samples. | sphingomonas is an organism of major interest for the degradation of organic contaminants in soils and other environments. a medium based on the aminoglycoside antibiotic streptomycin (sm) was developed, which, together with the yellow pigmentation of sphingomonas, facilitated the detection, recovery and quantification of culturable sphingomonas from soils. all 29 previously described bacterial strains belonging to 17 different sphingomonas species were able to grow on mineral media containing 2 ... | 2004 | 15479246 |
| sphingopyxis flavimaris sp. nov., isolated from sea water of the yellow sea in korea. | a gram-negative, motile, yellow-pigmented, slightly halophilic bacterial strain, sw-151t, was isolated from sea water of the yellow sea in korea, and subjected to a polyphasic taxonomic study. the isolate grew optimally at 30 degrees c and in the presence of 2-3 % nacl. strain sw-151t was characterized chemotaxonomically as having q-10 as the predominant respiratory lipoquinone and c(18 : 1)omega7c, c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh and c(17 : 1)omega6c as the major fatty acids. sphingo ... | 2005 | 15653902 |
| sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the yellow sea in korea. | a gram-negative, motile, slightly halophilic bacterial strain, sw-150(t), was isolated from sea water of the yellow sea, korea, and was characterized by a polyphasic taxonomic approach. strain sw-150(t) grew optimally at 25-30 degrees c and in the presence of 2 % (w/v) nacl. the isolate could be distinguished from other sphingopyxis species in producing an orange pigment. it contained ubiquinone-10 as the predominant respiratory lipoquinone and c(18 : 1)omega7c and c(17 : 1)omega6c as the major ... | 2005 | 15879259 |
| sphingopyxis granuli sp. nov., a beta-glucosidase-producing bacterium in the family sphingomonadaceae in alpha-4 subclass of the proteobacteria. | strain kw07t, a gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an up-flow anaerobic sludge blanket (uasb) bioreactor used in the treatment of brewery wastewater. 16s rrna gene sequence analysis revealed that strain kw07t belongs to the alpha-4 subclass of the proteobacteria, and the highest degree of sequence similarity was determined to be to sphingopyxis macrogoltabida ifo 15033t(97.8%). chemotaxonomic data revealed that strain kw07t possesses a quinone s ... | 2005 | 15880090 |
| biosynthesis of poly-beta-hydroxyalkanoates by sphingopyxis chilensis s37 and wautersia sp. pzk cultured in cellulose pulp mill effluents containing 2,4,6-trichlorophenol. | poly-beta-hydroxyalkanoates (pha) polymer is synthesized by different bacterial species. there has been considerable interest in the development and production of biodegradable polymers; however, the high cost of pha production has restricted its applications. kraft cellulose industry effluents containing 2,4,6-trichlorophenol (10 or 20 microg ml(-1)) were used by the bacteria sphingopyxis chilensis s37 and wautersia sp. pzk to synthesize pha. in this condition, s. chilensis s37 was able to grow ... | 2005 | 16044293 |
| 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 |
| 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 |
| isolation and characterization of a novel poly(vinyl alcohol)-degrading bacterium, sphingopyxis sp. pva3. | we have isolated a poly(vinyl alcohol) (pva)-degrading bacterium from an activated sludge sample obtained from the drainage of a dyeing factory. enrichment cultures were performed in media containing pva as the sole or major carbon source. after several rounds of cultivation on liquid and solid media, we were able to isolate a single colony with pva-degrading ability (strain pva3). the bacterium could degrade pva in the absence of symbionts or cofactors such as pyrroloquinoline quinone (pqq). ov ... | 2006 | 16583228 |
| analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants. | polyethylene glycol dehydrogenase (pegdh) from sphingopyxis terrae (formerly sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a homodimeric structure. its amino acid sequence shows 28.5 to 30.5% identity with glucose oxidases from aspergillus niger and penicillium amagasakiense. the adp-binding site and the signature 1 and 2 consensus sequences of glucose-methanol-choline oxidoreductases are present in pegdh. based on three-di ... | 2006 | 16751555 |
| genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. | to investigate the diversity of dioxygenase genes involved in polycyclic aromatic hydrocarbon (pah)-degradation, a total of 32 bacterial strains were isolated from surface mangrove sediments, from the genera mycobacterium, sphingomonas, terrabacter, sphingopyxis, sphingobium and rhodococcus. two sets of pcr primers were constructed to detect the nida-like and nahac-like sequences of the alpha subunit of the pah ring-hydroxylating dioxygenase. pcr amplified the dna fragments from all gram-positiv ... | 2006 | 16923069 |
| description of sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of sphingomonas cloacae as sphingobium cloacae comb. nov. | a phenanthrene-degrading bacterium, strain tkp(t), was isolated from a fly ash dumping site of the thermal power plant in panki, kanpur, india, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. phylogenetic analysis based on 16s rrna gene sequences indicated that the strain belonged to the genus sphingobium, as it showed highest sequence similarity to sphingobium herbicidovorans dsm 11019(t) (97.3 %) and sphingomonas cloacae jcm 10874(t) (96.5 %), compar ... | 2006 | 16957112 |
| cooperative biodegradation of geosmin by a consortium comprising three gram-negative bacteria isolated from the biofilm of a sand filter column. | to isolate and identify bacteria from a sand filter column capable of degrading the taste and odour compound, geosmin. in doing so, to investigate if these organisms degrade geosmin either individually or if an alternative mechanism is utilized. | 2006 | 16965373 |
| dual regulation of a polyethylene glycol degradative operon by arac-type and galr-type regulators in sphingopyxis macrogoltabida strain 103. | the genes for polyethylene glycol (peg) catabolism (pegb, c, d, a and e) in sphingopyxis macrogoltabida strain 103 were shown to form a peg-inducible operon. the pegr gene, encoding an arac-type regulator in the downstream area of the operon, is transcribed in the reverse direction. the transcription start sites of the operon were mapped, and three putative sigma(70)-type promoter sites were identified in the pegb, pega and pegr promoters. a promoter activity assay showed that the pegb promoter ... | 2006 | 17005983 |
| isolation of bacteria able to grow on both polyethylene glycol (peg) and polypropylene glycol (ppg) and their peg/ppg dehydrogenases. | two bacterial consortia growing on a random copolymer of ethylene glycol and propylene glycol units were obtained by enrichment cultures from various microbial samples. six major strains included in both consortia were purified and identified as sphingomonads, pseudomonas sp. and stenotrophomonas maltophilia. three of them (sphingobium sp. strain ek-1, sphingopyxis macrogoltabida strain ey-1, and pseudomonas sp. strain pe-2) utilized both peg and polypropylene glycol (ppg) as a sole carbon sourc ... | 2007 | 17043822 |
| description of sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus sphingosinicella and the species sphingosinicella microcystinivorans. | a gram-negative, rod-shaped bacterium, strain 3-2w4(t), was isolated from the aeration tank of a wastewater treatment plant in zurich and was found to have the exceptional capacity to degrade synthetic beta-peptides. 16s rrna gene sequence analysis showed that strain 3-2w4(t) is closely related to sphingosinicella microcystinivorans y2(t), but dna-dna hybridization experiments between these two strains revealed that they belong to two different species. the two strains displayed different finger ... | 2007 | 17220451 |
| structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. | sphingopyxis terrae, and sphingopyxis macrogoltabida strains 103 and 203, can degrade polyethylene glycols (pegs). they differ in the following respects: (i) different substrate specificities (chain length) of assimilable peg, (ii) peg-inducible or constitutive peg-degradative proteins, and (iii) symbiotic or axenic degradation of peg. s. terrae was able to incorporate peg 6000, but strain 103 could not incorporate more than peg 4000, suggesting that the difference in assimilable peg chain lengt ... | 2007 | 17259605 |
| cell surface structure enhancing uptake of polyvinyl alcohol (pva) is induced by pva in the pva-utilizing sphingopyxis sp. strain 113p3. | polyvinyl alcohol (pva)-utilizing sphingopyxis sp. 113p3 (re-identified from sphingomonas sp. 113p3) removed almost 0.5% pva from culture supernatants in 4 days. faster degradation of 0.5% pva was performed by the periplasmic fraction. the average molecular size of pva in the culture supernatant or cell-bound pva was gradually shifted higher, suggesting that lower molecular size molecules are degraded faster. depolymerized products were found in neither the culture supernatant nor the cell-bound ... | 2007 | 17453173 |
| identification of yellow-pigmented bacteria isolated from hospital tap water in japan and their chlorine resistance. | twenty-five yellow chromogenic strains isolated from hospital tap water samples collected nationwide were identified by partial 16s rdna sequencing. in addition, the chlorine resistance of the isolates was experimentally investigated. the results showed that of the strains tested, 12 strains (48.0%) were sphingomonas ursincola/natatoria, which was most frequently identified, followed by 2 strains (8.0%) of mycobacterium frederiksbergense and 1 strain (4.0%) each of sphingomonas adhaesiva, sphing ... | 2007 | 17629244 |
| biosynthesis of poly-beta-hydroxyalkanoate by brevundimonas vesicularis lmg p-23615 and sphingopyxis macrogoltabida lmg 17324 using acid-hydrolyzed sawdust as carbon source. | poly-beta-hydroxyalkanoate (pha) is a biodegradable polymer accumulated in intracellular granules by different bacterial species. its physical and chemical properties are similar to those of petroleum-derived plastics. material generated by the acid hydrolysis of wood was evaluated for use in the bacterial synthesis of pha. acid-hydrolyzed sawdust was prepared and adjusted to ph 7. mineral salts with carbon:nitrogen (c:n) proportions of 100:1, 100:3.5, 100:10, 100:30, or 100:50 and trace element ... | 2007 | 17630126 |
| isolation and identification of a novel microcystin-degrading bacterium from a biological sand filter. | a novel bacterium capable of degrading two microcystin analogues, microcystin-lr and -la (mclr and mcla), was isolated from a biological sand filter which was previously shown to effectively remove these toxins from source waters. based on phylogenetic analysis of the 16s rrna gene sequence, the isolated organism, lh21, most likely belonged to the genus sphingopyxis and of the previously cultured species clustered with sphingopyxis witflariensis. using polymerase chain reaction (pcr), isolate lh ... | 2007 | 17640697 |
| [isolation and characterization of marine oligotrophic bacteria]. | a significant part of the world ocean is characterized by low absolute nutrients and chlorophyll concentrations. in these oligotrophic environments, bacteria are very abundant and play a vital role in the remineralization of the dissolved organic matter. bacteria adapted to oligotrophic waters differ from those adapted to richer environments by some genetic and metabolic characteristics. culture techniques in bacteriology are based on rich media and do not allow the growth of most marine bacteri ... | 2007 | 17762823 |
| polyethylene glycol (peg)-carboxylate-coa synthetase is involved in peg metabolism in sphingopyxis macrogoltabida strain 103. | sphingopyxis macrogoltabida strain 103 possesses polyethylene-glycol (peg)-inducible pegbcdae operon encoding the genes relevant to peg degradation. peg is converted to peg-carboxylate by pega (peg dehydrogenase) and pegc (peg-aldehyde dehydrogenase). in this study, the recombinant pege (homologous to acyl-coa synthetases) was characterized. pege was an acyl-coa synthetase active for peg-carboxylate and fatty acids. judging from the nature of this kind of protein (located on the cytoplasmic memb ... | 2008 | 17985114 |
| the pva operon is located on the megaplasmid of sphingopyxis sp. strain 113p3 and is constitutively expressed, although expression is enhanced by pva. | the upstream and downstream regions of the tentative pva operon including genes encoding oxidized polyvinyl alcohol (pva) hydrolase (oph), pva dehydrogenase (pvaa) and cytochrome c (cytc) from sphingopyxis sp. strain 113p3 were sequenced. the resultant 7.9 kb sequence contained orf1 in the upstream region and orf2 and orf3 in the downstream region. reverse transcription-polymerase chain reaction (pcr) analyses revealed that the intergenic regions between orf1 and oph or between cytc and orf2 wer ... | 2008 | 18214469 |
| cloning and expression of soluble cytochrome c and its role in polyvinyl alcohol degradation by polyvinyl alcohol-utilizing sphingopyxis sp. strain 113p3. | the gene encoding cytocrome c in the pva operon of sphingopyxis sp. strain 113p3 was cloned, on the basis of the sequence of the gene for cytochrome c (genbank accession no. ab190288). the deduced amino acid sequence of the gene showed homologies (37% and 47% identities) with two cytochromes c of different origins. the recombinant cytochrome c tagged with hexahistidines was expressed in the periplasm of escherichia coli bl21(de3) harboring pt-groe, which was in accordance with the localization o ... | 2008 | 18343342 |
| [search of streptomycin-resistant bacteria in creek water and application of maldi-tof ms to grouping of the isolated bacteria]. | a search of streptomycin-resistant bacteria was carried out using ten creek water samples collected in saga prefecture by spreading the sample water on an r2a medium containing 10 microg/ml of streptomycin. it was clarified that such streptomycin-resistant bacteria as bacillus, novosphigobium, sphingopyxis and oceanobacillus were distributed in the creek water. further, 60% of the isolates didn't form an inhibitory zone by the application of 700 microg/ml streptomycin solution in the cup method ... | 2008 | 18350749 |
| a common soil flagellate (cercomonas sp.) grows slowly when feeding on the bacterium rhodococcus fascians in isolation, but does not discriminate against it in a mixed culture with sphingopyxis witflariensis. | flagellates are very important predators on bacteria in soil. because of their high growth rates, flagellate populations respond rapidly to changes in bacterial numbers. previous results indicate that actinobacteria are generally less suitable than proteobacteria as food for flagellates. in this study, we investigated the growth of the flagellate cercomonas sp. (atcc 50334) on each of the two bacteria sphingopyxis witflariensis (alphaproteobacteria) and rhodococcus fascians (actinobacteria) sepa ... | 2008 | 18462400 |
| sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field. | a gram-negative, strictly aerobic, motile bacterial strain, designated gsoil 124t, was isolated from a soil sample taken from a ginseng field in pocheon province (south korea). the isolate contained q-10 as the predominant lipoquinone, plus c18:1 7c and summed feature 4 (c16:1 6c and/or iso- c15:0 2-oh) as the major fatty acids. the g+c content of the genomic dna was 68.1 mol%, and the major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, and phosphatidyle ... | 2008 | 18600040 |
| involvement of peg-carboxylate dehydrogenase and glutathione s-transferase in peg metabolism by sphingopyxis macrogoltabida strain 103. | sphingopyxis terrae and the sphingopyxis macrogoltabida strains 103 and 203 are able to degrade polyethylene glycol (peg). they possess the peg operon, which is responsible for the conversion of peg to peg-carboxylate-coenzyme a (coa). the upstream (3.0 kb) and downstream (6.5 kb) regions of the operon in strain 103 were cloned and sequenced. the structure was well conserved between s. macrogoltabida strain 203 and s. terrae, except that two sets of transposases are absent in strain 203. the dow ... | 2008 | 18719904 |
| influence of size, shape, and flexibility on bacterial passage through micropore membrane filters. | sterilization of fluids by means of microfiltration is commonly applied in research laboratories as well as in pharmaceutical and industrial processes. sterile micropore filters are subject to microbiological validation, where brevundimonas diminuta is used as a standard test organism. however, several recent reports on the ubiquitous presence of filterable bacteria in aquatic environments have cast doubt on the accuracy and validity of the standard filter-testing method. six different bacterial ... | 2008 | 18800559 |
| sphingopyxis ginsengisoli sp. nov., isolated from soil of a ginseng field in south korea. | a gram-negative, aerobic, motile, rod-shaped bacterium (strain gsoil 250(t)) was isolated from soil of a ginseng field in pocheon province (south korea) and was characterized using a polyphasic approach in order to determine its taxonomic position. comparative analysis of 16s rrna gene sequences showed that strain gsoil 250(t) belonged to the family sphingomonadaceae of the class alphaproteobacteria, and was related to sphingopyxis macrogoltabida (98.7 %), sphingopyxis chilensis (98.2 %), sphing ... | 2008 | 18842853 |
| sphingopyxis marina sp. nov. and sphingopyxis litoris sp. nov., isolated from seawater. | two yellow-pigmented, gram-negative, aerobic bacterial strains, designated fr1087(t) and fr1093(t), were isolated from surface seawater off jeju island, republic of korea. both strains required sea salts for growth. phylogenetic analysis based on 16s rrna gene sequences indicated that the two isolates belong to the genus sphingopyxis, showing the highest level of sequence similarity with respect to sphingopyxis flavimaris sw-151(t) (97.9 %). the two isolates shared 98.5 % sequence similarity. dn ... | 2008 | 18842866 |
| biodegradation of geosmin by a novel gram-negative bacterium; isolation, phylogenetic characterisation and degradation rate determination. | biologically active sand filters within water treatment plants (wtps) are now recognised as an effective barrier for the removal of geosmin. however, little is known regarding the actual microbiological processes occurring or the bacteria capable of degrading geosmin. this study reports the enrichment and isolation of a gram-negative bacterium, geo48, from the biofilm of a wtp sand filter where the isolate was shown to effectively degrade geosmin individually. experiments revealed that geo48 deg ... | 2009 | 19439338 |
| carbon and nitrogen substrate utilization in the marine bacterium sphingopyxis alaskensis strain rb2256. | sphingopyxis alaskensis is a marine member of the alphaproteobacteria that is adapted to heterotrophic growth under nutrient-depleted (oligotrophic) conditions. s. alaskensis strain rb2256 is an ultramicrobacterium (cell volume <0.1 microm(3)), and has a genome size larger than that of the ultramicrobacterium 'candidatus pelagibacter ubique' htcc1062 (sar11 clade of alphaproteobacteria): 3.35 versus 1.31 mbp. in this study, we investigate the carbon and nitrogen metabolism of strain rb2256 using ... | 2009 | 19458655 |
| biochemistry of microbial polyvinyl alcohol degradation. | effect of minor chemical structures such as 1,2-diol content, ethylene content, tacticity, a degree of polymerization, and a degree of saponification of the main chain on biodegradability of polyvinyl alcohol (pva) is summarized. most pva-degraders are gram-negative bacteria belonging to the pseudomonads and sphingomonads, but gram-positive bacteria also have pva-degrading abilities. several examples show symbiotic degradation of pva by different mechanisms. penicillium sp. is the only reported ... | 2009 | 19590867 |
| the response of the marine bacterium sphingopyxis alaskensis to solar radiation assessed by quantitative proteomics. | the adaptive response of the marine bacterium sphingopyxis alaskensis rb2256 to solar radiation (both visible and ultraviolet) was assessed by a quantitative proteomic approach using itraq (isobaric tags for relative and absolute quantification). both growth phase (mid-log and stationary phase) and duration (80 min or 8 h) of different light treatments (combinations of visible light, uv-a and uv-b) were assessed relative to cultures maintained in the dark. rates of total protein synthesis and vi ... | 2009 | 19601963 |
| normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling. | comparative proteomics is a powerful analytical method for learning about the responses of biological systems to changes in growth parameters. to make confident inferences about biological responses, proteomics approaches must incorporate appropriate statistical measures of quantitative data. in the present work we applied microarray-based normalization and statistical analysis (significance testing) methods to analyze quantitative proteomics data generated from the metabolic labeling of a marin ... | 2009 | 19605365 |
| sphingopyxis ummariensis sp. nov., isolated from a hexachlorocyclohexane dump site. | a gram-negative, motile, rod-shaped, yellow-pigmented bacterium, strain ui2(t), was isolated from a hexachlorocyclohexane (hch) dump site located in ummari, in northern india. 16s rrna gene sequence analysis revealed that strain ui2(t) belongs to the genus sphingopyxis and showed highest 16s rrna gene sequence similarity with sphingopyxis terrae ifo 15098(t) (98.6 %). dna-dna relatedness values between strain ui2(t) and sphingopyxis terrae ifo 15098(t) and other related strains were found to be ... | 2010 | 19656938 |
| remarkable resistance to uvb of the marine bacterium photobacterium angustum explained by an unexpected role of photolyase. | dna damage and cell survival was assessed in the marine bacteria, photobacterium angustum (gc%=39.6) and sphingopyxis alaskensis (gc%=65.5) following uvb irradiation and recovery in the presence or absence of visible light. the extent of bipyrimidine photoproduct formation was analyzed by hplc-ms/ms. s. alaskensis was chosen as a reference species since it was previously shown to be photoresistant. interestingly, p. angustum exhibited an even higher level of survival to uvb irradiation than s. a ... | 2009 | 19707619 |
| characterization and phylogenetic analysis of biodemulsifier-producing bacteria. | based on demulsification performance, twenty biodemulsifier-producing strains were isolated from various environmental sources. five of them achieved nearly or over 90% of emulsion breaking ratio within 24 h. with the aid of biochemical and physiological tests and 16s rdna analysis, these isolates were classified into eleven genera, in which six genera (brevibacillus sp., dietzia sp., ochrobactrum sp., pusillimonas sp., sphingopyxis sp. and achromobacter sp.) were firstly reported as demulsifyin ... | 2010 | 19720525 |
| poly-beta-hydroxyalkanoate exert a protective effect against carbon starvation and frozen conditions in sphingopyxis chilensis. | several bacterial species have developed physiological response to avoid the cellular damage when are exposed to carbon starvation or frozen stress. for example survival to inanition has been related to endogenous substrates consumptions. the aim of this study was to evaluate if poly-beta-hydroxylkanoates (pha) consumption enable sphingopyxis chilensis s37 to survive under carbon starvation or frozen condition. bacterial cells were grown in r(2)a broth for 48 h, and suspended in mineral saline s ... | 2009 | 19727947 |
| sphingopyxis soli sp. nov., isolated from landfill soil. | a gram-negative, aerobic, rod-shaped, motile, oxidase-positive, catalase-negative bacterium, designated strain bl03(t), was isolated from landfill soil in pohang, republic of korea. colonies on luria-bertani agar plates were yellow. the strain grew in the presence of 0-3 % (w/v) nacl, at 15-42 degrees c and at ph 5.0-9.5. the predominant ubiquinone was q-10, and the major cellular fatty acids were c(17 : 1)omega6c, c(15 : 0) 2-oh and c(18 : 1)omega7c. polar lipids detected were phosphatidylmonom ... | 2010 | 19734286 |
| the genomic basis of trophic strategy in marine bacteria. | many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. here, we compare the genome sequences of two bacteria, photobacterium angustum s14 and sphingopyxis alaskensis rb2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms an ... | 2009 | 19805210 |
| degradation of fumonisin b1 by the consecutive action of two bacterial enzymes. | detoxification of the mycotoxin fumonisin b(1) comprises at least two enzymatic steps, an initial deesterification reaction, followed by deamination of the resulting hydrolyzed fumonisin b(1). in this study, two genes that are responsible for degradation of fumonisin b(1) by the bacterium sphingopyxis sp. mta144 were identified within a gene cluster, assumed to be associated with fumonisin degradation. the first gene encodes a protein which shows similarity to carboxylesterases, type b. the seco ... | 2010 | 19922747 |
| sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. | a gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in daejeon, south korea, and characterized in order to determine its taxonomic position. phylogenetic analysis based on 16s rrna gene sequence analysis revealed that strain dcy34(t) belonged to the family sphingomonadaceae, and the highest degree of sequence similarity was found with sphingopyxis witflariensis w-50(t) (97.1 %), sphingopyxis ginsengisoli gsoil 250(t) (97.0 %), sphingopyxis chilensis s37(t) ... | 2010 | 19933588 |
| sphingopyxis bauzanensis sp. nov., a psychrophilic bacterium isolated from soil. | strain bz30(t) was isolated from hydrocarbon-contaminated soil. the gram-negative, aerobic bacterium was psychrophilic and able to grow at temperatures ranging from 1 to 30 °c. the predominant cellular fatty acids of strain bz30(t) were summed feature 3 (c(16 : 1)ω7c and/or iso-c(15 : 0) 2-oh) (37.4 %), c(18 : 1)ω7c (19.6 %), c(16 : 0) (8.2 %), c(14 : 0) 2-oh (8.0 %) and c(16 : 0) 2-oh (5.0 %). the predominant ubiquinone was q-10. major polar lipids were sphingoglycolipids, diphosphatidyl ... | 2010 | 20023054 |
| changes in pelagic bacteria communities due to leaf litter addition. | in many limnetic systems, the input of allochthonous organic matter, e.g., leaf litter, is a substantial source of dissolved organic carbon (doc) for pelagic bacteria, especially in fall and winter when autochthonous doc production is low. however, relatively little is known about community changes of pelagic lake bacteria due to leaf litter input which includes both the release of leaf leachates and microorganisms from the leaf litter into the surrounding water. therefore, we have experimentall ... | 2010 | 20198369 |
| characteristics of a microcystin-degrading bacterium under alkaline environmental conditions. | the ph of the water associated with toxic blooms of cyanobacteria is typically in the alkaline range; however, previously only microcystin-degrading bacteria growing in neutral ph conditions have been isolated. therefore, we sought to isolate and characterize an alkali-tolerant microcystin-degrading bacterium from a water bloom using microcystin-lr. analysis of the 16s rrna gene sequence revealed that the isolated bacterium belonged to the genus sphingopyxis, and the strain was named c-1. sphing ... | 2010 | 20224628 |
| microbial biodegradation of microcystin-rr by bacterium sphingopyxis sp. ustb-05. | a strain, ustb-05, isolated from lake dianchi, china, degraded the cyanobacterial toxin microcystin-rr (mc-rr) at the rate of 16.7 mg/l per day. analysis of 16s rdna sequence showed that the strain was sphingopyxis sp. enzymatic degradation pathways for mc-rr by sphingopyxis sp. ustb-05 were identified. adda-arg peptide bond of mc-rr was cleaved and then a hydrogen and a hydroxyl were combined onto the nh2 group of adda and the carboxyl group of arginine to form a linear molecule as intermediate ... | 2010 | 20397402 |
| cold adaptation in the marine bacterium, sphingopyxis alaskensis, assessed using quantitative proteomics. | the cold marine environment constitutes a large proportion of the earth's biosphere. sphingopyxis alaskensis was isolated as a numerically abundant bacterium from several cold marine locations, and has been extensively studied as a model marine bacterium. recently, a metabolic labelling platform was developed to comprehensively identify and quantify proteins from s. alaskensis. the approach incorporated data normalization and statistical validation for the purpose of generating highly confident ... | 2010 | 20482592 |
| influence of growth temperature and starvation state on survival and dna damage induction in the marine bacterium sphingopyxis alaskensis exposed to uv radiation. | despite the considerable volume of literature describing the individual effects of temperature or uv light on aquatic bacteria, little is known about their combined effects. the current study was conducted to learn about the effects of growth temperature and duration of starvation on the response of a marine bacterium, sphingopyxis alaskensis to uv-b or simulated solar radiation. cells grown at 12 degrees c or 24 degrees c, and harvested at early or late stationary phase, were exposed to uv-b or ... | 2010 | 20570167 |
| bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study. | microorganisms in drinking water sources may colonize in gastrointestinal (gi) tracts and this phenomenon may pose a potential health risk especially to immunocompromised population. the microbial community diversity of the drinking water was compared with the gi tracts of the mice using phylogenetic and statistical analyses of 16s rrna gene sequences. a group of germ-free mice were fed with drinking water from public water supply that passed through an automated watering system with documented ... | 2010 | 20705313 |
| enhancement of solubility in escherichia coli and purification of an aminotransferase from sphingopyxis sp. mta144 for deamination of hydrolyzed fumonisin b(1). | fumonisin b(1) is a cancerogenic mycotoxin produced by fusarium verticillioides and other fungi. sphingopyxis sp. mta144 can degrade fumonisin b(1), and a key enzyme in the catabolic pathway is an aminotransferase which removes the c2-amino group from hydrolyzed fumonisin b(1). in order to study this aminotransferase with respect to a possible future application in enzymatic fumonisin detoxification, we attempted expression of the corresponding fumi gene in e. coli and purification of the enzyme ... | 2010 | 20718948 |
| culture-independent study of the diversity of microbial populations in brines during fermentation of naturally-fermented aloreña green table olives. | aloreña table olives are naturally fermented traditional green olives with a denomination of protection (dop). the present study focused on aloreña table olives manufactured by small and medium enterprises (smes) from valle del guadalhorce (southern spain) under three different conditions (cold storage, and ambient temperature fermentations in small vats and in large fermentation tanks). the microbial load of brines during fermentation was studied by plate counting, and the microbial diversity w ... | 2010 | 21122933 |
| metagenomic analysis of 0.2-µm-passable microorganisms in deep-sea hydrothermal fluid. | we pyrosequenced the bulk dna extracted from microorganisms that passed through 0.2-µm-pore-size filters and trapped by 0.1-µm-pore-size filters in the hydrothermal fluid of the mariana trough. using the 454-flx sequencer, we generated 202,648 sequences with an average length of 173.8 bases. functional profiles were assigned by the seed annotation engine. in the metagenome of the 0.2-µm-passable microorganisms, genes related to membrane function, including potassium homeostasis classified as mem ... | 2011 | 21279410 |
| characterization of a cryptic plasmid, psm103mini, from polyethylene-glycol degrading sphingopyxis macrogoltabida strain 103. | a cryptic plasmid, psm103mini, was found in polyethylene-glycol degrading bacterium sphingopyxis macrogoltabida, strain 103. the plasmid was 4,328-bp long and its gc content was 57.5%. it contained four open reading frames, but only two of them showed significant similarity to reported proteins. orf3 and orf4 were assumed to encode resolvase and replication protein (repa) respectively. downstream of orf4 we found complex repeat sequences. these together with orf3 and 4 were necessary and suffici ... | 2011 | 21307601 |
| culturable diversity of heterotrophic bacteria in forlidas pond (pensacola mountains) and lundström lake (shackleton range), antarctica. | cultivation techniques were used to study the heterotrophic bacterial diversity in two microbial mat samples originating from the littoral zone of two continental antarctic lakes (forlidas pond and lundström lake) in the dufek massif (within the pensacola mountains group of the transantarctic mountains) and shackleton range, respectively. nearly 800 isolates were picked after incubation on several growth media at different temperatures. they were grouped using a whole-genome fingerprinting techn ... | 2011 | 21424822 |
| enzyme characteristics of aminotransferase fumi of sphingopyxis sp. mta144 for deamination of hydrolyzed fumonisin b(1). | fumonisins are carcinogenic mycotoxins that are frequently found as natural contaminants in maize from warm climate regions around the world. the aminotransferase fumi is encoded as part of a gene cluster of sphingopyxis sp. mta144, which enables this bacterial strain to degrade fumonisin b(1) and related fumonisins. fumi catalyzes the deamination of the first intermediate of the catabolic pathway, hydrolyzed fumonisin b(1). we used a preparation of purified, his-tagged fumi, produced recombinan ... | 2011 | 21503761 |
| diversity and antibiotic resistance patterns of sphingomonadaceae isolates from drinking water. | sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). the bacterial isolates were identified based on analysis of the 16s rrna gene sequence, and intraspecies variation was assessed on the basis of atpd gene sequence analysis. the isolates were identified as members of the genera sphingomonas (n = 27), sphingobium (n = 28), novosphingobium (n = 12), sphingopy ... | 2011 | 21705522 |
| expression and fermentation optimization of oxidized polyvinyl alcohol hydrolase in e. coli. | oxidized polyvinyl alcohol (pva) hydrolase (oph) is a key enzyme in the degradation of pva, suggesting that oph has a great potential for application in textile desizing processes. in this study, the oph gene from sphingopyxis sp. 113p3 was modified, by artificial synthesis, for overexpression in escherichia coli. the oph gene, lacking the sequence encoding the original signal peptide, was inserted into pet-20b (+) expression vector, which was then used to transform e. coli bl21 (de3). oph expre ... | 2011 | 21695541 |
| parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine organism in kagoshima bay, japan. | a gram-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain jamh 0132t, was isolated from a tubeworm trophosome in kagoshima bay, japan, and subjected to polyphasic taxonomic characterization. the isolate grew optimally at 28-30 °c and in the presence of 2-3 % nacl. chemotaxonomic analysis showed that q-10 was the predominant respiratory quinone and that c18:1 ω7c, c16:0 2-oh and c16:0 were the major fatty acids. sphingoglycolipids, phosphatid ... | 2011 | 22081711 |
| Characterization of the first step involved in enzymatic pathway for microcystin-RR biodegraded by Sphingopyxis sp. USTB-05. | Enzymes encoded by genes biodegrading microcystins (MCs) can help reveal the function of genes and biodegradation pathway of MCs. Here the first and important gene (USTB-05-A, 1,008bp) involved in biodegradation of microcystin-RR (MC-RR) was cloned from Sphingopyxis sp. USTB-05 and firstly expressed in Escherichia coli BL21 (DE3) with an expression vector of pGEX4T-1 successfully. The nucleotide sequences of cloned USTB-05-A possessed 92.5% homology to that of mlA reported in Sphingomonas sp. st ... | 2011 | 22177937 |