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At least 19 recordsLinked to original sources

PubMed1990

Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas.

Based on the partial nucleotide sequence analysis of 16S ribosomal ribonucleic acid (rRNA), presence of unique sphingoglycolipids in cellular lipid, and the major type of ubiquinone (Q10), we propose Sphingomonas gen. nov. with the type species Sphingomonas paucimobilis (Holmes et al, 1977) comb. nov. From the homology values of deoxyribonucleic acid-deoxyribonucleic acid hybridization and the phenotypic characteristics, three new species, Sphingomonas parapaucimobilis, Sphingomonas yanoikuyae, Sphingomonas adhaesiva, and one new combination, Sphingomonas capsulata, are described. S. parapaucimobilis JCM 7510 (= GIFU 11387), S. yanoikuyae JCM 7371 (= GIFU 9882), and S. adhaesiva JCM 7370 (= GIFU 11458) are designated as the type strains of the three new species. Emended description of the type strain of S. capsulata is presented.

Base Composition↗

PubMed2003

Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas.

Seven psychrotolerant, Gram-negative bacterial strains, five dust- and airborne isolates (MA101b(T), MA306a, MA405/90, MA-olki(T) and NW12(T)) and two from the Antarctic (Ant 20 and M3C203B-B), were subjected to a polyphasic characterization to determine their taxonomic position. High 16S rDNA sequences similarities (99.3-100.0 %) demonstrated that they were closely related to each other. Phylogenetic evaluation of their 16S rDNA sequences revealed that they are members of the genus Sphingomonas sensu stricto, encompassing a separate branch within this genus. They shared 94.4-96.6 % 16S rDNA sequence similarity with species of this genus. All Sphingomonas-specific signature nucleotides were also detected. The presence of the major ubiquinone Q-10, sym-homospermidine as the predominant polyamine, Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns and a fatty acid profile containing C(14 : 0) 2-OH and lacking 3-OH fatty acids were in agreement with identification of these strains as members of the genus Sphingomonas sensu stricto. Results from DNA-DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species. One species is represented by strains MA101b(T), MA306a and MA405/90, the second by strains NW12(T), Ant 20 and M3C203B-B and the third by one strain, MA-olki(T). Their distinction at the species level was also supported by results of biochemical characterization and partly supported by riboprints and genomic fingerprints. On the basis of these results, three novel species of the genus Sphingomonas are proposed: Sphingomonas aurantiaca sp. nov., consisting of strains MA101b(T) (=DSM 14748(T)=LMG 21377(T)), MA306a and MA405/90 (=DSM 14749=LMG 21378), Sphingomonas faeni sp. nov. MA-olki(T) (=DSM 14747(T)=LMG 21379(T)) and Sphingomonas aerolata sp. nov., represented by strains NW12(T) (=DSM 14746(T)=LMG 21376(T)), Ant 20 (=ICMP 13599) and M3C203B-B (=SMCC M3C203B-B).

Air Microbiology↗

PubMed1995

Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.

The taxonomic positions of 10 strains of 3-ketolactose-forming bacteria which were isolated from the roots of plants (Rosa sp., Psychotria nairobiensis, Ardisia crispa, Prunus persica, and apple trees) were investigated. The DNA base compositions of these strains ranged from 64.0 to 65.7 mol%, the isoprenoid quinone of each strain was ubiquinone 10, 3-hydroxy fatty acids were lacking in the cellular fatty acids of these organisms, and all of the strains contained a sphingolipid with the long-chain base dihydrosphingosin. These are characteristics of the genus Sphingomonas. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S ribosomal DNA sequence comparison data, we propose the following four new species of the genus Sphingomonas: Sphingomonas rosa (type strain, IFO 15208) for the strains isolated from rose plants and formerly named [Agrobacterium rhizogenes]; Sphingomonas pruni (type strain, IFO 15498) for the strains isolated from Prunus persica; and Sphingomonas asaccharolytica (type strain, IFO 15499) and Sphingomonas mali (type strain, IFO 15500) for the strains isolated from apple trees. Two strains which were isolated from Psychotria nairobiensis and formerly named [Chromobacterium lividum] were identified as Sphingomonas yanoikuyae strains.

DNA, Bacterial↗

PubMed1999

Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas.

Based on the results of a phylogenetic analysis of 16S rRNA and the presence of sphingoglycolipid in cellular lipids of the type strains, transfer of "Rhizomonas" suberifaciens, Blastomonas natatoria and Erythromonas ursincola to the genus Sphingomonas as Sphingomonas suberifaciens (van Bruggen et al 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., and Sphingomonas ursincola (Yurkov et al 1997) comb. nov. are herein proposed together with the emendation of genus Sphingomonas. The type strain of S. suberifaciens is van Bruggen Cal=ATCC 49382=NCPPB 3629=IFO 15211=JCM 8521, that of S. natatoria is ATCC 35951 =DSM 3183=NCIMB 12085=JCM10396, and that of S. ursincola is DSM 9006= KR-99.

Base Composition↗

PubMed1997

Taxonomic study of aromatic-degrading bacteria from deep-terrestrial-subsurface sediments and description of Sphingomonas aromaticivorans sp. nov., Sphingomonas subterranea sp. nov., and Sphingomonas stygia sp. nov.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that six strains of bacteria isolated from deep saturated Atlantic coastal plain sediments were closely related to the genus Sphingomonas. Five of the strains clustered with, but were distinct from, Sphingomonas capsulata, whereas the sixth strain was most closely related to Blastobacter natatorius. The five strains that clustered with S. capsulata, all of which could degrade aromatic compounds, were gram-negative, non-spore-forming, non-motile, rod-shaped organisms that produced small, yellow colonies on complex media. Their G + C contents ranged from 60.0 to 65.4 mol%, and the predominant isoprenoid quinone was ubiquinone Q-10. All of the strains were aerobic and catalase positive. Indole, urease, and arginine dihydrolase were not produced. Gelatin was not liquified, and glucose was not fermented. Sphingolipids were present in all strains; 2OH14:0 was the major hydroxy fatty acid, and 18:1 was a major constituent of cellular lipids. Acid was produced oxidatively from pentoses, hexoses, and disaccharides, but not from polyalcohols and indole. All of these characteristics indicate that the five aromatic-degrading strains should be placed in the genus Sphingomonas as currently defined. Phylogenetic analysis of 16S rRNA gene sequences, DNA-DNA reassociation values, BOX-PCR genomic fingerprinting, differences in cellular lipid composition, and differences in physiological traits all indicated that the five strains represent three previously undescribed Sphingomonas species. Therefore, we propose the following new species: Sphingomonas aromaticivorans (type strain, SMCC F199), Sphingomonas subterranea (type strain, SMCC B0478), and Sphingomonas stygia (type strain, SMCC B0712).

Alcohols↗

PubMed2001

Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water.

The taxonomic status of four strains from several mineral water sources in Taejon, Korea, was examined. The DNA base compositions of these strains ranged from 62 to 66 mol %. All of the strains contained sphingolipids and ubiquinone 10 as the main respiratory quinone. The cellular fatty acids of these strains included octadecenoic acid, hexadecanoic acid and 2-hydroxymyristic acid, without 3-hydroxy fatty acids. On the basis of morphological, physiological and chemotaxonomic characteristics, together with 16S rDNA sequence comparison and DNA-DNA reassociation data, three new species of the genus Sphingomonas are proposed for the strains isolated from natural mineral water: Sphingomonas aquatilis sp. nov. for strain JSS7T (= KCTC 2881T = KCCM 41067T), Sphingomonas koreensis sp. nov. for strains JSS26T (= KCTC 2882T = KCCM 41069T) and JSS28 (= KCTC 2883 = KCCM 41066) and Sphingomonas taejonensis sp. nov. for strain JSS54T (= KCTC 2884T = KCCM 41068T).

Base Composition↗

PubMed2000

Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.

Pseudomonas sp. strain DJ77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. Phylogenetic analysis based on 16S rDNA sequences indicated that the strain belonged to the genus Sphingomonas and formed a monophyletic clade with the type strains of Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae with sequence similarity values of 98.1, 96.1 and 95.6%, respectively. Genomic relatedness based on DNA-DNA hybridization of strain DJ77 to these strains is 7-14%. Strain DJ77 contained ubiquinone 10 as the main respiratory quinone, and the G+C content of DNA was 63 mol%. The organism contained octadecenoic acid (67%) as major cellular fatty acid. Strain DJ77 can be readily differentiated from representative members of the genus Sphingomonas using a battery of biochemical tests. On the basis of polyphasic evidence, it is proposed that strain DJ77, previously known as Pseudomonas sp., be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. The type strain is strain DJ77T (= KCTC 2955T = IMSNU 11152T).

Base Composition↗

PubMed1996

Description of chlorophenol-degrading Pseudomonas sp. strains KF1T, KF3, and NKF1 as a new species of the genus Sphingomonas, Sphingomonas subarctica sp. nov.

Gram-negative polychlorophenol-degrading bacterial strains KF1T (T = type strain), KF3, and NKF1, which were described previously as Pseudomonas saccharophila strains, were studied by chemotaxonomic, genetic, and physiological methods and by electron microscopy and compared with selected xenobiotic compound-degrading bacteria. These strains contained sphingolipids with d-18:0, d-20:1, and d-21:1 as the main dihydrosphingosines, ubiquinone 10 as the main respiratory quinone, and spermidine as the major polyamine, and the DNA G + C content was 66 mol%. The cellular fatty acids included about 60% octadecenoic acid, 9% 2-hydroxymyristic acid, 14% cis-9-hexadecenoic acid, and 10% hexadecanoic acid. These strains exhibited less than 97% 16S ribosomal DNA sequence similarity to all of the other taxa studied. In the DNA-DNA reassociation studies the highest levels of reassociation between these strains and previously described species were less than 40%. Thin sections of cells of strains KF1T, KF3, and NKF1 were examined by electron microscopy, and the results showed that the cells had peculiar concentrically arranged layered membranous blebs that extruded from the outer membrane, especially at the cell division points. On the basis of the results of this study, polychlorophenol-degrading strains KF1T, KF3, and NKF1 are considered members of a new species of the genus Sphingomonas, Sphingomonas subarctica. The polycyclic aromatic hydrocarbon-degrading organism Sphingomonas paucimobilis EPA 505 was closely related to Sphingomonas chlorophenolica as determined by chemotaxonomic, phylogenetic, and physiological criteria. The xenobiotic compound degraders Alcaligenes sp. strain A175 and Pseudomonas sp. strain BN6 were identified as members of species of the genus Sphingomonas.

Base Sequence↗

PubMed2002

Correction of the connecting vowel and gender of the specific epithet in the name Sphingomonas macrogoltabidus Takeuchi et al. 1993 to Sphingomonas macrogolitabida.

In accordance with the Bacteriological Code (1990 Revision), the connecting vowel and gender of the specific epithet macrogoltabidus in combination with the generic name Sphingomonas must be -i- and the ending must be changed to -a to agree with the gender of the generic name, respectively. Thus Sphingomonas macroboltabidus Takeuchi et al. 1993 should be Sphingomonas macrogolitabida corrig. Takeuchi et al. 1993.

Species Specificity↗

PubMed1997

Classification of "Pseudomonas azotocolligans" Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov.

"Pseudomonas azotocolligans" ATCC 12417T (T = type strain), which was described as a diazotrophic bacterium, was reinvestigated to clarify its taxonomic position. 16S ribosomal DNA sequence comparisons demonstrated that this strain clusters phylogenetically with species of the genus Sphingomonas and represents a new species. The results of investigations of the fatty acid patterns, polar lipid profiles, and quinone system supported this placement. The substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of any previously described species of the genus Sphingomonas. The new name Sphingomonas trueperi is proposed on the basis of these results and previously published data for the G + C content of the genomic DNA and the polyamine pattern.

Base Composition↗

PubMed1999

Reclassification of Pseudomonas echinoides Heumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov.

[Pseudomonas] echinoides DSM 1805T (= ATTC 14820T, DSM 50409T, ICBP 2835T, NCIB 9420T) has been reinvestigated to clarify its taxonomic position. 16S rDNA sequence comparisons demonstrated that this species clusters phylogenetically with species of the genus Sphingomonas. Investigation of fatty acid patterns, polar lipid profiles, polyamine patterns and quinone systems supported this delineation. Substrate utilization profiles and biochemical characteristics displayed no distinct overall similarity to any validly described species of the genus Sphingomonas. Therefore, the reclassification of [Pseudomonas] echinoides as Sphingomonas echinoides comb. nov. is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data, chemotaxonomic data and previously published genomic DNA G+C content data.

Bacterial Typing Techniques↗

PubMed2000

Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990.

Based on the results of phylogenetic analysis of the 16S rDNA sequences and the presence of N-2'-hydroxymyristoyl dihydrosphingosine 1-glucuronic acid (SGL-1) and 2-hydroxymyristic acid (non-hydroxymyristic acid in Zymomonas) in cellular lipids, a new family, Sphingomonadaceae, for Group 4 of the alpha-subclass of the class Proteobacteria is herein proposed and a description of the family is given. The family consists of six genera, Sphingomonas, Erythrobacter, Erythromicrobium, Porphyrobacter, Sandaracinobacter and Zymomonas. Thus, all the validly published and currently known genera in Group 4 of the alpha-subclass of Proteobacteria belong to Sphingomonadaceae fam. nov. Among them, type strains of two species, Porphyrobacter and Erythrobacter, Sandaracinobacter sibiricus and Sphingomonas ursincola, respectively, are facultatively photosynthetic due to bacteriochlorophyll (Bchl)-a. The type strains of two subspecies of Zymomonas mobilis are facultative anaerobes. The presence of SGL-1 together with the results of a phylogenetic analysis of the 16S rDNA sequences recommends a new criteria by which to define the new family Sphingomonadaceae. The type genus is Sphingomonas Yabuuchi et al. 1990.

DNA, Ribosomal↗

PubMed2000

Chemotaxonomic and phylogenetic analyses of Sphingomonas strains isolated from ears of plants in the family Gramineae and a proposal of Sphingomonas roseoflava sp. nov.

Chemotaxonomic and phylogenetic characteristics of Sphingomonas strains isolated from plants of the family Gramineae were investigated. All strains contained the monosaccharide (glucuronic acid) type of glycosphingolipid (GSL-1). Most were found also to contain the oligosaccharide-type glycosphingolipids. Fatty acid and sphingosine profiles of the isolates were identical, although the ratio of the contents varies among the isolates. They all contained ubiquinone Q-10, and the G1C contents were from 66 to 68%. Phylogenetic analysis using 16S rRNA gene base sequences revealed that all the isolates were placed in the phylogenetic group of Sphingomonas paucimobilis in the alpha-4 subclass of Proteobacteria. By DNA-DNA hybridization experiments, the plant isolates were divided into five genotypic groups (groups 1 to 5). The strains of group 5 showed common physiological characteristics and formed pink-yellow colored colonies. Based on these results, Sphingomonas roseoflava sp. nov. was proposed for that homology group.

Journal Article↗

PubMed2001

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 herbicidovorans and Sphingomonas yanoikuyae. The genus Novosphingobium is proposed for Sphingomonas aromaticivorans, Sphingomonas capsulata, Sphingomonas rosa, Sphingomonas stygia, Sphingomonas subarctica and Sphingomonas subterranea. Sphingomonas macrogoltabidus and Sphingomonas terrae are reclassified in the genus Sphingopyxis. The type species of Sphingobium, Novosphingobium and Sphingopyxis are Sphingobium yanoikuyae, Novosphingobium capsulatum and Sphingopyxis macrogoltabida, respectively.

Alphaproteobacteria↗

PubMed2001

Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer.

A polyphasic taxonomic study was performed on Sphingomonas sp. strain RW1T. The organism was isolated from water of the River Elbe and has been known as a potent metabolizer of dibenzo-p-dioxin and its relatives. TLC of a mild alkaline hydrolysate of extractable cellular lipids of strain RW1T and type strains of 21 Sphingomonas species gave a spot of sphingoglycolipid (SGL)-1 (glucuronosyl ceramide), which is characteristic of sphingomonads. In addition, strain RW1T and type strains of three Sphingomonas species (Sphingomonas yanoikuyae, Sphingomonas terrae and Sphingomonas macrogoltabidus) showed a second spot of SGL (SGL-1') identified as galacturonosyl ceramide. The presence of SGL-1 in cellular lipids suggested that strain RW1T is a member of the genus Sphingomonas. DNA-DNA reassociation rates between strain RW1T and each type strain of 14 Sphingomonas species including Sphingomonas paucimobilis, type species for the genus, revealed that strain RW1T is independent from these species. Results of phylogenetic analysis of 16S rDNA sequences of strain RW1T and type strains of 21 named Sphingomonas species verified that strain RW1T belongs to the genus Sphingomonas. Strain RW1T could be differentiated from named species of the genus by phenotypic characteristics and has been assigned to a new species, Sphingomonas wittichii sp. nov. The type strain is DSM 6014T (= JCM 10273T = EY 4224T). DNA G+C content is 67 mol %.

Bacterial Typing Techniques↗

PubMed2002

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 strains of all 28 Sphingomonas species tested contained glucuronosyl-(1 --> 1)-ceramide together with 2-hydroxymyristic acid, other molecular species of sphingoglycolipids were distributed randomly. Sphingomonas natatoria and Sphingomonas ursincola, bacteriochlorophyll a-containing, gram-negative facultative phototrophs, belong to the cluster of the genus Sphingomonas. Other phototrophic Porphyrobacter and Erythrobacter species in the Sphingomonadaceae were classified into a cluster different from the genus Sphingomonas, as reported previously. None of the physiological and biochemical characteristics considered, including cellular lipids and fatty acid composition, provided evidence for the division of the current genus Sphingomonas. It is therefore concluded that the genus Sphingomonas should remain undivided at this time. The species of three recently proposed genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastobacter ursincola, are junior objective synonyms of species of the genus Sphingomonas.

Alphaproteobacteria↗

PubMed2000

A novel sphingoglycolipid containing galacturonic acid and 2-hydroxy fatty acid in cellular lipids of Sphingomonas yanoikuyae.

A novel sphingoglycolipid was isolated from Sphingomonas yanoikuyae, and its structure was identified as a galacturonosyl-beta (1-->1)-ceramide. This was a characteristic sphingoglycolipid present in S. yanoikuyae and certain other species of Sphingomonas, such as Sphingomonas mali, Sphingomonas terrae, and Sphingomonas macrogoltabidus, but not in the type species of Sphingomonas, Sphingomonas paucimobilis.

Carbohydrates↗

PubMed1999

Detection of Sphingomonas spp in soil by PCR and sphingolipid biomarker analysis.

Sphingomonas spp possess unique abilities to degrade refractory contaminants and are found ubiquitously in the environment. We developed Sphingomonas genus-specific PCR primers (SPf-190 and SPr1-852) which showed specific amplification of a 627-bp 16S rDNA fragment from Sphingomonas spp. A PCR assay using these Sphingomonas specific primers was developed to detect Sphingomonas aromaticivorans B0695R in three texturally distinct soil types, showing detection limits between 1.3-2.2 x 10(3) CFU g(-1) dry soil. A sphingolipid extraction protocol was also developed to monitor Sphingomonas populations in soil quantitatively. The detection limit of the assay was 20 pmol g(-1) dry soil, equivalent to about 3 x 10(5) cells g(-1) dry soil. Survival of S. aromaticivorans B0695R was monitored in the three different soils by antibiotic selective plate counting, PCR and sphingolipid analysis. All three approaches showed that the B0695R cells persisted in the low biomass Sequatchie sub-soil at about 3-5 x 10(7)cells g(-1) dry soil. In comparison to the plate counting assay, both the PCR and sphingolipid analysis detected a significantly higher level of B0695R cells in the clay soil and Sequatchie top-soil, indicating the possibility of the presence of viable but non-culturable B0695R cells in the soils. The combination of PCR and sphingolipid analysis may provide a more realistic estimation of Sphingomonas population in the environment.

Journal Article↗