Genus Sphingobium Research Articles

Sphingobium quisquiliarum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH-contaminated soil

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterial strain, P25(T), was isolated from an HCH dump site located in the northern part of India. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the strain belongs to the genus Sphingobium, as it showed highest sequence similarity to Sphingobium amiense IAM 15006(T) (97.7 %). The 16S rRNA gene sequence similarity between strain P25(T) and members of other species of the genus Sphingobium with validly published names ranged from 94.0 to 97.7 %. The DNA-DNA relatedness between strain P25(T) and Sphingobium amiense IAM 15006(T) and other related strains was found be less than 30 %, confirming it to represent a novel species. The DNA G+C content of strain P25(T) was 65 mol%. The polyamine profile showed the presence of spermidine. The predominant cellular fatty acids were summed feature 8 (18 : 1omega7c and/or 18 : 1omega6c; 48.3 %), 16 : 0 (13.7 %) and 14 : 0 2-OH (8.8 %). The polar lipid profile of strain P25(T) also corresponded to those reported for sphingomonads (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid), supporting its identification as a member of the family Sphingomonadaceae. The results obtained from DNA-DNA hybridization and biochemical and physiological tests clearly distinguished strain P25(T) from closely related members of the genus Sphingobium. Thus, a novel species of the genus Sphingobium is proposed, Sphingobium quisquiliarum sp. nov. The type strain is P25(T) (=MTCC 9472(T) =CCM 7543(T)).

Sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil

This study characterized strain WP01(T), a Gram-staining-negative, rod-shaped, aerobic bacterium isolated from a polycyclic aromatic hydrocarbon-contaminated soil in New Zealand. Strain WP01(T) shared many characteristics of the genus Sphingobium: the predominant respiratory quinone (89 %) was ubiquinone with ten isoprene units (Q-10); the major fatty acids were C(18 : 1)omega7c, C(16 : 1)omega7c, C(16 : 0) and C(14 : 0) 2-OH; spermidine was the major polyamine; the DNA G+C content was 63.8 mol%; and the Sphingobium-specific 16S rRNA signatures were conserved. A point of difference from other species of the genus Sphingobium was that strain WP01(T) reduced nitrate to nitrite. The polar lipid pattern consisted of the predominant compounds diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipids. 16S rRNA gene sequence analysis showed that, amongst the recognized species of the genus Sphingobium, strain WP01(T) was most similar to Sphingobium yanoikuyae GIFU 9882(T) and Sphingobium amiense YT(T) (>97 % 16S rRNA gene sequence similarities). The low DNA-DNA relatedness values between strain WP01(T) and S. yanoikuyae GIFU 9882(T) (46.6 %) and S. amiense DSM 16289(T) (25.6 %) indicated no relatedness at the species level. On the basis of these characteristics, it is concluded that strain WP01(T) should be considered as representing a novel species within the genus Sphingobium, for which the name Sphingobium scionense sp. nov. is proposed. The type strain is WP01(T) (=DSM 19371(T)=ICMP 13533(T)).

Sphingobium faniae sp. nov., a pyrethroid-degrading bacterium isolated from activated sludge treating wastewater from pyrethroid manufacture

A bacterial strain capable of degrading pyrethroid, designated JZ-2(T), was isolated from activated sludge treating pyrethroid-contaminated wastewater. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JZ-2(T) belongs to the genus Sphingobium. It showed the highest levels of 16S rRNA gene sequence similarity to Sphingobium cloacae JCM 10874(T) (98.3 %) and Sphingobium ummariense CCM 7431(T) (97.1 %), and 94.8-96.9 % similarity to the type strains of other members of the genus Sphingobium. Strain JZ-2(T) contained C(18 : 1)omega7c as the predominant fatty acid, C(14 : 0) 2-OH as the major 2-hydroxy fatty acid, ubiquinone Q-10 as the main respiratory quinone, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and two sphingoglycolipids as the predominant polar lipids and spermidine as the major polyamine. DNA-DNA hybridization results showed that strain JZ-2(T) had low genomic relatedness with S. cloacae JCM 10874(T) (34 %) and S. ummariense CCM 7431(T) (23 %). Based on the phenotypic, genotypic and phylogenetic data presented, strain JZ-2(T) is considered to represent a novel species of the genus Sphingobium, for which the name Sphingobium faniae sp. nov. is proposed. The type strain is JZ-2(T) (=CGMCC 1.7749(T) =DSM 21829(T)).

Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, strain IP26(T), was isolated from an HCH dumpsite and subjected to a polyphasic analysis in order to determine its taxonomic position. Strain IP26(T) showed maximum 16S rRNA gene sequence similarity with Sphingobium francense Sp+(T) (98.5 %), Sphingobium japonicum UT26(T) (98.4 %) and Sphingobium indicum B90A(T) (98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences also showed that strain IP26(T) formed a cluster with these three HCH-degrading strains. Chemotaxonomic data (major polyamine, spermidine; major quinone, ubiquinone with ten isoprene units; major polar lipids, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphotidylcholine; and presence of 2-hydroxy fatty acid) supported inclusion of strain IP26(T) in the genus Sphingobium. However, the results of DNA-DNA hybridization and morphological and biochemical tests clearly allowed phenotypic and genotypic differentiation of strain IP26(T) from recognized species of the genus Sphingobium. Strain IP26(T) thus represents a novel species of the genus Sphingobium for which the name Sphingobium chinhatense sp. nov. is proposed. The type strain is IP26(T) (=MTCC8598(T) =CCM 7432(T)).

Sphingobium vermicomposti sp. nov., isolated from vermicompost

Strain VC-230(T) was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15-37 degrees C and pH 6-8. On the basis of 16S rRNA gene sequence analysis, strain VC-230(T) was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790(T) (97.7 %) and Sphingobium herbicidovorans DSM 11019(T) (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C(18 : 1)omega7c/9t/12t, C(16 : 1)omega7c and C(16 : 0) and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA-DNA hybridization analyses verify that strain VC-230(T) represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230(T) (=CCUG 55809(T) =DSM 21299(T)).

Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil

The taxonomic position of a yellow-pigmented bacterial strain, designated DS20T, isolated from a hexachlorocyclohexane dump site at Lucknow, India was determined based on a polyphasic taxonomic characterization. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain DS20T occupied a distinct phylogenetic position in the Sphingobium cluster, showing highest similarity with 'Pseudomonas abikonensis' IAM 12404 (98.8%), followed by Sphingobium rhizovicinum CC-FH12-1T (97.4%) and Sphingobium olei IMMIB HF-1T (97.2%). Therefore, the taxonomic characterization of 'P. abikonensis' NBRC 16140 was also undertaken. Phylogenetic, chemotaxonomic and morphological analyses, based on signature sequences, DNA-DNA hybridizations, fatty acid profiles, physiological characterizations and polar lipid profiles confirmed that both strains DS20T and 'P. abikonensis' NBRC 16140 represent two distinct species of the genus Sphingobium. Therefore, two novel Sphingobium species are proposed, Sphingobium lactosutens sp. nov. (type strain, DS20T=CCM 7540T=MTCC 9471T) and Sphingobium abikonense sp. nov. (type strain, NBRC 16140T=IAM 12404T=KCTC 2864T).

Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil

A hexachlorocyclohexane (HCH)-degrading bacterial strain (RL-3T) was isolated from an HCH dump site located in the northern part of India. Resting cell assays and analytical GC studies confirmed the ability of strain RL-3T to degrade HCH isomers. Southern blot hybridization studies revealed the presence of lin genes, which are involved in the HCH degradation pathway, in this bacterium. The 16S rRNA gene sequence of strain RL-3T showed that it was most closely related to Sphingobium cloacae JCM 10874T (97.3 %) and Sphingobium fuliginis MTCC 7295T (96.4 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain RL-3T between S. cloacae JCM 10874T and S. fuliginis MTCC 7295T. The DNA G+C content of strain RL-3T was 62 mol%. The DNA-DNA relatedness values of strain RL-3T with S. cloacae JCM 10874T and S. fuliginis CCM 7327T were 8.65 and 7.47 %, respectively. SGL1 was the major sphingolipid and spermidine was the major polyamine in strain RL-3T. The major fatty acids in strain RL-3T were C(18 : 1)omega7c (56.6 %), C(16 : 0) (14 %) and C(14 : 0) 2-OH (7.4 %). Ubiquinone Q-10 was the major respiratory quinone. Phylogenetic distinctiveness, DNA-DNA relatedness values, biochemical and physiological characterization and unique phenotypic characteristics suggest that strain RL-3T represents a novel species of the genus Sphingobium, for which the name Sphingobium ummariense sp. nov. is proposed. The type strain is RL-3T (=MTCC 8599T=CCM 7431T).

Organization of three rRNA (rrn) operons from Sphingobium chungbukense DJ77

The nucleotide sequences of all three rRNA operons (rrnA, rrnB, and rrnC) of Sphingobium chungbukense DJ77 were determined. The three rrn operons have the same gene order (16S rRNA-tRNAIle-tRNAAla-23S rRNA-5S rRNA-tRNAfMet). The nucleotide sequences were identical over a 5,468 bp region spanning the 16S rRNA gene to the 5S rRNA gene. Variability was observed in the 5S rRNA-tRNAfMet spacer sequence of rrnB. The tRNAfMet gene sequences were identical except for two bases (T5794 and A5871 in rrnB, T5942 and A5956 in rrnA, but C5942 and G5956 in rrnC). Comparative sequence analyses of ribosomal RNA operons from DJ77 with those of the class Alphaproteobacteria, to which the genus Sphingobium belongs, reveal close evolutionary relationships with other members of the order Sphingomonadales.

Sphingobium rhizovicinum sp. nov., isolated from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle

The taxonomic status of a pale-yellow-coloured bacterial isolate from rhizosphere soil of Fortunella hindsii (Champ. ex Benth.) Swingle was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that the isolate constituted a distinct branch within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile that was characteristic for the genus Sphingobium, consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids and the lack of 3-OH fatty acids, ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone, and a polar lipid pattern that consisted of the predominant compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, diphosphatidylglycerol, sphingoglycolipid and an unknown glycolipid. Spermidine was the major polyamine component. The genotypic and phenotypic data (physiology and fatty acid and polar lipid profiles) showed that the isolate merits classification as representing a novel species of the genus Sphingobium, for which the name Sphingobium rhizovicinum sp. nov. is proposed. The type strain is CC-FH12-1T (=CCM 7491(T)=BCRC 17770T) [corrected]

Sphingobium olei sp. nov., isolated from oil-contaminated soil

The taxonomic status of a yellow-coloured bacterial isolate from an oil-contaminated soil sample was determined using a polyphasic taxonomic approach. Comparative analysis of 16S rRNA gene sequences showed that the novel isolate formed a distinct phyletic line within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed: a fatty acid profile that is characteristic of the genus Sphingobium consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids; a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone; a polar lipid pattern consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid, and spermidine as the major polyamine component. Genotypic and phenotypic data show that the new isolate merits classification as a representative of a novel species of the genus Sphingobium, for which the name Sphingobium olei sp. nov. is proposed. The type strain is IMMIB HF-1T (=DSM 18999T=CCUG 54329T).

Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment

A bacterial strain capable of degrading some monochlorinated dibenzofurans, designated RW16T, was isolated from aerobic River Elbe sediments. The strain was characterized based on 16S rRNA gene sequence analysis, DNA G+C content, physiological characteristics, polyamines, ubiquinone and polar lipid pattern and fatty acid composition. This analysis revealed that strain RW16T represents a novel species of the genus Sphingobium. The DNA G+C content of strain RW16T, 60.7 mol%, is the lowest yet reported for the genus. 16S rRNA gene sequence analysis placed strain RW16T as an outlier in the genus Sphingobium. The name Sphingobium aromaticiconvertens sp. nov. is proposed for this dibenzofuran-mineralizing organism, with type strain RW16T (=DSM 12677T=CIP 109198T).

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 %), compared with only 91-93 % similarity to members of other genera such as Sphingomonas sensu stricto, Novosphingobium, Sphingopyxis and Sphingosinicella. In DNA-DNA hybridization experiments with strains that were closely related phylogenetically and in terms of 16S rRNA gene sequences, i.e. Sphingobium herbicidovorans DSM 11019(T) and Sphingomonas cloacae JCM 10874(T), strain TKP(T) showed less than 70 % relatedness. Strain TKP(T) contained sphingoglycolipids SGL-1 and SGL-2 and 18 : 1omega7c as the predominant fatty acid, with 16 : 0 as a minor component and 14 : 0 2-OH as the major 2-hydroxy fatty acid. Thus, phylogenetic analysis, DNA-DNA hybridization, fatty acid and polar lipid profiles and differences in physiological and morphological features from the most closely related members of the Sphingobium group showed that strain TKP(T) represents a distinct species of Sphingobium. The name Sphingobium fuliginis sp. nov. is proposed, with the type strain TKP(T) (=MTCC 7295(T)=CCM 7327(T)). Sphingomonas cloacae JCM 10874(T) formed a coherent cluster with members of Sphingobium, did not reduce nitrate to nitrite and had a fatty acid profile similar to those of Sphingobium species; hence Sphingomonas cloacae should be transferred to the genus Sphingobium as Sphingobium cloacae comb. nov., with the type strain JCM 10874(T) (=DSM 14926(T)).

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 analysis of the 16S rRNA gene sequences of all the members of the group of sphingomonads encompassed in the genera Sphingomonas sensu stricto, Sphingobium, Novosphingobium and Sphingopyxis was inferred by using tree-making algorithms. [Sphingomonas] xenophaga DSM 6383T was found to form a distinct clade with the members of the genus Sphingobium, whereas [Sphingomonas] taejonensis DSM 15583T forms a clade with the members of the genus Sphingopyxis. The respective positions of these strains were also supported by the data for signature nucleotides, 2-hydroxy fatty acid profiles, polyamine patterns and the nitrate reduction properties of the strains. We therefore propose the reclassification of [Sphingomonas] xenophaga and [Sphingomonas] taejonensis as Sphingobium xenophagum comb. nov. (type strain DSM 6383T = CIP 107206T) and Sphingopyxis taejonensis comb. nov. (type strain DSM 15583T = KCTC 2884T = KCCM 41068T), respectively.

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 DNA-DNA relatedness values with Sphingomonas paucimobilis ATCC 29837(T) (8-25%), [Sphingomonas] chungbukensis IMSNU 11152(T) (10-17%), Sphingobium chlorophenolicum ATCC 33790(T) (23-54%) and Sphingomonas xenophaga DSM 6383(T) (10-28%), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99.1-99.4%), DNA-DNA relatedness (19-59%) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152(T) formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364(T)=CCM 7286(T)), Sphingobium japonicum sp. nov. (=MTCC 6362(T)=CCM 7287(T)) and Sphingobium francense sp. nov. (=MTCC 6363(T)=CCM 7288(T)), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.

Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment.

A nonylphenol-degrading bacterial strain (YT(T)) was isolated previously from a river sediment sample obtained in Ami-machi, Ibaraki, Japan, and identified as a Sphingomonas species. In this study, the taxonomic relationship between strain YT(T), a recently described nonylphenol-degrading strain, Sphingomonas cloacae, and Sphingobium yanoikuyae, which is phylogenetically related, was examined. Their phenotypic characteristics were compared and levels of DNA-DNA relatedness between these strains were determined. Based on the results of physiological and biochemical tests and DNA-DNA hybridization, it is proposed that strain YT(T) (=IAM 15006(T)=JCM 11777(T)=CIP 107839(T)) represents a novel species of the genus Sphingobium, Sphingobium amiense sp. nov.