Reclassification of a Polycyclic Aromatic Hydrocarbon-Metabolizing Bacterium, Beijerinckia sp. Strain B1, as Sphingomonas yanoikuyae by Fatty Acid Analysis, Protein Pattern Analysis, DNA-DNA Hybridization, and 16S Ribosomal DNA Sequencing

Abstract

A bacterium isolated from a polluted stream, capable of metabolizing biphenyl, naphthalene, phenanthrene, and higher-molecular-weight polycyclic aromatic hydrocarbons (D. Gibson, V. Mahadevan, D. Jerina, H. Yagi, and H. Yeh, Science 189:295-297, 1975), was previously identified as Beijerinckiu sp. strain B1. In this investigation, 16s rRNA gene sequencing, biochemical tests, fatty acid methyl ester analysis, polyacrylamide gel electrophoresis of protein, and DNA-DNA hybridization were used to determine the taxonomic relationship of Beijerinckiu sp. strain Bl. The sequence of the 16s rRNA gene of B1 was identical to that of Sphingomonas yanoikuyae ATCC 51230T. The biochemical tests, fatty acid analysis, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis profile of soluble proteins of strain B1 showed results similar to those of S. yanoikuyae. DNA-DNA hybridization indicated that B1 and S. yanoikuyae ATCC 51230T are 75% homologous at the DNA level. We propose that Beijerinckia sp. strain B1 be reclassified as S. yanoikuyae.A strain designated Beijerinckia sp. strain B1 was originally isolated for its ability to grow with biphenyl as a carbon and energy source (6). This organism can utilize biphenyl, naphthalene, and phenanthrene as sole sources of carbon and energy and co-oxidize a wide variety of polycyclic aromatic hydrocarbons to carbon dioxide and mixtures of ring fission products (1, 6, 8, 9, 12). Biphenyl-induced cells of a mutant of this strain, B8/36, oxidize biphenyl, anthracene, phenanthrene, benzo[a]pyrene, and benz [a]anthracene to cis-dihydrodiols (1, 6, 8, 9, 12, 17). The metabolic pathway for the degradation of benz [a]anthracene is inducible by biphenyl, salicylate, and mxylene (12). Because of the wide range of polycyclic aromatic hydrocarbons degraded by this organism, extensive genetic and metabolic pathway studies have been done (1, 3, 6, 8, 9). Molecular analysis of the enzymes involved in aromatic degradation has been reported by Kim and Zylstra (10).Since strain B1 has potential use in the bioremediation of polycyclic aromatic hydrocarbon-contaminated environmental sites, we reevaluated the identification of Beijerinckia sp. strain B1 by using biochemical tests, DNA-DNA hybridization, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) soluble protein analysis, fatty acid methyl ester (FAME) analysis, and 16s rRNA gene sequence analysis. FAME analysis. Bacterial cultures were harvested from Trypticase soy broth-5% sheep blood agar for total cellular fatty acid analysis. Fatty acids were extracted by following the Microbial Identification System (MIDI; Microbial ID, Inc., Newark, Del.) instructions. MATERIALS AND METHODSPreparation of soluble protein fractions. The bacterial strains listed above were grown on Trypticase soy broth-5% sheep blood agar plates for 16 h at 30°C. Several colonies were combined in 300 p1 of Tris-HC1 (20 mM, pH 6.8) and sonicated for 4 30-s pulses at maximum power with 30-s cooling intervals in an ice bath. Unbroken cells and large fragm...

Biodiversity of Dioxin-Degrading Microorganisms and Potential Utilization in Bioremediation.

“…32,50,52) . This strain was later reclassified as Sphingomonas yanoikuyae on the basis of phylogenetic and chemotaxonomic data 104) . The genus Sphingomonas has recently been split into four genera with three new generic names, Novosphingobium, Sphingobium and Sphingopyxis 180) .…”

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

“…It was later found that this group of bacteria could also be isolated from natural sources, such as soil, rhizosphere, sediment, freshwater and marine environments [26]. Many Sphingomonas strains isolated from the environment possess broad catabolic capabilities towards recalcitrant organic pollutants, which include dibenzo-p-dioxin and dibenzofuran [27], carbofuran [6], hexachlorocyclohexane [9], chlorinated biphenyls [24], polychlorophenols [11,16], 2,4-dichlorophenoxyacetic acid [10], halogenated diphenyl ethers [21], and single-ring aromatic and polyaromatic hydrocarbons [7,13]. Despite the catabolic diversity of the genus Sphingomonas, its members are related phylogenetically.…”

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

“…A comparative study showed that the genes and gene orders for aromatic hydrocarbon degradation of strain DJ77 T were strikingly similar to the corresponding genes of Sphingomonas species, such as Sphingomonas paucimobilis EPA505, Sphingomonas yanoikuyae B1, ' Sphingomonas agrestis ' HV3 and Sphingomonas aromaticivorans F199 (Mueller et al, 1990 ;Kim, 1996 ;Yrja$ la$ et al, 1997 ;Romine et al, 1999). The members of the genus Sphingomonas have been reported to degrade various aromatic hydrocarbons (Wittich et al, 1992 ;Ka et al, 1994 ; Fredrickson et al, 1995 ;Khan et al, 1996). In this study, we applied a polyphasic approach to identify strain DJ77 T .…”