title: 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.
abstract: 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).
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee 32306-3043, USA. balkwill@bio.fsu.edu
authors.forename: D L
authors.initials: DL
authors.lastname: Balkwill
authors.forename: G R
authors.initials: GR
authors.lastname: Drake
authors.forename: R H
authors.initials: RH
authors.lastname: Reeves
authors.forename: J K
authors.initials: JK
authors.lastname: Fredrickson
authors.forename: D C
authors.initials: DC
authors.lastname: White
authors.forename: D B
authors.initials: DB
authors.lastname: Ringelberg
authors.forename: D P
authors.initials: DP
authors.lastname: Chandler
authors.forename: M F
authors.initials: MF
authors.lastname: Romine
authors.forename: D W
authors.initials: DW
authors.lastname: Kennedy
authors.forename: C M
authors.initials: CM
authors.lastname: Spadoni
mesh_terms: D000438:Alcohols / Q000378:metabolism; D001431:Bacteriological Techniques; D001482:Base Composition; D002374:Catalase / Q000378:metabolism; D003470:Culture Media / Q000378:metabolism; D016172:DNA Fingerprinting; D004187:Disaccharides / Q000378:metabolism; D005227:Fatty Acids / Q000032:analysis; D005285:Fermentation; D005780:Gelatin / Q000378:metabolism; D005947:Glucose / Q000378:metabolism; D006088:Gram-Negative Aerobic Bacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D006601:Hexoses / Q000378:metabolism; D006867:Hydrolases / Q000378:metabolism; D007211:Indoles / Q000378:metabolism; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010429:Pentoses / Q000378:metabolism; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D014510:Urease / Q000378:metabolism; D014871:Water Microbiology
chemical_list: D000438:Alcohols; D003470:Culture Media; D004187:Disaccharides; D005227:Fatty Acids; D006601:Hexoses; D007211:Indoles; D010429:Pentoses; D012336:RNA, Ribosomal, 16S; C030374:indole; D005780:Gelatin; D002374:Catalase; D006867:Hydrolases; D014510:Urease; C019723:arginine deiminase; D005947:Glucose