Skip to main content
NCBI home page
Applied and Environmental Microbiology logoLink to Applied and Environmental Microbiology
. 1995 May;61(5):1917–1922. doi: 10.1128/aem.61.5.1917-1922.1995

Aromatic-degrading Sphingomonas isolates from the deep subsurface.

J K Fredrickson 1, D L Balkwill 1, G R Drake 1, M F Romine 1, D B Ringelberg 1, D C White 1
PMCID: PMC167454  PMID: 7544095

Abstract

An obligately aerobic chemoheterotrophic bacterium (strain F199) previously isolated from Southeast Coastal Plain subsurface sediments and shown to degrade toluene, naphthalene, and other aromatic compounds (J. K. Fredrickson, F. J. Brockman, D. J. Workman, S. W. Li, and T. O. Stevens, Appl. Environ. Microbiol. 57:796-803, 1991) was characterized by analysis of its 16S rRNA nucleotide base sequence and cellular lipid composition. Strain F199 contained 2-OH14:0 and 18:1 omega 7c as the predominant cellular fatty acids and sphingolipids that are characteristic of the genus Sphingomonas. Phylogenetic analysis of its 16S rRNA sequence indicated that F199 was most closely related to Sphingomonas capsulata among the bacteria currently in the Ribosomal Database. Five additional isolates from deep Southeast Coastal Plain sediments were determined by 16S rRNA sequence analysis to be closely related to F199. These strains also contained characteristic sphingolipids. Four of these five strains could also grow on a broad range of aromatic compounds and could mineralize [14C]toluene and [14C]naphthalene. S. capsulata (ATCC 14666), Sphingomonas paucimobilis (ATCC 29837), and one of the subsurface isolates were unable to grow on any of the aromatic compounds or mineralize toluene or naphthalene. These results indicate that bacteria within the genus Sphingomonas are present in Southeast Coastal Plain subsurface sediments and that the capacity for degrading a broad range of substituted aromatic compounds appears to be common among Sphingomonas species from this environment.

Full Text

The Full Text of this article is available as a PDF (206.1 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Amy P. S., Haldeman D. L., Ringelberg D., Hall D. H., Russell C. Comparison of Identification Systems for Classification of Bacteria Isolated from Water and Endolithic Habitats within the Deep Subsurface. Appl Environ Microbiol. 1992 Oct;58(10):3367–3373. doi: 10.1128/aem.58.10.3367-3373.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. doi: 10.1073/pnas.75.10.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Devereux R., He S. H., Doyle C. L., Orkland S., Stahl D. A., LeGall J., Whitman W. B. Diversity and origin of Desulfovibrio species: phylogenetic definition of a family. J Bacteriol. 1990 Jul;172(7):3609–3619. doi: 10.1128/jb.172.7.3609-3619.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science. 1967 Jan 20;155(3760):279–284. doi: 10.1126/science.155.3760.279. [DOI] [PubMed] [Google Scholar]
  5. Fredrickson J. K., Balkwill D. L., Zachara J. M., Li S. M., Brockman F. J., Simmons M. A. Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the atlantic coastal plain. Appl Environ Microbiol. 1991 Feb;57(2):402–411. doi: 10.1128/aem.57.2.402-411.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fredrickson J. K., Brockman F. J., Workman D. J., Li S. W., Stevens T. O. Isolation and characterization of a subsurface bacterium capable of growth on toluene, naphthalene, and other aromatic compounds. Appl Environ Microbiol. 1991 Mar;57(3):796–803. doi: 10.1128/aem.57.3.796-803.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Fredrickson J. K., Hicks R. J., Li S. W., Brockman F. J. Plasmid incidence in bacteria from deep subsurface sediments. Appl Environ Microbiol. 1988 Dec;54(12):2916–2923. doi: 10.1128/aem.54.12.2916-2923.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ghiorse W. C., Wilson J. T. Microbial ecology of the terrestrial subsurface. Adv Appl Microbiol. 1988;33:107–172. doi: 10.1016/s0065-2164(08)70206-5. [DOI] [PubMed] [Google Scholar]
  9. Guckert J. B., Ringelberg D. B., White D. C., Hanson R. S., Bratina B. J. Membrane fatty acids as phenotypic markers in the polyphasic taxonomy of methylotrophs within the Proteobacteria. J Gen Microbiol. 1991 Nov;137(11):2631–2641. doi: 10.1099/00221287-137-11-2631. [DOI] [PubMed] [Google Scholar]
  10. Haigler B. E., Pettigrew C. A., Spain J. C. Biodegradation of mixtures of substituted benzenes by Pseudomonas sp. strain JS150. Appl Environ Microbiol. 1992 Jul;58(7):2237–2244. doi: 10.1128/aem.58.7.2237-2244.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Imai R., Nagata Y., Fukuda M., Takagi M., Yano K. Molecular cloning of a Pseudomonas paucimobilis gene encoding a 17-kilodalton polypeptide that eliminates HCl molecules from gamma-hexachlorocyclohexane. J Bacteriol. 1991 Nov;173(21):6811–6819. doi: 10.1128/jb.173.21.6811-6819.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kawahara K., Seydel U., Matsuura M., Danbara H., Rietschel E. T., Zähringer U. Chemical structure of glycosphingolipids isolated from Sphingomonas paucimobilis. FEBS Lett. 1991 Nov 4;292(1-2):107–110. doi: 10.1016/0014-5793(91)80845-t. [DOI] [PubMed] [Google Scholar]
  13. Kuhm A. E., Stolz A., Ngai K. L., Knackmuss H. J. Purification and characterization of a 1,2-dihydroxynaphthalene dioxygenase from a bacterium that degrades naphthalenesulfonic acids. J Bacteriol. 1991 Jun;173(12):3795–3802. doi: 10.1128/jb.173.12.3795-3802.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955–6959. doi: 10.1073/pnas.82.20.6955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Larsen N., Olsen G. J., Maidak B. L., McCaughey M. J., Overbeek R., Macke T. J., Marsh T. L., Woese C. R. The ribosomal database project. Nucleic Acids Res. 1993 Jul 1;21(13):3021–3023. doi: 10.1093/nar/21.13.3021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. McBride L. J., Koepf S. M., Gibbs R. A., Salser W., Mayrand P. E., Hunkapiller M. W., Kronick M. N. Automated DNA sequencing methods involving polymerase chain reaction. Clin Chem. 1989 Nov;35(11):2196–2201. [PubMed] [Google Scholar]
  17. Mueller J. G., Chapman P. J., Blattmann B. O., Pritchard P. H. Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl Environ Microbiol. 1990 Apr;56(4):1079–1086. doi: 10.1128/aem.56.4.1079-1086.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Schmidt S., Wittich R. M., Erdmann D., Wilkes H., Francke W., Fortnagel P. Biodegradation of diphenyl ether and its monohalogenated derivatives by Sphingomonas sp. strain SS3. Appl Environ Microbiol. 1992 Sep;58(9):2744–2750. doi: 10.1128/aem.58.9.2744-2750.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stanier R. Y., Palleroni N. J., Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol. 1966 May;43(2):159–271. doi: 10.1099/00221287-43-2-159. [DOI] [PubMed] [Google Scholar]
  20. Steiert J. G., Crawford R. L. Catabolism of pentachlorophenol by a Flavobacterium sp. Biochem Biophys Res Commun. 1986 Dec 15;141(2):825–830. doi: 10.1016/s0006-291x(86)80247-9. [DOI] [PubMed] [Google Scholar]
  21. Taira K., Hayase N., Arimura N., Yamashita S., Miyazaki T., Furukawa K. Cloning and nucleotide sequence of the 2,3-dihydroxybiphenyl dioxygenase gene from the PCB-degrading strain of Pseudomonas paucimobilis Q1. Biochemistry. 1988 May 31;27(11):3990–3996. doi: 10.1021/bi00411a015. [DOI] [PubMed] [Google Scholar]
  22. Takeuchi M., Sawada H., Oyaizu H., Yokota A. Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria. Int J Syst Bacteriol. 1994 Apr;44(2):308–314. doi: 10.1099/00207713-44-2-308. [DOI] [PubMed] [Google Scholar]
  23. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991 Jan;173(2):697–703. doi: 10.1128/jb.173.2.697-703.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wittich R. M., Wilkes H., Sinnwell V., Francke W., Fortnagel P. Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl Environ Microbiol. 1992 Mar;58(3):1005–1010. doi: 10.1128/aem.58.3.1005-1010.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. 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. Microbiol Immunol. 1990;34(2):99–119. doi: 10.1111/j.1348-0421.1990.tb00996.x. [DOI] [PubMed] [Google Scholar]

Articles from Applied and Environmental Microbiology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES