1887

Abstract

In the present study, a yellow-pigmented, Gram-negative, short rod-shaped novel bacterium that was capable of degrading a wide range of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) was isolated from agricultural soil located in Yunlin County, Taiwan. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus as an independent lineage adjacent to a subclade containing K101, UM2, RW1 and A175. 16S rRNA gene sequence analysis of strain CC-Nfb-2 showed highest sequence similarity to K101 (96.2 %), UM2 (96.1 %), RW1 (95.9 %), A175 (95.7 %), and RL-3 (94.7 %); lower sequence similarities were observed with strains of all other species. The strain contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and diphosphatidylglycerol. The predominant fatty acids were summed feature 8 (Cω7 and/or Cω6) C and 11-methyl Cω7; C 2-OH was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus . The serine palmitoyl transferase gene () was also detected and sphingolipid synthesis was confirmed. The predominant isoprenoid quinone system was ubiquinone (Q-10) and the isolate contained -homospermidine as the major polyamine. The DNA G+C content of the isolate was 62.8±0.8 mol%. On the basis of chemotaxonomic, phenotypic and phylogenetic data, strain CC-Nfb-2 represents a novel species within the genus , for which the name sp. nov. is proposed; the type strain is CC-Nfb-2 ( = BCRC 80272 = DSM 24164).

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2012-07-01
2020-01-25
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References

  1. Anzai Y. , Kim H. , Park J.-Y. , Wakabayashi H. , Oyaizu H. . ( 2000; ). Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. . Int J Syst Evol Microbiol 50:, 1563–1589. [CrossRef] [PubMed]
    [Google Scholar]
  2. Busse H.-J. , Kämpfer P. , Denner E. B. M. . ( 1999; ). Chemotaxonomic characterisation of Sphingomonas . . J Ind Microbiol Biotechnol 23:, 242–251. [CrossRef] [PubMed]
    [Google Scholar]
  3. Collins M. D. . ( 1985; ). Isoprenoid quinone analysis in classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by Goodfellow M. , Minnikin D. E. . . London:: Academic Press;.
    [Google Scholar]
  4. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  5. Heiner C. R. , Hunkapiller K. L. , Chen S. M. , Glass J. I. , Chen E. Y. . ( 1998; ). Sequencing multimegabase-template DNA with BigDye terminator chemistry. . Genome Res 8:, 557–561.[PubMed]
    [Google Scholar]
  6. Hung M.-H. , Bhagwath A. A. , Shen F.-T. , Devasya R. P. , Young C.-C. . ( 2005; ). Indigenous rhizobia associated with native shrubby legumes in Taiwan. . Pedobiologia (Jena) 49:, 577–584. [CrossRef]
    [Google Scholar]
  7. Lee K.-B. , Liu C.-T. , Anzai Y. , Kim H. , Aono T. , Oyaizu H. . ( 2005; ). The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov.. Int J Syst Evol Microbiol 55:, 1907–1919. [CrossRef] [PubMed]
    [Google Scholar]
  8. Lin S.-Y. , Young C.-C. , Hupfer H. , Siering C. , Arun A. B. , Chen W.-M. , Lai W.-A. , Shen F.-T. , Rekha P. D. , Yassin A. F. . ( 2009; ). Azospirillum picis sp. nov., isolated from discarded tar. . Int J Syst Evol Microbiol 59:, 761–765. [CrossRef] [PubMed]
    [Google Scholar]
  9. Maruyama T. , Park H.-D. , Ozawa K. , Tanaka Y. , Sumino T. , Hamana K. , Hiraishi A. , Kato K. . ( 2006; ). Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. . Int J Syst Evol Microbiol 56:, 85–89. [CrossRef] [PubMed]
    [Google Scholar]
  10. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  11. Miller L. T. . ( 1982; ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16:, 584–586.[PubMed]
    [Google Scholar]
  12. Minnikin D. E. , O’Donnell A. G. , Goodfellow M. , Alderson G. , Athalye M. , Schaal A. , Parlett J. H. . ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  13. Murray R. G. E. , Doetsch R. N. , Robinow F. . ( 1994; ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 21–41. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  14. Nigam A. , Jit S. , Lal R. . ( 2010; ). Sphingomonas histidinilytica sp. nov., isolated from a hexachlorocyclohexane dump site. . Int J Syst Evol Microbiol 60:, 1038–1043. [CrossRef] [PubMed]
    [Google Scholar]
  15. Paisley R. . ( 1996; ). MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual. Newark, DE:: MIDI;.
    [Google Scholar]
  16. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  17. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  18. Scherer P. , Kneifel H. . ( 1983; ). Distribution of polyamines in methanogenic bacteria. . J Bacteriol 154:, 1315–1322.[PubMed]
    [Google Scholar]
  19. Singh A. , Lal R. . ( 2009; ). Sphingobium ummariense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium, isolated from HCH-contaminated soil. . Int J Syst Evol Microbiol 59:, 162–166. [CrossRef] [PubMed]
    [Google Scholar]
  20. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  21. Takeuchi M. , Hamana K. , Hiraishi A. . ( 2001; ). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. . Int J Syst Evol Microbiol 51:, 1405–1417.[PubMed]
    [Google Scholar]
  22. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24:, 1596–1599. [CrossRef] [PubMed]
    [Google Scholar]
  23. Thompson J. D. , Gibson T. J. , Plewniak F. , Jeanmougin F. , Higgins D. G. . ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25:, 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  24. Watts D. , MacBeath J. R. . ( 2001; ). Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. . Methods Mol Biol 167:, 153–170.[PubMed]
    [Google Scholar]
  25. White D. C. , Sutton S. D. , Ringelberg D. B. . ( 1996; ). The genus Sphingomonas: physiology and ecology. . Curr Opin Biotechnol 7:, 301–306. [CrossRef] [PubMed]
    [Google Scholar]
  26. Wittich R.-M. , Busse H.-J. , Kämpfer P. , Macedo A. J. , Tiirola M. , Wieser M. , Abraham W.-R. . ( 2007; ). Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas . . Int J Syst Evol Microbiol 57:, 1740–1746. [CrossRef] [PubMed]
    [Google Scholar]
  27. Yabuuchi E. , Yano I. , Oyaizu H. , Hashimoto Y. , Ezaki T. , Yamamoto H. . ( 1990; ). 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 34:, 99–119.[PubMed] [CrossRef]
    [Google Scholar]
  28. Yabuuchi E. , Yamamoto H. , Terakubo S. , Okamura N. , Naka T. , Fujiwara N. , Kobayashi K. , Kosako Y. , Hiraishi A. . ( 2001; ). Proposal of Sphingomonas wittichii sp. nov. for strain RW1T, known as a dibenzo-p-dioxin metabolizer. . Int J Syst Evol Microbiol 51:, 281–292.[PubMed]
    [Google Scholar]
  29. Yim M.-S. , Yau Y. C. W. , Matlow A. , So J.-S. , Zou J. , Flemming C. A. , Schraft H. , Leung K. T. . ( 2010; ). A novel selective growth medium-PCR assay to isolate and detect Sphingomonas in environmental samples. . J Microbiol Methods 82:, 19–27. [CrossRef] [PubMed]
    [Google Scholar]
  30. Young C.-C. , Ho M.-J. , Arun A. B. , Chen W.-M. , Lai W.-A. , Shen F.-T. , Rekha P. D. , Yassin A. F. . ( 2007; ). Sphingobium olei sp. nov., isolated from oil-contaminated soil. . Int J Syst Evol Microbiol 57:, 2613–2617. [CrossRef] [PubMed]
    [Google Scholar]
  31. Zhang D.-C. , Busse H.-J. , Liu H.-C. , Zhou Y.-G. , Schinner F. , Margesin R. . ( 2011; ). Sphingomonas glacialis sp. nov., a psychrophilic bacterium isolated from alpine glacier cryoconite. . Int J Syst Evol Microbiol 61:, 587–591. [CrossRef] [PubMed]
    [Google Scholar]
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