1887

Abstract

During the study of hydrocarbon-degrading bacteria in the oil-contaminated soil of Gunsan, North Jeolla Province, South Korea, a light-grey-pigmented, Gram-staining-negative, aerobic, non-motile and rod-shaped bacterium, designated strain D39, was isolated. This strain was non-sporulating, catalase-negative and oxidase-positive. It was able to grow at 12–42 °C, pH 5.5–8.5 and with 0–1 % (w/v) NaCl. This strain was characterized taxonomically by a polyphasic approach. Based on the results of 16S rRNA gene sequence analysis, strain D39 belongs to the genus Novosphingobium and is closely related to ‘ Novosphingobium ginsenosidimutans' FW-6 (97.30 % sequence similarity), Novosphingobium mathurense SM117 (97.17 % sequence similarity) and Novosphingobium aquiterrae E-II-3 (97.01 % sequence similarity). The only respiratory quinone was ubiquinone-10 and the major polyamine was spermidine. The polar lipid profile revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phosphatidyl-N-methylethanolamine. The predominant fatty acids of strain D39 were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and C14 : 0 2-OH. The genomic DNA G+C content of this novel strain was 66.7 mol%. The DNA–DNA relatedness between strain D39 and ‘N. ginsenosidimutans' KACC 16615, N. mathurense KACC 14598, N. aquiterrae KACC 17599 and Novosphingobium kunmingense DSM 25975 were 33.7 %, 29.0 %, 22.3 % and 18.3 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain D39 represents a novel species of the genus Novosphingobium , for which the name Novosphingobium naphthae sp. nov. is proposed. The type strain is D39 (=KEMB 9005-346=KACC 18593=JCM 31158).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001164
2016-08-01
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/8/3170.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001164&mimeType=html&fmt=ahah

References

  1. Breznak J. A. , Costilow R. N. . ( 2007;). Physicochemical factors in growth. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 309–329. Edited by Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt. T. M. , Snyder L. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  2. Busse H. J. , Auling G. . ( 1988;). Polyamine patterns as a chemotaxonomic marker within the Proteobacteria. . Syst Appl Microbiol 11: 1–8.[CrossRef]
    [Google Scholar]
  3. Busse H. J. , Bunka S. , Hensel A. , Lubitz W. . ( 1997;). Discrimination of members of the family Pasteurellaceae based on polyamine patterns. . Int J Syst Bacteriol 47: 698–708.[CrossRef]
    [Google Scholar]
  4. Collins M. D. , Jones D. . ( 1981;). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. . Microbiol Rev 45: 316–354.[PubMed]
    [Google Scholar]
  5. Cowan S. T. , Steel K. J. . ( 1965;). Manual for the Identification of Medical Bacteria, London:: Cambridge University Press;.
    [Google Scholar]
  6. Doetsch R. N. . ( 1981;). Determinative methods of light microscopy. . In Manual of Methods for General Bacteriology, pp. 21–33. Edited by Gerhardt. P. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  7. Ezaki T. , Hashimoto Y. , Yabuuchi E. . ( 1989;). Fluorometric deoxyribonucleic acid deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39: 224–229.[CrossRef]
    [Google Scholar]
  8. Felsenstein J. . ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17: 368–376.[PubMed] [CrossRef]
    [Google Scholar]
  9. Felsenstein J. . ( 1985;). Confidence limits on Phylogenies: an approach using the bootstrap. . Evolution 39: 783–791.[CrossRef]
    [Google Scholar]
  10. Fitch W. M. . ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20: 406–416.[CrossRef]
    [Google Scholar]
  11. Frank J. A. , Reich C. I. , Sharma S. , Weisbaum J. S. , Wilson B. A. , Olsen G. J. . ( 2008;). Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. . Appl Environ Microbiol 74: 2461–2470. [CrossRef] [PubMed]
    [Google Scholar]
  12. Gordon R. E. , Barnett D. A. , Handerhan J. E. , Pang C. H. N. . ( 1974;). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Syst Bacteriol 24: 54–63.[CrossRef]
    [Google Scholar]
  13. Gupta S. K. , Lal D. , Lal R. . ( 2009;). Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. . Int J Syst Evol Microbiol 59: 156–161. [CrossRef] [PubMed]
    [Google Scholar]
  14. Hall T. A. . ( 1999;). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41: 95–98.
    [Google Scholar]
  15. Kim J. K. , He D. , Liu Q. M. , Park H. Y. , Jung M. S. , Yoon M. H. , Kim S. C. , Im W. T. . ( 2013;). Novosphingobium ginsensosidimutans sp. nov., with the ability to convert ginsenoside. . Int J Syst Evol Microbiol 23: 444–450.
    [Google Scholar]
  16. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. et al. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62: 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  17. Kimura M. . ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16: 111–120.[PubMed] [CrossRef]
    [Google Scholar]
  18. Komagata K. , Suzuki K. . ( 1987;). Lipids and cell wall analysis in bacterial systematics. . Methods Microbiol 19: 161–203.[CrossRef]
    [Google Scholar]
  19. Lee J. C. , Kim S. G. , Whang K. S. . ( 2014;). Novosphingobium aquiterrae sp. nov., isolated from ground water. . Int J Syst Evol Microbiol 64: 3282–3287. [CrossRef] [PubMed]
    [Google Scholar]
  20. Lin S. Y. , Hameed A. , Liu Y. C. , Hsu Y. H. , Lai W. A. , Huang H. I. , Young C. C. . ( 2014;). Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana . . Int J Syst Evol Microbiol 64: 594–598. [CrossRef] [PubMed]
    [Google Scholar]
  21. Marmur J. . ( 1961;). A procedure for the isolation of deoxyribonucleic acid from micro-organisms. . J Mol Biol 3: 208–218.[CrossRef]
    [Google Scholar]
  22. 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]
  23. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int Syst Bacteriol 39: 159–167.[CrossRef]
    [Google Scholar]
  24. 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]
  25. Pham V. H. T. , Kim J. . ( 2012;). Cultivation of unculturable soil bacteria. . Trends Biotechnol 30: 475–484. [CrossRef] [PubMed]
    [Google Scholar]
  26. Pham V. H. T. , Kim J. , Jeong S. W. . ( 2014;). Enhanced isolation and culture of highly efficient psychrophilic oil-degrading bacteria from oil-contaminated soils in South Korea. . J Environ Biol 35: 1145–1149.[PubMed]
    [Google Scholar]
  27. Powers E. M. . ( 1995;). Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. . Appl Environ Microbiol 61: 3756–3758.[PubMed]
    [Google Scholar]
  28. Saitou N. , Nei M. . ( 1987;). The neighbour-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4: 406–425.[PubMed]
    [Google Scholar]
  29. Sasser M. . ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids. . MIDI Technical Note 101, Newark, DE:: MIDI Inc;.
    [Google Scholar]
  30. Smibert R. M. , Krieg N. R. . ( 1994;). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. , Murray R. G. E. , Wood. W. A. , Krieg N. R. . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  31. Stolz A. , Busse H. J. , Kämpfer P. . ( 2007;). Pseudomonas knackmussii sp. nov. . Int J Syst Evol Microbiol 57: 572–576. [CrossRef] [PubMed]
    [Google Scholar]
  32. 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. [CrossRef] [PubMed]
    [Google Scholar]
  33. Tamura K. , Stecher G. , Peterson D. , Filipski A. , Kumar S. . ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30: 2725–2729. [CrossRef] [PubMed]
    [Google Scholar]
  34. 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.[PubMed] [CrossRef]
    [Google Scholar]
  35. Tindall B. J. , Sikorski J. , Smibert R. A. , Krieg N. R. . ( 2007;). Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Bacteriology, , 3rd edn., pp. 330–393. Edited by Reddy C. A. , Beveridge T. J. , Breznak J. A. , Marzluf G. A. , Schmidt. T. M. , Snyder L. R. . Washington, DC:: ASM Press;.
    [Google Scholar]
  36. Vaughn R. H. , Mitchell N. B. , Levine M. . ( 1939;). The Voges-Proskauer and methyl red reactions in the coli-aerogenes group. . J Am Water Works Assoc 31: 993–1001.
    [Google Scholar]
  37. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. et al. ( 1987;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. . Int J Syst Bacteriol 37: 463–464.[CrossRef]
    [Google Scholar]
  38. Xie F. , Quan S. , Liu D. , He W. , Wang Y. , Ma H. , Chen G. , Chao Y. , Quian S. . ( 2014;). Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. . Int J Syst Evol Microbiol 64: 2324–2329. [CrossRef] [PubMed]
    [Google Scholar]
  39. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001164
Loading
/content/journal/ijsem/10.1099/ijsem.0.001164
Loading

Data & Media loading...

Supplements

Supplementary File 1



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error