1887

Abstract

A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of (98.6 % similarity), (98.5 %), (98.4 %), (98.3 %), (98.1 %) and (97.5 %); the phylogenetic distance from other species with validly published names within the genus was greater than 3 %. Strain 2C1-5 was characterized chemotaxonomically as having -2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H) as the predominant menaquinone and iso-C, C and Cω6 as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5 to the genus . The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5 from existing species with validly published names. Therefore, strain 2C1-5 represents a novel species of the genus , for which the name sp. nov. is proposed, with the type strain 2C1-5 ( = JCM 17460 = KCTC 19799).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.047043-0
2013-10-01
2019-10-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/10/3727.html?itemId=/content/journal/ijsem/10.1099/ijs.0.047043-0&mimeType=html&fmt=ahah

References

  1. Bae H. S. , Lee J. M. , Kim Y. B. , Lee S.-T. . ( 1996; ). Biodegradation of the mixtures of 4-chlorophenol and phenol by Comamonas testosteroni CPW301. . Biodegradation 7:, 463–469. [CrossRef] [PubMed]
    [Google Scholar]
  2. Boyd S. A. , Shelton D. R. . ( 1984; ). Anaerobic biodegradation of chlorophenols in fresh and acclimated sludge. . Appl Environ Microbiol 47:, 272–277.[PubMed]
    [Google Scholar]
  3. Buck J. D. . ( 1982; ). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol 44:, 992–993.[PubMed]
    [Google Scholar]
  4. Cole J. R. , Cascarelli A. L. , Mohn W. W. , Tiedje J. M. . ( 1994; ). Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol. . Appl Environ Microbiol 60:, 3536–3542.[PubMed]
    [Google Scholar]
  5. Cui Y. S. , Lee S.-T. , Im W.-T. . ( 2009; ). Nocardioides ginsengisoli sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 59:, 3045–3050. [CrossRef] [PubMed]
    [Google Scholar]
  6. 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]
  7. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  8. Felsenstein J. . ( 1985; ). Confidence limit on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Felsenstein J. . ( 2009; ). phylip (phylogeny inference package), version 3.69. . Distributed by the author. Department of Genome Sciences, University of Washington;, Seattle, USA:.
  10. Fitch W. M. . ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Biol 20:, 406–416. [CrossRef]
    [Google Scholar]
  11. 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]
  12. Hiraishi A. , Ueda Y. , Ishihara J. , Mori T. . ( 1996; ). Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. . J Gen Appl Microbiol 42:, 457–469. [CrossRef]
    [Google Scholar]
  13. Im W. T. , Kim S. Y. , Liu Q. M. , Yang J. E. , Lee S. T. , Yi T. H. . ( 2010; ). Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field. . J Microbiol 48:, 623–628. [CrossRef] [PubMed]
    [Google Scholar]
  14. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. . & other authors ( 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]
  15. Komagata K. , Suzuki K. . ( 1987; ). Lipids and cell-wall analysis in bacterial systematics. . Methods Microbiol 19:, 161–207. [CrossRef]
    [Google Scholar]
  16. Kimura M. . ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press. .
    [Google Scholar]
  17. Kubota M. , Kawahara K. , Sekiya K. , Uchida T. , Hattori Y. , Futamata H. , Hiraishi A. . ( 2005; ). Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments. . Syst Appl Microbiol 28:, 165–174. [CrossRef] [PubMed]
    [Google Scholar]
  18. Lee D. W. , Lee S. Y. , Yoon J. H. , Lee S. D. . ( 2011; ). Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil. . Int J Syst Evol Microbiol 61:, 1933–1937. [CrossRef] [PubMed]
    [Google Scholar]
  19. Lee S. H. , Liu Q. M. , Lee S. T. , Kim S. C. , Im W. T. . ( 2012; ). Nocardioides ginsengagri sp. nov., isolated from the soil of a ginseng field. . Int J Syst Evol Microbiol 62:, 591–595. [CrossRef] [PubMed]
    [Google Scholar]
  20. Madsen T. , Aamand H. . ( 1992; ). Anaerobic transformation and toxicity of trichlorophenols in a stable enrichment culture. . Appl Environ Microbiol 58:, 557–561.[PubMed]
    [Google Scholar]
  21. 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]
  22. Mikesell M. D. , Boyd S. A. . ( 1986; ). Complete reductive dechlorination and mineralization of pentachlorophenol by anaerobic microorganisms. . Appl Environ Microbiol 52:, 861–865.[PubMed]
    [Google Scholar]
  23. Moore D. D. , Dowhan D. . ( 1995; ). Preparation and analysis of DNA. . In Current Protocols in Molecular Biology, pp. 2–11. Edited by Ausubel F. M. , Brent R. , Kingston R. E. , Moore D. D. , Seidman J. G. , Smith J. A. , Struhl K. . . New York:: Wiley;.
    [Google Scholar]
  24. Prauser H. . ( 1976; ). Nocardioides, a new genus of the order Actinomycetales . . Int J Syst Bacteriol 26:, 58–65. [CrossRef]
    [Google Scholar]
  25. 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]
  26. Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.
  27. Sei K. , Asano K. , Tateishi N. , Mori K. , Ike M. , Fujita M. . ( 1999; ). Design of PCR primers and gene probes for the general detection of bacterial populations capable of degrading aromatic compounds via catechol cleavage pathways. . J Biosci Bioeng 88:, 542–550. [CrossRef] [PubMed]
    [Google Scholar]
  28. Song G. C. , Yasir M. , Bibi F. , Chung E. J. , Jeon C. O. , Chung Y. R. . ( 2011; ). Nocardioides caricicola sp. nov., an endophytic bacterium isolated from a halophyte, Carex scabrifolia Steud.. Int J Syst Evol Microbiol 61:, 105–109. [CrossRef] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Tóth E. M. , Kéki Z. , Makk J. , Homonnay Z. G. , Márialigeti K. , Schumann P. . ( 2011; ). Nocardioides hungaricus sp. nov., isolated from a drinking water supply system. . Int J Syst Evol Microbiol 61:, 549–553. [CrossRef] [PubMed]
    [Google Scholar]
  33. 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. . & other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464.[CrossRef]
    [Google Scholar]
  34. Woo S. G. , Srinivasan S. , Yang J. , Jung Y. A. , Kim M. K. , Lee M. . ( 2012; ). Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant. . Int J Syst Evol Microbiol 62:, 1199–1203. [CrossRef] [PubMed]
    [Google Scholar]
  35. Woods S. L. , Ferguson J. F. , Benjamin M. M. . ( 1989; ). Characterization of chlorophenol and chloromethoxybenzene biodegradation during anaerobic treatment. . Environ Sci Technol 23:, 62–68. [CrossRef]
    [Google Scholar]
  36. Yamamura H. , Ohkubo S. Y. , Nakagawa Y. , Ishida Y. , Hamada M. , Otoguro M. , Tamura T. , Hayakawa M. . ( 2011; ). Nocardioides iriomotensis sp. nov., an actinobacterium isolated from forest soil. . Int J Syst Evol Microbiol 61:, 2205–2209. [CrossRef] [PubMed]
    [Google Scholar]
  37. Yoon J.-H. , Lee J.-S. , Shin Y.-K. , Park Y.-H. , Lee S.-T. . ( 1997; ). Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis . . Int J Syst Bacteriol 47:, 904–907. [CrossRef] [PubMed]
    [Google Scholar]
  38. Yoon J.-H. , Cho Y.-G. , Lee S.-T. , Suzuki K. , Nakase T. , Park Y.-H. . ( 1999; ). Nocardioides nitrophenolicus sp. nov., a p-nitrophenol-degrading bacterium. . Int J Syst Bacteriol 49:, 675–680. [CrossRef] [PubMed]
    [Google Scholar]
  39. Yoon J.-H. , Lee J.-K. , Jung S.-Y. , Kim J.-A. , Kim H.-K. , Oh T.-K. . ( 2006; ). Nocardioides kongjuensis sp. nov., an N-acylhomoserine lactone-degrading bacterium. . Int J Syst Evol Microbiol 56:, 1783–1787. [CrossRef] [PubMed]
    [Google Scholar]
  40. Yoon J.-H. , Kang S.-J. , Park S. , Kim W. , Oh T.-K. . ( 2009; ). Nocardioides caeni sp. nov., isolated from wastewater. . Int J Syst Evol Microbiol 59:, 2794–2797. [CrossRef] [PubMed]
    [Google Scholar]
  41. Zhang D. C. , Schumann P. , Redzic M. , Zhou Y. G. , Liu H. C. , Schinner F. , Margesin R. . ( 2012; ). Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite. . Int J Syst Evol Microbiol 62:, 445–450. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.047043-0
Loading
/content/journal/ijsem/10.1099/ijs.0.047043-0
Loading

Data & Media loading...

Supplements

Supplementary material 

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