1887

Abstract

Two bacterial isolates from Kuwaiti soil contaminated by crude oil were analysed by using a polyphasic taxonomic approach. The isolates, designated OFN N11 and OFN N12, were shown to have molecular, chemical and morphological properties typical of members of the genus . Based on a multigenic approach that included 16S rRNA, and gene sequencing, these novel isolates formed a monophyletic clade within the genus . The closest species was (with 99.4 %, 99.5 %, 98.6 % gene sequence similarity to the 16S rRNA, and genes, respectively). The novel isolates could be distinguished phenotypically from the type strains of recognized species of the genus . The novel isolates were not related to the type strain of in DNA–DNA hybridization experiments (26 % relatedness). On the basis of these genotypic and phenotypic data, the two isolates appear to represent a novel species, for which the name sp. nov. is proposed. The type strain is OFN N12 (=DSM 44960=CIP 108996).

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2007-07-01
2020-01-29
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References

  1. Boiron, P., Provost, F. & Dupont, B. ( 1993; ). Technical protocols. In Méthodes de Laboratoire pour le Diagnostic de la Nocardiose, pp. 107–126. Edited by Institut Pasteur. Paris: Institut Pasteur (in French).
  2. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. ( 1977; ). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461–466.[CrossRef]
    [Google Scholar]
  3. De Ley, J., Cattoir, H. & Reynaerts, A. ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133–142.[CrossRef]
    [Google Scholar]
  4. Devulder, G., Perrière, G., Baty, F. & Flandrois, J. P. ( 2003; ). bibi, a bioinformatics bacterial identification tool. J Clin Microbiol 41, 1785–1787.[CrossRef]
    [Google Scholar]
  5. Devulder, G., Perouse de Montclos, M. & Flandrois, J. P. ( 2005; ). A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol 55, 293–302.[CrossRef]
    [Google Scholar]
  6. Escara, J. F. & Hutton, J. R. ( 1980; ). Thermal stability and renaturation of DNA in dimethyl sulphoxide solutions: acceleration of renaturation rate. Biopolymers 19, 1315–1327.[CrossRef]
    [Google Scholar]
  7. Felsenstein, J. ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef]
    [Google Scholar]
  8. 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]
  9. Galtier, N., Gouy, M. & Gautier, C. ( 1996; ). seaview and phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12, 543–548.
    [Google Scholar]
  10. Goodfellow, M. ( 1992; ). The family Nocardiaceae. In The Prokaryotes, 2nd edn, pp. 1188–1213. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  11. Goodfellow, M. ( 1998; ). The genus Nocardia Trevisan 1889. In Topley & Wilson's Microbiology & Microbial Infections, 9th edn, pp. 464–489. Edited by A. Balows & B. I. Duerden. London: Edward Arnold.
  12. Goodfellow, M. & Lechevalier, M. P. ( 1989; ). Genus Nocardia Trevisan. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2350–2361. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  13. Huß, V. A. R., Festl, H. & Schleifer, K. H. ( 1983; ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184–192.[CrossRef]
    [Google Scholar]
  14. Isik, K., Chun, J., Hah, Y. C. & Goodfellow, M. ( 1999; ). Nocardia salmonicida nom. rev., a fish pathogen. Int J Syst Bacteriol 49, 833–837.[CrossRef]
    [Google Scholar]
  15. Jahnke, K. D. ( 1992; ). Basic computer program for evaluation of spectroscopic DNA renaturation data from GILFORD System 2600 spectrometer on a PC/XT/AT type personal computer. J Microbiol Methods 15, 61–73.[CrossRef]
    [Google Scholar]
  16. Jahnke, K. D. & Bahnweg, G. ( 1986; ). Assessing natural relationships in the Basidiomycetes by DNA analysis. Trans Br Mycol Soc 87, 175–191.[CrossRef]
    [Google Scholar]
  17. Khan, Z. U., Neil, L., Chandy, R., Chugh, T. D., Al-Sayer, H., Provost, F. & Boiron, P. ( 1997; ). Nocardia asteroides in the soil of Kuwait. Mycopathologia 137, 159–163.[CrossRef]
    [Google Scholar]
  18. Kroppenstedt, R. M. ( 1982; ). Separation of bacterial menaquinones by HPLC using reverse phase (RP-18) and a silver loaded ion exchanger. J Liq Chromatogr 5, 2359–2367.[CrossRef]
    [Google Scholar]
  19. Kroppenstedt, R. M. ( 1985; ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics (Society for Applied Microbiology Technical Series no. 20), pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  20. Kumar, S., Tamura, K. & Nei, M. ( 2004; ). mega3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef]
    [Google Scholar]
  21. Kurup, P. V. & Schmitt, J. A. ( 1971; ). Isolation of Nocardia from soil by a modified paraffin bait method. Mycologia 63, 175–177.[CrossRef]
    [Google Scholar]
  22. Laurent, F. J., Provost, F. & Boiron, P. ( 1999; ). Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR. J Clin Microbiol 37, 99–102.
    [Google Scholar]
  23. Maldonado, L., Hookey, J. V., Ward, A. C. & Goodfellow, M. ( 2000; ). The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. Antonie van Leeuwenhoek 78, 367–377.[CrossRef]
    [Google Scholar]
  24. Minnikin, D. E., Alshamaony, L. & Goodfellow, M. ( 1975; ). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analyses of whole-cell methanolysates. J Gen Microbiol 88, 200–204.[CrossRef]
    [Google Scholar]
  25. 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 isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  26. Nocard, M. E. ( 1888; ). Note sur la maladie des boeufs de la guadeloupe connue sous le nom de farcin. Ann Inst Pasteur (Paris) 2, 293–302.
    [Google Scholar]
  27. Rodríguez-Nava, V., Couble, A., Molinard, C., Sandoval, H., Boiron, P. & Laurent, F. ( 2004; ). Nocardia mexicana sp. nov., a new pathogen isolated from human mycetomas. J Clin Microbiol 42, 4530–4535.[CrossRef]
    [Google Scholar]
  28. Rodríguez-Nava, V., Couble, A., Khan, Z. U., Pérouse de Montclos, M., Brasme, L., Villuendas, C., Molinard, C., Boiron, P. & Laurent, F. ( 2005; ). Nocardia ignorata, a new agent of human nocardiosis isolated from respiratory specimens in Europe and soil samples from Kuwait. J Clin Microbiol 43, 6167–6170.[CrossRef]
    [Google Scholar]
  29. Rodríguez-Nava, V., Couble, A., Devulder, G., Flandrois, J.-P., Boiron, P. & Laurent, F. ( 2006; ). Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species. J Clin Microbiol 44, 536–546.[CrossRef]
    [Google Scholar]
  30. Roth, A., Andrees, S., Kroppenstedt, R. M., Harmsen, D. & Mauch, H. ( 2003; ). Phylogeny of the genus Nocardia based on reassessed 16S rRNA gene sequences reveals underspeciation and division of strains classified as Nocardia asteroides into three established species and two unnamed taxons. J Clin Microbiol 41, 851–856.[CrossRef]
    [Google Scholar]
  31. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  32. Stackebrandt, E., Rainey, F. A. & Ward-Rainey, N. L. ( 1997; ). Proposal for a new hierarchic classification system, Actinobacteria class nov. Int J Syst Bacteriol 47, 479–491.[CrossRef]
    [Google Scholar]
  33. Steingrube, V. A., Wilson, R. W., Brown, B. A., Jost, K. C., Jr, Blacklock, Z., Gibson, J. L. & Wallace, R. J., Jr ( 1997; ). Rapid identification of clinically significant species and taxa of aerobic actinomycetes, including Actinomadura, Gordona, Nocardia, Rhodococcus, Streptomyces, and Tsukamurella isolates, by DNA amplification and restriction endonuclease analysis. J Clin Microbiol 35, 817–822.
    [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.[CrossRef]
    [Google Scholar]
  35. Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevski, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E., Stackebrandt, E., Starr, M. P. & Trüper, H. G. ( 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]
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Additional phylogenetic trees based on analysis of the 16S rRNA, and gene sequences of sp. nov. [ PDF] (72 KB)



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