1887

Abstract

The taxonomic position of two soil actinomycetes, strains A2012 and A2019, isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family . Strains A2012 and A2019 were most closely related to DSM 44831 (98.9 %) and CIP 108295 (98.6 %), respectively; similarity to other type strains of the genus ranged from 96.9 to 97.9 %. However, DNA–DNA relatedness and phenotypic data demonstrated that strains A2012 and A2019 could be clearly distinguished from members of the most closely related species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus . It is proposed, therefore, that strains A2012 and A2019 be classified in the genus as representatives of sp. nov. (type strain A2012 = DSM 45516 = NRRL B-24833 = KCTC 19986) and sp. nov. (type strain A2019 = DSM 45517 = NRRL B-24834 = KCTC 19985), respectively.

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2012-06-01
2019-12-09
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References

  1. Aoki H. , Sakai H. , Kohsaka M. , Konomi T. , Hosoda J. , Kubochi Y. , Iguchi E. , Imanaka H. . ( 1976; ). Nocardicin A, a new monocyclic beta-lactam antibiotic. I. Discovery, isolation and characterization. . J Antibiot (Tokyo) 29:, 492–500. [CrossRef] [PubMed]
    [Google Scholar]
  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] [PubMed]
    [Google Scholar]
  3. Chun J. , Goodfellow M. . ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. . Int J Syst Bacteriol 45:, 240–245. [CrossRef] [PubMed]
    [Google Scholar]
  4. Chun J. , Lee J.-H. , Jung Y. , Kim M. , Kim S. , Kim B. K. , Lim Y. W. . ( 2007; ). EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. . Int J Syst Evol Microbiol 57:, 2259–2261. [CrossRef] [PubMed]
    [Google Scholar]
  5. Collins M. D. , Pirouz T. , Goodfellow M. , Minnikin D. E. . ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100:, 221–230.[PubMed] [CrossRef]
    [Google Scholar]
  6. De Ley J. , Cattoir H. , Reynaerts A. . ( 1970; ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12:, 133–142.[PubMed] [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 limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  9. Felsenstein J. . ( 1993; ). phylip (phylogeny inference package), version 3.5c. 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 Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  11. Gauze G. F. , Preobrazhenskaya T. P. , Kudrina E. S. , Blinov N. O. , Ryabova I. D. , Sveshnikova M. A. . ( 1957; ). Problems of Classification of Actinomycete-Antagonists. Moscow:: Government Publishing House of Medical Literature, Mediz;.
    [Google Scholar]
  12. Gerhardt P. . ( 1981; ). Manual of Methods for General Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  13. Gonzalez J. M. , Saiz-Jimenez C. . ( 2005; ). A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. . Extremophiles 9:, 75–79. [CrossRef] [PubMed]
    [Google Scholar]
  14. Goodfellow M. . ( 1992; ). The family Nocardiaceae . . In The Prokaryotes, , 2nd edn., pp. 1188–1213. Edited by Balows A. , Trüper H. G. , Dworkin M. , Harder W. , Schleifer K. H. . . New York:: Springer;.
    [Google Scholar]
  15. Goodfellow M. . ( 1998; ). Nocardia and related genera. . In Topley & Wilson’s Microbiology & Microbial Infections, , 9th edn., vol. 2, pp. 463–489. Edited by Balows A. , Duerden B. I. . . London:: Edward Arnold;.
    [Google Scholar]
  16. Goodfellow M. , Lechevalier M. P. . ( 1989; ). Genus Nocardia. Trevisan 1889, 9AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 2, pp. 1458–1471. Edited by Williams S. T. , Sharpe M. E. , Holt J. G. . . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  17. Goodfellow M. , Isik K. , Yates E. . ( 1999; ). Actinomycete systematics: an unfinished synthesis. . Nova Acta Leopold 312:, 47–82.
    [Google Scholar]
  18. Gordon R. E. . ( 1967; ). The taxonomy of soil bacteria. . In The Ecology of Soil Bacteria, pp. 293–321. Edited by Gray T. R. G. , Parkinson D. . . Liverpool:: Liverpool University Press;.
    [Google Scholar]
  19. Gordon R. E. , Mihm J. M. . ( 1957; ). A comparative study of some strains received as nocardiae. . J Bacteriol 73:, 15–27.[PubMed]
    [Google Scholar]
  20. Gordon R. E. , Mihm J. M. . ( 1962; ). The type species of the genus Nocardia . . J Gen Microbiol 27:, 1–10.[PubMed] [CrossRef]
    [Google Scholar]
  21. 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]
  22. Huß V. A. R. , Festl H. , Schleifer K. H. . ( 1983; ). Studies on the spectrometric determination of DNA hybridisation from renaturation rates. . Syst Appl Microbiol 4:, 184–192. [CrossRef]
    [Google Scholar]
  23. Igarashi M. , Hayashi C. , Homma Y. , Hattori S. , Kinoshita N. , Hamada M. , Takeuchi T. . ( 2000; ). Tubelactomicin A, a novel 16-membered lactone antibiotic, from Nocardia sp. I. Taxonomy, production, isolation and biological properties. . J Antibiot (Tokyo) 53:, 1096–1101. [CrossRef] [PubMed]
    [Google Scholar]
  24. 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] [PubMed]
    [Google Scholar]
  25. Jones K. L. . ( 1949; ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. . J Bacteriol 57:, 141–145.
    [Google Scholar]
  26. Jukes T. H. , Cantor C. R. . ( 1969; ). Evolution of protein molecules. . In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by Munro H. N. . . New York:: Academic Press;.
    [Google Scholar]
  27. Kageyama A. , Yazawa K. , Nishimura K. , Mikami Y. . ( 2005; ). Nocardia anaemiae sp. nov. isolated from an immunocompromised patient and the first isolation report of Nocardia vinacea from humans. . Nippon Ishinkin Gakkai Zasshi 46:, 21–26. [CrossRef] [PubMed]
    [Google Scholar]
  28. Kämpfer P. , Kroppenstedt R. M. . ( 1996; ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. . Can J Microbiol 42:, 989–1005. [CrossRef]
    [Google Scholar]
  29. Komaki H. , Nemoto A. , Tanaka Y. , Takagi H. , Yazawa K. , Mikami Y. , Shigemori H. , Kobayashi J. , Ando A. , Nagata Y. . ( 1999; ). Brasilicardin A, a new terpenoid antibiotic from pathogenic Nocardia brasiliensis: fermentation, isolation and biological activity. . J Antibiot (Tokyo) 52:, 13–19. [CrossRef] [PubMed]
    [Google Scholar]
  30. Kumar S. , Tamura K. , Nei M. . ( 2004; ). mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. . Brief Bioinform 5:, 150–163. [CrossRef] [PubMed]
    [Google Scholar]
  31. Lechevalier M. P. . ( 1976; ). The taxonomy of the genus Nocardia: some light at the end of the tunnel?. In The Biology of the Nocardiae, pp. 1–33. Edited by Goodfellow M. , Brownell G. H. , Serrano J. A. . . London:: Academic Press;.
    [Google Scholar]
  32. Lechevalier M. P. , Lechevalier H. A. . ( 1980; ). The chemotaxonomy of actinomycetes. . In Actinomycete Taxonomy (Special Publication no. 6), pp. 227–291. Edited by Dietz A. , Thayer J. . . Arlington, VA:: Society for Industrial Microbiology;.
    [Google Scholar]
  33. 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] [PubMed]
    [Google Scholar]
  34. McNeil M. M. , Brown J. M. . ( 1994; ). The medically important aerobic actinomycetes: epidemiology and microbiology. . Clin Microbiol Rev 7:, 357–417.[PubMed]
    [Google Scholar]
  35. Minnikin D. E. , Hutchinson I. G. , Caldicott A. B. , Goodfellow M. . ( 1980; ). Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. . J Chromatogr A 188:, 221–233. [CrossRef]
    [Google Scholar]
  36. Orchard V. A. . ( 1979; ). Effect of sewage sludge additions on Nocardia in soil. . Soil Biol Biochem 11:, 217–220. [CrossRef]
    [Google Scholar]
  37. Orchard V. A. . ( 1981; ). The ecology of Nocardia and related taxa. . Zentralbl Bakteriol 11: (Suppl.), 167–180.
    [Google Scholar]
  38. Orchard V. A. , Goodfellow M. , Williams S. T. . ( 1977; ). Selective isolation and occurrence of Nocardiae in soil. . Soil Biol Biochem 9:, 233–238. [CrossRef]
    [Google Scholar]
  39. Saintpierre D. . ( 2001; ). Identification de souches originales d’actinomycétes isolées de sols ultramafiques de Nouvelle-Calédonie. Caractérisation chimique de quelques antibiotiques produits . . PhD thesis, Institut National Polytechnique de Toulouse, France (in French).
  40. 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]
  41. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. . Newark, DE:: MIDI Inc;.
  42. Shirling E. B. , Gottlieb D. . ( 1966; ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16:, 313–340. [CrossRef]
    [Google Scholar]
  43. Stackebrandt E. , Rainey F. A. , Ward-Rainey N. L. . ( 1997; ). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47:, 479–491. [CrossRef]
    [Google Scholar]
  44. Staneck J. L. , Roberts G. D. . ( 1974; ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28:, 226–231.[PubMed]
    [Google Scholar]
  45. Thompson J. D. , Higgins D. G. , Gibson T. J. . ( 1994; ). clustal_w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22:, 4673–4680. [CrossRef] [PubMed]
    [Google Scholar]
  46. Trevisan V. . ( 1889; ). I Generi e le Specie delle Batteriacee. Milan:: Zanaboni & Gabuzzi;.
    [Google Scholar]
  47. Wang Y. , Zhang Z. S. , Ruan J. S. , Wang Y. M. , Ali S. M. . ( 1999; ). Investigation of actinomycete diversity in the tropical rainforests of Singapore. . J Ind Microbiol Biotechnol 23:, 178–187. [CrossRef]
    [Google Scholar]
  48. Williams S. T. , Goodfellow M. , Alderson G. , Wellington E. M. H. , Sneath P. H. A. , Sackin M. J. . ( 1983; ). Numerical classification of Streptomyces and related genera. . J Gen Microbiol 129:, 1743–1813.[PubMed]
    [Google Scholar]
  49. Wu C. , Lu X. , Qin M. , Wang Y. , Ruan J. . ( 1989; ). Analysis of menaquinone compound in microbial cells by HPLC. . Microbiology (English translation of Mikrobiologiia) 16:, 176–178.
    [Google Scholar]
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