1887

Abstract

An actinomycete, strain L1505, was isolated from a limnetic lake sediment and found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with its classification in the genus . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain L1505 formed a distinct lineage within the genus . The isolate belonged to a cluster containing MA140/96, MT8 and N1350, with which the isolate shared 99.0–98.2 % 16S rRNA gene sequence similarity. Genotypic and phenotypic data also indicated that the isolate was different from known members of the genus . On the basis of these data, strain 1505 is considered to represent a novel species of the genus , for which the name sp. nov. is proposed (type strain L1505 = DSM 45521 = NRRL B-24829 = KCTC 19981).

Funding
This study was supported by the:
  • , Ondokuz Mayis University (OMU) , (Award PYO. FEN. 1901.09.003)
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2012-06-01
2020-10-19
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References

  1. 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]
  2. 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]
  3. 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]
  4. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  5. Felsenstein J. 1985; Confidence limits on phylogeny: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
    [Google Scholar]
  6. Felsenstein J. 1993; phylip (phylogenetic inference package), version 3.5c.. Seattle:: Department of Genetics, University of Washington, USA;
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Jones A. L., Payne G. D., Goodfellow M. 2010; Williamsia faeni sp. nov., an actinomycete isolated from a hay meadow. Int J Syst Evol Microbiol 60:2548–2551 [CrossRef][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Kämpfer P., Andersson M. A., Rainey F. A., Kroppenstedt R. M., Salkinoja-Salonen M. 1999; Williamsia muralis gen. nov., sp. nov., isolated from the indoor environment of a children’s day care centre. Int J Syst Bacteriol 49:681–687 [CrossRef][PubMed]
    [Google Scholar]
  17. Kelly K. L. 1964 Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;
    [Google Scholar]
  18. Klatte S., Rainey F. A., Kroppenstedt R. M. 1994; Transfer of Rhodococcus aichiensis Tsukamura 1982 and Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov.. Int J Syst Bacteriol 44:769–773 [CrossRef][PubMed]
    [Google Scholar]
  19. Kroppenstedt R. M., Goodfellow M. 1991; The family Thermomonosporaceae . In The Prokaryotes, 2nd edn. pp. 1085–1114 Edited by Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K. H. New York: Springer;
    [Google Scholar]
  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][PubMed]
    [Google Scholar]
  21. Küster E. 1959; Outline of a comparative study of criteria used in characterization of the actinomycetes. Int Bull Bacteriol Nomencl Taxon 9:97–104 [CrossRef]
    [Google Scholar]
  22. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443 [CrossRef]
    [Google Scholar]
  23. Lechevalier M. P., De Bievre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [CrossRef]
    [Google Scholar]
  24. Mikami H., Ishida Y. 1983; Post-column fluorometric detection of reducing sugars in high-performance liquid chromatography using arginine. Bunseki Kagaku 32:E207–E210 [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 bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [CrossRef]
    [Google Scholar]
  26. Pathom-aree W., Nogi Y., Sutcliffe I. C., Ward A. C., Horikoshi K., Bull A. T., Goodfellow M. 2006; Williamsia marianensis sp. nov., a novel actinomycete isolated from the Mariana Trench. Int J Syst Evol Microbiol 56:1123–1126 [CrossRef][PubMed]
    [Google Scholar]
  27. 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]
  28. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. Technical Note 101. Newark, DE: MIDI Inc;
  29. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [CrossRef]
    [Google Scholar]
  30. Stach J. E., Maldonado L. A., Ward A. C., Bull A. T., Goodfellow M. 2004; Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan. Int J Syst Evol Microbiol 54:191–194 [CrossRef][PubMed]
    [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
  34. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [CrossRef]
    [Google Scholar]
  35. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [CrossRef]
    [Google Scholar]
  36. 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; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  37. Weyland H. 1969; Actinomycetes in North Sea and Atlantic Ocean sediments. Nature 223:858 [CrossRef][PubMed]
    [Google Scholar]
  38. 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]
  39. Wu C., Lu X., Qin M., Wang Y., Ruan J. 1989; Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 16:176–178
    [Google Scholar]
  40. Yassin A. F., Hupfer H. 2006; Williamsia deligens sp. nov., isolated from human blood. Int J Syst Evol Microbiol 56:193–197 [CrossRef][PubMed]
    [Google Scholar]
  41. Yassin A. F., Young C. C., Lai W.-A., Hupfer H., Arun A. B., Shen F.-T., Rekha P. D., Ho M.-J. 2007; Williamsia serinedens sp. nov., isolated from an oil-contaminated soil. Int J Syst Evol Microbiol 57:558–561 [CrossRef][PubMed]
    [Google Scholar]
  42. Zhi X.-Y., Li W.-J., Stackebrandt E. 2009; An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 59:589–608 [CrossRef][PubMed]
    [Google Scholar]
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