1887

Abstract

A novel actinobacterial strain, designated, NIO-1009, was isolated from a marine sediment sample collected from Chorao Island, Goa, India. Phylogenetic analysis comparisons based on 16S rRNA gene sequences between strain NIO-1009 and other members of the genus revealed that strain NIO-1009 had the closest sequence similarity to DSM 44908 and DSM 20151 with 99.2 and 99.1 %, respectively. Furthermore, DNA–DNA hybridization results showed that DSM 44908 and DSM 20151 were 39.5 (3.0 %) and 41.7 (2.0 %) with strain NIO-1009, respectively, which were well below the 70 % limit for any novel species proposal. Phylogenetically strain NIO-1009 forms a stable clade with and DSM 44908 and DSM 20151 with 100 % bootstrap values. Strain NIO-1009 contained -diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose as the cell wall sugars. The major fatty acids were C, Cω9, C(ω6 and/or ω7) and 10-methyl C. The only menaquinone detected was MK-8(H), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 66.9 mol%. The phenotypic and genotypic data showed that strain NIO-1009 warrants recognition as a novel species of the genus for which the name sp. nov., is proposed; the type strain is NIO-1009 ( = NCIM 5452 = DSM 45688).

Funding
This study was supported by the:
  • Council for Scientific and Industrial Research -National Chemical Laboratory
  • Council for Scientific and Industrial Research (CSIR)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.061390-0
2014-08-01
2021-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/8/2693.html?itemId=/content/journal/ijsem/10.1099/ijs.0.061390-0&mimeType=html&fmt=ahah

References

  1. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  2. Dong X. Z., Cai M. Y. ( 2001 ). Manual of Systematics and Identification of General Bacteria. Beijing:: Science Press;.
    [Google Scholar]
  3. Embley T. M., Stackebrandt E. ( 1994 ). The molecular phylogeny and systematics of the actinomycetes. . Annu Rev Microbiol 48, 257289. [View Article] [PubMed]
    [Google Scholar]
  4. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  5. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  6. Finnerty W. R. ( 1992 ). The biology and genetics of the genus Rhodococcus . . Annu Rev Microbiol 46, 193218. [View Article] [PubMed]
    [Google Scholar]
  7. Fitch W. M. ( 1971 ). Toward defining the course of evolution: minimum change for a specified tree topology. . Syst Zool 20, 406416. [View Article]
    [Google Scholar]
  8. Gillis M., De Ley J., De Cleene M. ( 1970 ). The determination of molecular weight of bacterial genome DNA from renaturation rates. . Eur J Biochem 12, 143153. [View Article] [PubMed]
    [Google Scholar]
  9. Goodfellow M. ( 1989 ). Genus Rhodococcus. . In Bergey’s Manual of Systematic Bacteriology, vol. 4. pp. 23622371. edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams and Wilkins;.
    [Google Scholar]
  10. Goodfellow M., Alderson G. ( 1977 ). The actinomycete-genus Rhodococcus: a home for the “rhodochrous” complex. . J Gen Microbiol 100, 99122. [View Article] [PubMed]
    [Google Scholar]
  11. Goodfellow M., Alderson G., Chun J. ( 1998 ). Rhodococcal systematics: problems and developments. . Antonie van Leeuwenhoek 74, 320. [View Article] [PubMed]
    [Google Scholar]
  12. Gürtler V., Mayall B. C., Seviour R. ( 2004 ). Can whole genome analysis refine the taxonomy of the genus Rhodococcus? . FEMS Microbiol Rev 28, 377403. [View Article] [PubMed]
    [Google Scholar]
  13. Hasegawa T., Takizawa M., Tanida S. ( 1983 ). A rapid analysis for chemical grouping of aerobic actinomycetes. . J Gen Appl Microbiol 29, 319322. [View Article]
    [Google Scholar]
  14. Hayakawa M., Nonomura H. ( 1987 ). Humic acid-vitamin agar, a new medium for selective isolation of soil actinomycetes. . J Ferment Technol 65, 501509. [View Article]
    [Google Scholar]
  15. 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, 184192. [View Article] [PubMed]
    [Google Scholar]
  16. Ivshina I. B., Oborin A. A., Nesterenko O. A., Kasumova S. A. ( 1981 ). Bacteria of the Rhodococcus genus from the ground water of oil-bearing deposits in the Perm region near the Urals. . 50, 709717.
    [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, 111120. [View Article] [PubMed]
    [Google Scholar]
  18. Klatte S., Kroppenstedt R. M., Rainey F. A. ( 1994 ). Rhodococcus opacus sp. nov., an unusual nutritionally versatile Rhodococcus species. . Syst Appl Microbiol 17, 355360. [View Article]
    [Google Scholar]
  19. Kroppenstedt R. M. ( 1982 ). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver-loaded ion exchanger. . J Liq Chromatogr 5, 23592367. [View Article]
    [Google Scholar]
  20. Lechevalier M. P., Lechevalier H. A. ( 1970 ). Chemical composition as criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20, 435443. [View Article]
    [Google Scholar]
  21. Lechevalier M. P., de Bievre C., Lechevalier H. A. ( 1977 ). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. . Biochem Syst Ecol 5, 249260. [View Article]
    [Google Scholar]
  22. Leifson E. ( 1960 ). Atlas of Bacterial Flagellation. London:: Academic Press;.
    [Google Scholar]
  23. Li W. J., Xu P., Schumann P., Zhang Y. Q., Pukall R., Xu L. H., Stackebrandt E., Jiang C. L. ( 2007 ). Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . . Int J Syst Evol Microbiol 57, 14241428. [View Article] [PubMed]
    [Google Scholar]
  24. Loveland-Curtze J., Miteva V. I., Brenchley J. E. ( 2011 ). Evaluation of a new fluorimetric DNA–DNA hybridization method. . Can J Microbiol 57, 250255. [View Article] [PubMed]
    [Google Scholar]
  25. Marmur J. ( 1961 ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. . J Mol Biol 3, 208218. [View Article]
    [Google Scholar]
  26. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109118. [View Article] [PubMed]
    [Google Scholar]
  27. Martínez-Murcia A. J., Rodríguez-Valera F. ( 1994 ). The use of arbitrarily primed PCR (AP-PCR) to develop taxa specific DNA probes of known sequence. . FEMS Microbiol Lett 124, 265269. [View Article] [PubMed]
    [Google Scholar]
  28. Mayilraj S., Krishnamurthi S., Saha P., Saini H. S. ( 2006 ). Rhodococcus kroppenstedtii sp. nov., a novel actinobacterium isolated from a cold desert of the Himalayas, India. . Int J Syst Evol Microbiol 56, 979982. [View Article] [PubMed]
    [Google Scholar]
  29. McMinn E. J., Alderson G., Dodson H. I., Goodfellow M., Ward A. C. ( 2000 ). Genomic and phenomic differentiation of Rhodococcus equi and related strains. . Antonie van Leeuwenhoek 78, 331340. [View Article] [PubMed]
    [Google Scholar]
  30. 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, 159167. [View Article]
    [Google Scholar]
  31. Minnikin D. E., Alshamaony L., Goodfellow M. ( 1975 ). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. . J Gen Microbiol 88, 200204. [View Article] [PubMed]
    [Google Scholar]
  32. 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, 221233. [View Article]
    [Google Scholar]
  33. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal K., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  34. Rainey F. A., Burghardt J., Kroppenstedt R. M., Klatte S., Stackebrandt E. ( 1995 ). Polyphasic evidence for the transfer of Rhodococcus roseus to Rhodococcus rhodochrous . . Int J Syst Bacteriol 45, 101103. [View Article]
    [Google Scholar]
  35. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  36. Sasser M. ( 1990 ). Identification of bacteria by gas chromatography of cellular fatty acids. . USFCC News Lett 20, 16.
    [Google Scholar]
  37. Smibert R. M., Krieg N. R. ( 1994 ). Phenotypic characterization. . In Methods for General and Molecular Bacteriology, pp. 607654. Edited by Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. . Washington, D.C.:: American Society for Microbiology;.
    [Google Scholar]
  38. 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, 479491. [View Article]
    [Google Scholar]
  39. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [View Article] [PubMed]
    [Google Scholar]
  40. 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, 48764882. [View Article] [PubMed]
    [Google Scholar]
  41. Uchida K., Aida K. ( 1977 ). Acyl type of bacterial cell wall: its simple identification by colorimetric method. . J Gen Appl Microbiol 23, 249260. [View Article]
    [Google Scholar]
  42. 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, 463464. [View Article]
    [Google Scholar]
  43. Xu P., Li W. J., Tang S. K., Zhang Y. Q., Chen G. Z., Chen H. H., Xu L. H., Jiang C. L. ( 2005 ). Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. . Int J Syst Evol Microbiol 55, 11491153. [View Article] [PubMed]
    [Google Scholar]
  44. Yassin A. F., Binder C., Schaal K. P. ( 1993 ). Identification of mycobacterial isolates by thin-layer and capillary gas-liquid chromatography under diagnostic routine conditions. . Zentralbl Bakteriol 278, 3448. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.061390-0
Loading
/content/journal/ijsem/10.1099/ijs.0.061390-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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