1887

Abstract

Two actinomycete strains were isolated from within the fynbos-rich area surrounded by the horseracing track at Kenilworth Racecourse in Cape Town, South Africa. Rapid molecular identification indicated that the isolates belonged to the family . Based on 16S rRNA gene sequence analysis, the isolates were identified as members of the genus . Phylogenetic analysis showed that the isolates clustered with each other and were most closely related to DSM 43909. Further 16S rRNA gene sequence analysis using EzTaxon revealed that the isolates are closely related to TT1-11, MC5-1, LK2-10, DSM 43818 and DSM 43868. DNA–DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of both isolates from related species; however, their high DNA–DNA relatedness showed that they belong to the same genomic species. Strain Y22 ( = DSM 45644 = NRRL B-24859) was selected as the type strain to represent this novel species, for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • National Research Foundation (NRF) (Award 2073133)
  • Medical Research Council of South Africa
  • University Research Committee (University of Cape Town)
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2013-03-01
2024-10-12
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References

  1. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. ( 1997 ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25, 33893402. [View Article] [PubMed]
    [Google Scholar]
  2. Atlas R. M. ( 2004 ). Handbook of Microbiological Media, , 3rd edn.. Boca Raton, FL:: CRC Press;. [View Article]
    [Google Scholar]
  3. 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, 22592261. [View Article] [PubMed]
    [Google Scholar]
  4. Cook A. E., Meyers P. R. ( 2003 ). Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S rRNA gene restriction fragment patterns. . Int J Syst Evol Microbiol 53, 19071915. [View Article] [PubMed]
    [Google Scholar]
  5. Cross T. ( 1981 ). The monosporic actinomycetes. . In The Prokaryotes: a Handbook on Habitats, Isolation and Identification of Bacteria, vol. 2, pp. 20912102. Edited by Starr M. P., Stolp H., Trüper H. G., Balows A., Schlegel H. G. . Berlin, Germany:: Springer-Verlag;.
    [Google Scholar]
  6. Euzéby J. P. ( 2012 ). List of prokaryote names with standing in nomenclature. ( http://www.bacterio.cict.fr/)
  7. Everest G. J., Meyers P. R. ( 2008 ). Kribbella hippodromi sp. nov., isolated from soil from a racecourse in South Africa. . Int J Syst Evol Microbiol 58, 443446. [View Article] [PubMed]
    [Google Scholar]
  8. Everest G. J., Meyers P. R. ( 2009 ). The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis . . Antonie van Leeuwenhoek 95, 111. [View Article] [PubMed]
    [Google Scholar]
  9. 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, 224229. [View Article]
    [Google Scholar]
  10. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  11. Garcia L. C., Martínez-Molina E., Trujillo M. E. ( 2010 ). Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum . . Int J Syst Evol Microbiol 60, 331337. [View Article] [PubMed]
    [Google Scholar]
  12. Gevers D., Huys G., Swings J. ( 2001 ). Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. . FEMS Microbiol Lett 205, 3136. [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. Jongrungruangchok S., Tanasupawat S., Kudo T. ( 2008 ). Micromonospora chaiyaphumensis sp. nov., isolated from Thai soils. . Int J Syst Evol Microbiol 58, 924928. [View Article] [PubMed]
    [Google Scholar]
  15. Kasai H., Tamura T., Harayama S. ( 2000 ). Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. . Int J Syst Evol Microbiol 50, 127134. [View Article] [PubMed]
    [Google Scholar]
  16. Kawamoto I. ( 1989 ). Genus Micromonospora Ørskov 1923, 147AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 4, pp. 24422450. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  17. Kawamoto I., Yamamoto M., Nara T. ( 1983 ). Micromonospora olivasterospora sp. nov.. Int J Syst Bacteriol 33, 107112. [View Article]
    [Google Scholar]
  18. Kirby B. M., Meyers P. R. ( 2010 ). Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea . . Int J Syst Evol Microbiol 60, 13281333. [View Article] [PubMed]
    [Google Scholar]
  19. Kirby B. M., Everest G. J., Meyers P. R. ( 2010 ). Phylogenetic analysis of the genus Kribbella based on the gyrB gene – proposal of a gyrB-sequence threshold for recognising new type strains of Kribbella . . Antonie van Leeuwenhoek 97, 131142. [View Article] [PubMed]
    [Google Scholar]
  20. Koch C., Kroppenstedt R. M., Rainey F. A., Stackebrandt E. ( 1996 ). 16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae . . Int J Syst Bacteriol 46, 765768. [View Article] [PubMed]
    [Google Scholar]
  21. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [View Article]
    [Google Scholar]
  22. Kroppenstedt R. M., Mayilraj S., Wink J. M., Kallow W., Schumann P., Secondini C., Stackebrandt E. ( 2005 ). Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.. Syst Appl Microbiol 28, 328339. [View Article] [PubMed]
    [Google Scholar]
  23. le Roes M., Goodwin C. M., Meyers P. R. ( 2008 ). Gordonia lacunae sp. nov., isolated from an estuary. . Syst Appl Microbiol 31, 1723. [View Article] [PubMed]
    [Google Scholar]
  24. Lechevalier M. P., Lechevalier H. ( 1970 ). Chemical composition as a criterion in the classification of aerobic actinomycetes. . Int J Syst Bacteriol 20, 435443. [View Article]
    [Google Scholar]
  25. 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]
  26. 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 quinines and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  27. Nonomura H., Ohara Y. ( 1971 ). Distribution of actinomycetes in soil. VIII. Green spore group of Microtetraspora, its preferential isolation and taxonomic characteristics. . J Ferment Technol 49, 17.
    [Google Scholar]
  28. Ørskov J. ( 1923 ). Investigations into the Morphology of the Ray Fungi. Copenhagen:: Levin and Munksgaard;.
    [Google Scholar]
  29. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  30. Sambrook J., Fritsch E. F., Maniatis T. ( 1989 ). Molecular Cloning: a Laboratory Manual, , 2nd edn.. Cold Spring Harbor, NY:: Cold Spring Harbor Laboratory;.
    [Google Scholar]
  31. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  32. Takahashi K., Nei M. ( 2000 ). Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. . Mol Biol Evol 17, 12511258. [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. Thawai C., Tanasupawat S., Itoh T., Suwanborirux K., Kudo T. ( 2004 ). Micromonospora aurantionigra sp. nov., isolated from a peat swamp forest in Thailand. . Actinomycetologica 18, 814. [View Article]
    [Google Scholar]
  35. Thawai C., Tanasupawat S., Itoh T., Suwanborirux K., Suzuki K., Kudo T. ( 2005 ). Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest. . Int J Syst Evol Microbiol 55, 417422. [View Article] [PubMed]
    [Google Scholar]
  36. Trujillo M. E., Fernández-Molinero C., Velázquez E., Kroppenstedt R. M., Schumann P., Mateos P. F., Martínez-Molina E. ( 2005 ). Micromonospora mirobrigensis sp. nov.. Int J Syst Evol Microbiol 55, 877880. [View Article] [PubMed]
    [Google Scholar]
  37. Trujillo M. E., Kroppenstedt R. M., Schumann P., Carro L., Martínez-Molina E. ( 2006 ). Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia . . Int J Syst Evol Microbiol 56, 23812385. [View Article] [PubMed]
    [Google Scholar]
  38. Wagman G. H., Weinstein M. J. ( 1980 ). Antibiotics from Micromonospora . . Annu Rev Microbiol 34, 537558. [View Article] [PubMed]
    [Google Scholar]
  39. 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]
  40. Williams S. T., Goodfellow M., Alderson G. ( 1989 ). Genus Streptomyces Waksman and Henrici 1943, 339AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 4, pp. 24522492. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  41. 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, 589608. [View Article] [PubMed]
    [Google Scholar]
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