1887

Abstract

In phylogenetic analyses of the genus using 16S rRNA gene sequences, NRRL B-1811 forms a cluster with five other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these other species, including NRRL B-1685, NRRL B-2465, NRRL B-1335 and NRRL B-12378 are quite similar. This cluster is of particular taxonomic interest because is the type species of the genus . The related strains were subjected to multilocus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes , , , and and confirmation of previously reported phenotypic characteristics. The five strains formed a coherent cluster supported by a 100 % bootstrap value in phylogenetic trees generated from sequence alignments prepared by concatenating the sequences of the housekeeping genes, and identical tree topology was observed using various different tree-making algorithms. Moreover, all but one strain, NRRL B-2465, exhibited identical sequences for all of the five housekeeping gene loci sequenced, but NRRL B-2465 still exhibited an MLSA evolutionary distance of 0.005 from the other strains, a value that is lower than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. These data support a proposal to reclassify , , and as later heterotypic synonyms of with NRRL B-1811 as the type strain. The MLSA sequence database also demonstrated utility for quickly and conclusively confirming that numerous strains within the ARS Culture Collection had been previously misidentified as subspecies of and that should be redescribed as a novel species, sp. nov., with the type strain NRRL B-24287.

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2014-03-01
2024-04-26
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References

  1. Darriba D., Taboada G. L., Doallo R., Posada D. ( 2012 ). jModelTest 2: more models, new heuristics and parallel computing. . Nat Methods 9, 772. [View Article] [PubMed]
    [Google Scholar]
  2. Doroghazi J. R., Buckley D. H. ( 2010 ). Widespread homologous recombination within and between Streptomyces species. . ISME J 4, 11361143. [View Article] [PubMed]
    [Google Scholar]
  3. Edgar R. C. ( 2004 ). muscle: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32, 17921797. [View Article] [PubMed]
    [Google Scholar]
  4. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  5. Guindon S., Gascuel O. ( 2003 ). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52, 696704. [View Article] [PubMed]
    [Google Scholar]
  6. Guo Y., Zheng W., Rong X., Huang Y. ( 2008 ). A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. . Int J Syst Evol Microbiol 58, 149159. [View Article] [PubMed]
    [Google Scholar]
  7. Jolley K. A., Maiden M. C. ( 2010 ). BIGSdb: Scalable analysis of bacterial genome variation at the population level. . BMC Bioinformatics 11, 595. [View Article] [PubMed]
    [Google Scholar]
  8. Kämpfer P. ( 2012 ). Genus Streptomyces Waksman and Henrici 1943, 339AL emend. Witt and Stackebrandt 1990, 370, emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen, 1992, 159. . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp. 14551767. Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M., Suzuki K. E., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  9. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  10. 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]
  11. Labeda D. P. ( 1992 ). DNA-DNA hybridization in the systematics of Streptomyces . . Gene 115, 249253. [View Article] [PubMed]
    [Google Scholar]
  12. Labeda D. P. ( 1993 ). DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. . Int J Syst Evol Microbiol 43, 822825. [View Article]
    [Google Scholar]
  13. Labeda D. P. ( 1998 ). DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. . Int J Syst Evol Microbiol 48, 829832. [View Article]
    [Google Scholar]
  14. Labeda D. P. ( 2011 ). Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces . . Int J Syst Evol Microbiol 61, 25252531. [View Article] [PubMed]
    [Google Scholar]
  15. Labeda D. P., Lyons A. J. ( 1991a ). Deoxyribonucleic acid relatedness among species of the “Streptomyces cyaneus” cluster. . Syst Appl Microbiol 14, 158164. [View Article]
    [Google Scholar]
  16. Labeda D. P., Lyons A. J. ( 1991b ). The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: Emendation of the descriptions of S. violaceusniger and Streptomyces hygroscopicus . . Int J Syst Bacteriol 41, 398401. [View Article]
    [Google Scholar]
  17. Labeda D. P., Goodfellow M., Brown R., Ward A. C., Lanoot B., Vanncanneyt M., Swings J., Kim S. B., Liu Z. & other authors ( 2012 ). Phylogenetic study of the species within the family Streptomycetaceae . . Antonie van Leeuwenhoek 101, 73104. [View Article] [PubMed]
    [Google Scholar]
  18. Lanoot B., Vancanneyt M., Van Schoor A., Liu Z., Swings J. ( 2005 ). Reclassification of Streptomyces nigrifaciens as a later synonym of Streptomyces flavovirens; Streptomyces citreofluorescens, Streptomyces chrysomallus subsp. chrysomallus and Streptomyces fluorescens as later synonyms of Streptomyces anulatus; Streptomyces chibaensis as a later synonym of Streptomyces corchorusii; Streptomyces flaviscleroticus as a later synonym of Streptomyces minutiscleroticus; and Streptomyces lipmanii, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces willmorei as later synonyms of Streptomyces microflavus . . Int J Syst Evol Microbiol 55, 729731. [View Article] [PubMed]
    [Google Scholar]
  19. Nagatsu J., Anzai K., Suzuki S. ( 1962 ). Pathocidin, a new antifungal antibiotic; II. Taxonomic studies on the pathocidin-producing organism Streptomyces albus var. pathocidicus . . J Antibiot (Tokyo) 15, 103106.
    [Google Scholar]
  20. Nei M., Kumar S. ( 2000 ). Molecular Evolution and Phylogenetics. New York:: Oxford University Press;.
    [Google Scholar]
  21. Rong X., Huang Y. ( 2010 ). Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. . Int J Syst Evol Microbiol 60, 696703. [View Article] [PubMed]
    [Google Scholar]
  22. Rong X., Huang Y. ( 2012 ). Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. . Syst Appl Microbiol 35, 718. [View Article] [PubMed]
    [Google Scholar]
  23. Rong X., Guo Y., Huang Y. ( 2009 ). Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens . . Syst Appl Microbiol 32, 314322. [View Article] [PubMed]
    [Google Scholar]
  24. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425. [PubMed]
    [Google Scholar]
  25. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  26. Tamura K., Nei M. ( 1993 ). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. . Mol Biol Evol 10, 512526. [PubMed]
    [Google Scholar]
  27. Tamura T., Ishida Y., Otoguro M., Hatano K., Suzuki K. ( 2008 ). Reclassification of Streptomyces flavidofuscus as a synonym of Nocardiopsis dassonvillei subsp. dassonvillei . . Int J Syst Evol Microbiol 58, 23212323. [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. 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, 17431813. [PubMed]
    [Google Scholar]
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