1887

Abstract

Previous phylogenetic analysis of species of the genus Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100 % bootstrap value) containing eight species that exhibited very similar gross morphology in producing open looped (RetinaculumApertum) to spiral (Spira) chains of spiny- to hairysurfaced, dark green spores on their aerial mycelium. The type strains of the species in this clade, specifically Streptomyces bambergiensis, Streptomyces cyanoalbus, Streptomyces emeiensis, Streptomyces hirsutus, Streptomyces prasinopilosus , , , , and Streptomyces prasinus , were subjected to multi-locus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB to clarify their taxonomic status. The type strains of several recently described species with similar gross morphology, including Streptomyces chlorus, Streptomyces herbaceus, Streptomyces incanus, Streptomyces pratens , , , and Streptomyces viridis , were also studied along with six unidentified green-spored Streptomyces strains from the ARS Culture Collection. The MLSAs suggest that three of the species under study ( S. bambergiensis, S. cyanoalbus , and S. emeiensis ) represent synonyms of other previously described species ( S. prasinus, S. hirsutus , and S. prasinopilosus , respectively). These relationships were confirmed through determination of in silico DNA–DNA hybridization estimates based on draft genome sequences. The five recently described species appear to be phylogenetically distinct but the unidentified strains from the ARS Culture Collection could be identified as representatives of S. hirsutus, S. prasinopilosus , or S. prasinus .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001017
2016-06-10
2019-10-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/6/2444.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001017&mimeType=html&fmt=ahah

References

  1. Auch A. F. , Klenk H. P. , Göker M. . ( 2010a;). Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. . Stand Genomic Sci 2: 142–148. [CrossRef] [PubMed]
    [Google Scholar]
  2. Auch A. F. , von Jan M. , Klenk H. P. , Göker M. . ( 2010b;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. . Stand Genomic Sci 2: 117–134. [CrossRef] [PubMed]
    [Google Scholar]
  3. Darriba D. , Taboada G. L. , Doallo R. , Posada D. . ( 2012;). jModelTest 2: more models, new heuristics and parallel computing. . Nat Methods 9: 772–772. [CrossRef] [PubMed]
    [Google Scholar]
  4. Edgar R. C. . ( 2004;). MUSCLE: multiple sequence alignment with high accuracy and high throughput. . Nucleic Acids Res 32: 1792–1797. [CrossRef] [PubMed]
    [Google Scholar]
  5. Felsenstein J. . ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39: 783–791.[CrossRef]
    [Google Scholar]
  6. Guindon S. , Gascuel O. . ( 2003;). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. . Syst Biol 52: 696–704.[PubMed] [CrossRef]
    [Google Scholar]
  7. 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: 149–159. [CrossRef]
    [Google Scholar]
  8. Jolley K. A. , Maiden M. C. . ( 2010;). Bigsdb: Scalable analysis of bacterial genome variation at the population level. . BMC Bioinformatics 11:. [CrossRef] [PubMed]
    [Google Scholar]
  9. Jukes T. H. , Cantor C. R. . ( 1969;). Evolution of protein molecules. . In Mammalian Protein Metabolism. pp. 21–132. Edited by Munro H. N . New York:: Academic Press;.[CrossRef]
    [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: 111–120.[PubMed] [CrossRef]
    [Google Scholar]
  11. 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. , 2.nd edn,vol. 5 pp. 1455–1767. Edited by Goodfellow M. , Kämpfer P. , Busse H.-J. , Trujillo M. , Suzuki K. E. , Ludwig W. , Whitman W. B. . New York:: Springer;.[CrossRef]
    [Google Scholar]
  12. Labeda D. P. . ( 2011;). Multilocus sequence analysis of phytopathogenic species of the genus streptomyces. . Int J Syst Evol Microbiol 61: 2525–2531. [CrossRef] [PubMed]
    [Google Scholar]
  13. 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: 73–104. [CrossRef] [PubMed]
    [Google Scholar]
  14. Labeda D. P. , Doroghazi J. R. , Ju K. S. , Metcalf W. W. . ( 2014;). Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. . Int J Syst Evol Microbiol 64: 894–900. [CrossRef] [PubMed]
    [Google Scholar]
  15. Lapage S. P. , Sneath P. H. A. , Lessel E. F. , Skerman V. B. D. , Seeliger H. P. R. , Clark W. A. . ( 1992;). International Code of Nomenclature of Bacteria: Bacteriological Code, 1990 Revision. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  16. Meier-Kolthoff J. P. , Auch J. P. , Klenk J. P. , Göker J. P. . ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. . BMC Bioinformatics 14: 60. [CrossRef] [PubMed]
    [Google Scholar]
  17. Nei M. , Kumar S. . ( 2000;). Molecular Evolution and Phylogenetics. New York:: Oxford University Press;.
    [Google Scholar]
  18. 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: 314–322. [CrossRef] [PubMed]
    [Google Scholar]
  19. 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: 696–703. [CrossRef] [PubMed]
    [Google Scholar]
  20. 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: 7–18. [CrossRef] [PubMed]
    [Google Scholar]
  21. 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]
  22. 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: 512–526.[PubMed]
    [Google Scholar]
  23. Tamura K. , Stecher G. , Peterson D. , Filipski A. , Kumar S. . ( 2013;). MEGA6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30: 2725–2729. [CrossRef] [PubMed]
    [Google Scholar]
  24. Williams S. T. , Goodfellow M. , Alderson G. , Wellington E. M. , Sneath P. H. , Sackin M. J. . ( 1983;). Numerical classification of Streptomyces and related genera. . J Gen Microbiol 129: 1743–1813. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001017
Loading
/content/journal/ijsem/10.1099/ijsem.0.001017
Loading

Data & Media loading...

Supplements

Supplementary File 1



PDF

Most Cited This Month

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