1887

Abstract

A Gram-stain-positive, non-endospore-forming actinobacterium (ARP1) was isolated from the phyllosphere of . On the basis of 16S rRNA gene sequence phylogeny strain ARP1 was placed into the genus and the closest related species were (98.5 % 16S rRNA gene sequence similarity), (98.5 %), (98.3 %) and (98.2 %). Genome-based comparison indicated a clear distinction to the type strains of those species with pairwise average nucleotide identities (ANI) between 76.4–78.4 %. The quinone system of strain ARP1 consisted predominantly of menaquinones MK-9(H), MK-7(H) and MK-8(H), and the polar lipid profile contained the major compound diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol and numerous unidentified lipids. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were Cω7, C C Cω9 and tuberculostearic acid supported the affiliation of strain ARP1 to the genus . Genotypic, physiological and biochemical testing revealed clear differences of strain ARP1 to the most closely related species of the genus . Therefore strain ARP1 represents a novel species of this genus, for which the name sp. nov. is proposed. The type strain is ARP1 (=DSM 46872=LMG 28679).

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2016-11-01
2024-04-20
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References

  1. Altenburger P., Kämpfer P., Makristathis A., Lubitz W., Busse H.-J. 1996; Classification of bacteria isolated from a medieval wall painting. J Biotechnol 47:39–52 [View Article]
    [Google Scholar]
  2. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. 1978; Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148:107–127 [View Article]
    [Google Scholar]
  3. Collins M. D., Goodfellow M., Minnikin D. E. 1982; A survey of the structures of mycolic acids in Corynebacterium and related taxa. J Gen Microbiol 128:129–149 [View Article][PubMed]
    [Google Scholar]
  4. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  5. Felsenstein J. 2005 phylip (phylogeny inference package), version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  6. Frischmann A., Knoll A., Hilbert F., Zasada A. A., Kampfer P., Busse H.-J. 2012; Corynebacterium epidermidicanis sp. nov., isolated from skin of a dog. Int J Syst Evol Microbiol 62:2194–2200 [View Article][PubMed]
    [Google Scholar]
  7. Gerhardt P., Murray R. G. E., Wood W. A., Krieg N. R. (editors) 1994 Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology;
    [Google Scholar]
  8. Goris J., Konstantinidis K. T., Klappenbach J. A., Coenye T., Vandamme P., Tiedje J. M. 2007; DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91 [View Article][PubMed]
    [Google Scholar]
  9. Hasegawa M., Kishino H., Yano T. 1985; Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174 [View Article][PubMed]
    [Google Scholar]
  10. Horn H., Keller A., Hildebrandt U., Kämpfer P., Riederer M., Hentschel U. 2016; Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1. Stand Genomic Sci 11:8 [View Article][PubMed]
    [Google Scholar]
  11. Jones A. L., Payne G. D., Goodfellow M. 2010; Williamsia faeni sp. nov., a novel actinomycete isolated from a hay meadow. Int J Syst Evol Microbiol 60:2548–2551 [View Article][PubMed]
    [Google Scholar]
  12. Jukes T. H., Cantor C. R. 1969; Evolution of the protein molecules. In Mammalian Protein Metabolism21–132 Edited by Munro H. N. New York: Academic Press; [CrossRef]
    [Google Scholar]
  13. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [View Article]
    [Google Scholar]
  14. Kämpfer P., Kroppenstedt R. M. 2004; Pseudonocardia benzenivorans sp. nov. Int J Syst Evol Microbiol 54:749–751 [View Article][PubMed]
    [Google Scholar]
  15. Kämpfer P., Steiof M., Dott W. 1991; Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21:227–251 [View Article][PubMed]
    [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 [View Article][PubMed]
    [Google Scholar]
  17. Kämpfer P., Wellner S., Lohse N., Lodders N., Martin K. 2011; Williamsia phyllosphaerae sp. nov., isolated from the surface of Trifolium repens leaves. Int J Syst Evol Microbiol 61:2702–2705 [View Article][PubMed]
    [Google Scholar]
  18. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  19. Kyrpides N. C., Woyke T., Eisen J. A., Garrity G., Lilburn T. G., Beck B. J., Whitman W. B., Hugenholtz P., Klenk H. P. 2014; Genomic encyclopedia of type strains, phase I: the one thousand microbial genomes (KMG-I) project. Stand Genomic Sci 9:1278–1284 [View Article][PubMed]
    [Google Scholar]
  20. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Buchner A., Lai T., Steppi S., Yadhu K. et al. 2004; ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  21. 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 [View Article][PubMed]
    [Google Scholar]
  22. Pruesse E., Peplies J., Glockner F. O. 2012; SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  23. Richter M., Rossello-Mora R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131 [View Article]
    [Google Scholar]
  24. Sazak A., Sahin N. 2012; Williamsia limnetica sp. nov., isolated from a limnetic lake sediment. Int J Syst Evol Microbiol 62:1414–1418 [View Article][PubMed]
    [Google Scholar]
  25. Stach J. E. M., 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 [View Article][PubMed]
    [Google Scholar]
  26. Stamatakis A. 2006; RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690 [View Article]
    [Google Scholar]
  27. Tindall B. J. 1990a; Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  28. Tindall B. J. 1990b; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  29. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R. 2008; The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250 [View Article][PubMed]
    [Google Scholar]
  30. Yassin A. F., Hupfer H. 2006; Williamsia deligens sp. nov., a novel species of the genus Williamsia isolated from human blood. Int J Syst Evol Microbiol 56:193–197 [CrossRef]
    [Google Scholar]
  31. 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 [View Article][PubMed]
    [Google Scholar]
  32. 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 [View Article][PubMed]
    [Google Scholar]
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