1887

Abstract

A novel actinobacterium, designated LHW52908, was isolated from a marine sponge, , collected in the South China Sea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LHW52908 was member of the family , with highest similarities to DSM 43160 (97.7 %), CF6 (97.6 %) and B12 (97.5 %). Multilocus sequence analysis confirmed that the strain should be a member of genus . Chemotaxonomic characteristics confirmed the genus-level affiliation of strain LHW52908. Based on phylogenetic data, average nucleotide identity and digital DNA–DNA hybridization results, strain LHW52908 could be distinguished from its closest neighbours, representing a novel species of the genus , for which the name sp. nov. is proposed, with the type strain LHW52908 (=DSM 106570=CCTCC AA 2018014).

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2019-10-01
2020-01-18
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References

  1. Normand P. Geodermatophilaceae fam. nov., a formal description. Int J Syst Evol Microbiol 2006;56:2277–2278 [CrossRef][PubMed]
    [Google Scholar]
  2. Geodermatophilus LGM. a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 1968;96:1848–1858
    [Google Scholar]
  3. Zhi XY, Li WJ, Stackebrandt E. 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 2009;59:589–608 [CrossRef][PubMed]
    [Google Scholar]
  4. Montero-Calasanz MDC, Meier-Kolthoff JP, Zhang DF, Yaramis A, Rohde M et al. Genome-scale data call for a taxonomic rearrangement of Geodermatophilaceae. Front Microbiol 2017;8:2501 [CrossRef][PubMed]
    [Google Scholar]
  5. Gtari M, Essoussi I, Maaoui R, Sghaier H, Boujmil R et al. Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species. FEMS Microbiol Ecol 2012;80:566–577 [CrossRef][PubMed]
    [Google Scholar]
  6. Castro JF, Nouioui I, Sangal V, Trujillo ME, Montero-Calasanz MDC et al. Geodermatophilus chilensis sp. nov., from soil of the Yungay core-region of the Atacama Desert, Chile. Syst Appl Microbiol 2018;41:427–436 [CrossRef][PubMed]
    [Google Scholar]
  7. Kim BY, Stach JE, Weon HY, Kwon SW, Goodfellow M. Dactylosporangium luridum sp. nov., Dactylosporangium luteum sp. nov. and Dactylosporangium salmoneum sp. nov., nom. rev., isolated from soil. Int J Syst Evol Microbiol 2010;60:1813–1823 [CrossRef][PubMed]
    [Google Scholar]
  8. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340
    [Google Scholar]
  9. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949;57:141–146[PubMed]
    [Google Scholar]
  10. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  11. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  12. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005;55:1149–1153 [CrossRef][PubMed]
    [Google Scholar]
  13. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
    [Google Scholar]
  14. Williams ST, Cross T. Actinomycetes. In Booth C. (editor) Methods in Microbiologyvol. 4, 270 London: Academic Press; 1971; pp.295–334
    [Google Scholar]
  15. Teather RM, Wood PJ. Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 1982;43:777–780[PubMed]
    [Google Scholar]
  16. Guo L, Tuo L, Habden X, Zhang Y, Liu J et al. Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 2015;65:206–213 [CrossRef][PubMed]
    [Google Scholar]
  17. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983;129:1743–1813 [CrossRef][PubMed]
    [Google Scholar]
  18. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991;21:227–251 [CrossRef][PubMed]
    [Google Scholar]
  19. Lechevalier MP, Lechevalier HA. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy, Special Publication 6 Arlington, VA: Society of Industrial Microbiology; 1980; pp.227–291
    [Google Scholar]
  20. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2:233–241
    [Google Scholar]
  21. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  22. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 1995;11:217–218[PubMed]
    [Google Scholar]
  23. Nakajima Y, Kitpreechavanich V, Suzuki K, Kudo T. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil. Int J Syst Bacteriol 1999;49 Pt 4:1761–1767 [CrossRef][PubMed]
    [Google Scholar]
  24. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67:1613–1617 [CrossRef][PubMed]
    [Google Scholar]
  25. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015;31:587–589 [CrossRef][PubMed]
    [Google Scholar]
  26. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5:113 [CrossRef][PubMed]
    [Google Scholar]
  27. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger Datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  28. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376[PubMed]
    [Google Scholar]
  30. Kluge AG, Farris FS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1–32
    [Google Scholar]
  31. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  32. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  33. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013;195:413–418 [CrossRef][PubMed]
    [Google Scholar]
  34. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014;64:352–356 [CrossRef][PubMed]
    [Google Scholar]
  35. Guo Y, Zheng W, Rong X, Huang Y. A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 2008;58:149–159 [CrossRef][PubMed]
    [Google Scholar]
  36. Wayne L, Brenner D, Colwell R, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology: Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464
    [Google Scholar]
  37. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  38. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
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