1887

Abstract

A novel Gram-stain-positive, aerobic, non-motile actinobacterium, designated GY0556, was isolated from deep-sea sediment collected from the western Pacific Ocean at a depth of 7118 m. Phylogenetic analysis based on 16S rRNA gene sequences revealed that this strain belongs to the genus , being most closely related to IMSNU 22140 (97.6 % similarity), DSM 44248 (97.6 %) and Y-16303 (97.6 %); similarity to other type strains of the genus was less than 97.5 %. Strain GY0556 contained MK-8(H) as the predominant menaquinone and iso-C and iso H-C as the major fatty acids. The polar lipids detected in strain GY0556 were phosphatidylcholine, phosphatidylinositol, one unknown glycolipid, one unknown phospholipid and two unknown lipids. The whole organism hydrolysates mainly consisted of -diaminopimelic acid, xylose, galactose and arabinose. The DNA G+C content of strain GY0556 was 76.9 mol%. The results of DNA–DNA hybridizations and phylogenetic analysis, together with the phenotypic and biochemical tests, allowed the differentiation of strain GY0556 from established members of the genus . Therefore, it is proposed that strain GY0556 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is GY0556 (=MCCC 1A10574=KCTC 39641).

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2017-06-01
2024-03-29
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References

  1. Henssen A. Morphology and system of thermophilic actinomycetes. Arch Mikrobiol 1957; 26:373–414[PubMed] [CrossRef]
    [Google Scholar]
  2. Liu ZP, Wu JF, Liu ZH, Liu SJ. Pseudonocardia ammonioxydans sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2006; 56:555–558 [View Article][PubMed]
    [Google Scholar]
  3. Tian XP, Long LJ, Li SM, Zhang J, Xu Y et al. Pseudonocardia antitumoralis sp. nov., a deoxynyboquinone-producing actinomycete isolated from a deep-sea sediment. Int J Syst Evol Microbiol 2013; 63:893–899 [View Article][PubMed]
    [Google Scholar]
  4. Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM et al. Pseudonocardia sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2014; 64:745–750 [View Article][PubMed]
    [Google Scholar]
  5. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article][PubMed]
    [Google Scholar]
  6. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  7. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  8. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
    [Google Scholar]
  9. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
    [Google Scholar]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  12. Cerny G. Studies on the aminopeptidase test for the distinction of gram-negative from gram-positive bacteria. Appl Microbiol Biotechnol 1978; 5:113–122 [View Article]
    [Google Scholar]
  13. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960 [CrossRef]
    [Google Scholar]
  14. Ruan JS, Huang Y. The classified methods of actinobacteria. In Rapid Identification and Systematics of Actinobacteria Beijing: Science Press; 2011 pp. 72–77
    [Google Scholar]
  15. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note No. 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  16. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microb Meth 1984; 2:233–241 [View Article]
    [Google Scholar]
  17. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  18. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  19. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
    [Google Scholar]
  20. Kaiser P, Geyer R, Surmann P, Fuhrmann H. LC-MS method for screening unknown microbial carotenoids and isoprenoid quinones. J Microbiol Methods 2012; 88:28–34 [View Article][PubMed]
    [Google Scholar]
  21. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic-acid by high-performance liquid-chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  22. Nie GX, Ming H, Wei DQ, Zhou EM, Tang X et al. Pseudonocardia yuanmoensis sp. nov., a novel actinobacterium isolated from soil in Yunnan, south-west China. Antonie van Leeuwenhoek 2012; 101:753–760 [View Article][PubMed]
    [Google Scholar]
  23. Warwick S, Bowen T, Mcveigh H, Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 1994; 44:293–299 [View Article][PubMed]
    [Google Scholar]
  24. Loveland-Curtze J, Miteva VI, Brenchley JE. Evaluation of a new fluorimetric DNA-DNA hybridization method. Can J Microbiol 2011; 57:250–255 [View Article][PubMed]
    [Google Scholar]
  25. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc-committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  26. Lechevalier MP, Prauser H, Labeda DP, Ruan JS. Two New Genera of Nocardioform Actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Evol Microbiol 1986; 36:29–37 [View Article]
    [Google Scholar]
  27. Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf K. Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Evol Microbiol 1998; 48:441–449 [View Article]
    [Google Scholar]
  28. Huang Y, Wang L, Lu Z, Hong L, Liu Z et al. Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov. Int J Syst Evol Microbiol 2002; 52:977–982 [View Article][PubMed]
    [Google Scholar]
  29. Lee SB, Strand SE, Stensel HD, Herwig RP. Pseudonocardia chloroethenivorans sp. nov., a chloroethene-degrading actinomycete. Int J Syst Evol Microbiol 2004; 54:131–139 [View Article][PubMed]
    [Google Scholar]
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