sp. nov., an actinobacterium isolated from lichen Free

Abstract

A Gram-stain-positive, yellow-pigmented, catalase-positive and oxidase-negative, strictly aerobic actinobacterium, designated strain YIM 131853, was isolated from lichen collected from the South Bank of the Baltic Sea. The novel strain was non-spore-forming, short rod-shaped and motile with a single polar flagellum. The strain could grow at 4–37 °C (optimum, 28 °C), at pH 4.0–12.0 (pH 6.0) and at 0–3 % (w/v) NaCl (1 %). The DNA G+C content of strain YIM 131853 based on the draft genome sequence was 68.3 mol%. Predominant cellular fatty acids (>10 %) were identified as anteiso-C, anteiso-C and iso-C. The polar lipid profile included diphosphatidylglycerol, dimannosyldiacylglycerol, three unknown glycolipids, two unknown phospholipids and one unknown lipid. Strain YIM 131853 had 2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, galactose and glucose as whole-cell sugars, and MK-10, MK-14, MK-13 and MK-12 as the major menaquinones. Although strain YIM 131853 exhibited a highest 16S rRNA gene sequence similarity (96.6 %) to NBRC 109360, phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a tight lineage with NBRC 108725 (96.5 % 16S rRNA gene sequence similarity), which was the only species of genus . Based on the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain YIM 131853 should belong to the genus and represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM 131853 (=CGMCC 4.7565=NBRC 113605).

Funding
This study was supported by the:
  • Major research project of Guangxi for science and technology (Award AA18242026)
    • Principle Award Recipient: Yi Jiang
  • National Natural Science Foundation of China (Award 31460005)
    • Principle Award Recipient: Yi Jiang
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2019-11-18
2024-03-28
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References

  1. Weon HY, Kim SJ, Jang YH, Hamada M, Tamura T et al. Naasia aerilata gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from air. Int J Syst Evol Microbiol 2013; 63:2436–2441 [View Article]
    [Google Scholar]
  2. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment 1987; 65:501–509 [View Article]
    [Google Scholar]
  3. Jiang Y, Tang SK, Wiese J, Xu LH, Imhoff JF et al. Streptomyces hainanensis sp. nov., a novel member of the genus Streptomyces . Int J Syst Evol Microbiol 2007; 57:2694–2698 [View Article]
    [Google Scholar]
  4. Liu C, Jiang Y, Wang X, Chen D, Chen X et al. Diversity, antimicrobial activity, and biosynthetic potential of cultivable actinomycetes associated with lichen symbiosis. Microb Ecol 2017; 74:570–584 [View Article]
    [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]
    [Google Scholar]
  6. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 1985; 82:6955–6959 [View Article]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article]
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [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]
    [Google Scholar]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  12. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article]
    [Google Scholar]
  13. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  14. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article]
    [Google Scholar]
  15. Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article]
    [Google Scholar]
  16. Doetsch RN. Determinative methods of light microscopy. In Gerhardt P. editor Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981 pp 21–33
    [Google Scholar]
  17. 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 [View Article]
    [Google Scholar]
  18. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington, DC: American Society for Microbiology; 2007
    [Google Scholar]
  19. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477
    [Google Scholar]
  20. Tang SK, Wang Y, Chen Y, Lou K, Cao LL et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article]
    [Google Scholar]
  21. 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 Microbiol Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  23. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
    [Google Scholar]
  24. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  25. Nakagawa Y, Yamasato K. Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. J Gen Microbiol 1993; 139:1155–1161 [View Article]
    [Google Scholar]
  26. Kim SJ, Lee SS. Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae . Int J Syst Evol Microbiol 2011; 61:155–159 [View Article]
    [Google Scholar]
  27. FN L, Tuo L, Lee MY et al. Amnibacterium endophyticum sp. nov. an endophytic actinobacterium isolated from Aegiceras corniculatum . Int J Syst Evol Microbiol 2018; 68:
    [Google Scholar]
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