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Abstract

A novel actinobacterial strain, SB3-45, was isolated from soil of rhizosphere, Jaecheon-si, Chungcheongbuk-do, Republic of Korea. Strain SB3-45, was Gram-stain-positive, aerobic and coccoid to short rod-shaped bacterium. Growth occurred at 4–37 °C (optimum 28 °C), pH 5–8 (optimum pH 7) and 0–2.5 % NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SB3-45 belonged to the genus and was closely related to OS-21 (96.2%) and Gsoil 616 (95.9%). -DAP as the diamino acid in the peptidoglycan and the menaquinone MK-8(H) as the predominant isoprenoid quinone were detected. The polar lipids of strain SB3-45 were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The major cellular fatty acids (>5%) of strain SB3-45 were iso-C, C ω9c and C. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-45 represents a novel species of the genus for which the name sp.nov. is proposed. The type strain is SB3-45 (=KCTC 49133=NBRC 114107).

Funding
This study was supported by the:
  • Semyung University
    • Principle Award Recipient: YongKook Shin
  • Korea Research Institute of Bioscience and Biotechnology
    • Principle Award Recipient: Jung-SookLee
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2021-01-20
2021-10-24
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References

  1. Lee H, Kim MH, Choi YY, Hong J, Yang WM. Effects of Cynanchum wilfordii on osteoporosis with inhibition of bone resorption and induction of bone formation. Mol Med Rep 2018; 17:3758–3762 [View Article][PubMed]
    [Google Scholar]
  2. Yoon M-Y, Choi NH, Min BS, Choi GJ, Choi YH et al. Potent in vivo antifungal activity against powdery mildews of pregnane glycosides from the roots of Cynanchum wilfordii. J Agric Food Chem 2011; 59:12210–12216 [View Article][PubMed]
    [Google Scholar]
  3. Nocardioides PH. A new genus of the order Actinomycetales. Int J Syst Bacteriol 1976; 26:58–65
    [Google Scholar]
  4. O'Donnell AG, Goodfellow M, Minnikin DE. Lipids in the classification of Nocardioides: reclassification of Arthrobacter simplex (Jensen) Lochhead in the genus Nocardioides (Prauser) emend. O'Donnell et al. as Nocardioides simplex comb. nov. Arch Microbiol 1982; 133:323–329 [View Article][PubMed]
    [Google Scholar]
  5. Urzì C, Salamone P, Schumann P, Stackebrandt E. Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 2000; 50 Pt 2:529–536 [View Article][PubMed]
    [Google Scholar]
  6. Zhang J-Y, Liu X-Y, Liu S-J. Nocardioides terrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2009; 59:2444–2448 [View Article][PubMed]
    [Google Scholar]
  7. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592 [View Article][PubMed]
    [Google Scholar]
  8. Xu H, Zhang S, Cheng J, Asem MD, Zhang M-Y et al. Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L. Int J Syst Evol Microbiol 2016; 66:2013–2018 [View Article][PubMed]
    [Google Scholar]
  9. Qu J-H, Li X-D, Li H-F. Nocardioides taihuensis sp. nov., isolated from fresh water lake sediment. Int J Syst Evol Microbiol 2017; 67:3535–3539 [View Article][PubMed]
    [Google Scholar]
  10. Chou J-H, Cho N-T, Arun AB, Young C-C, Chen W-M. Nocardioides fonticola sp. nov., a novel actinomycete isolated from spring water. Int J Syst Evol Microbiol 2008; 58:1864–1868 [View Article][PubMed]
    [Google Scholar]
  11. Dastager SG, Lee J-C, Ju Y-J, Park D-J, Kim C-J. Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea. Antonie van Leeuwenhoek 2008; 93:401–406 [View Article][PubMed]
    [Google Scholar]
  12. Dastager SG, Lee J-C, Ju Y-J, Park D-J, Kim C-J. Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea. Int J Syst Evol Microbiol 2008; 58:2292–2296 [View Article][PubMed]
    [Google Scholar]
  13. Yoon S-H, Ha S-M, 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 [View Article][PubMed]
    [Google Scholar]
  14. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  18. Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Mol Biol Evol 1992; 9:678–687 [View Article][PubMed]
    [Google Scholar]
  19. 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][PubMed]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  21. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  22. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  23. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  24. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  25. Gomori G. Preparation of buffers for use in enzyme studies. Methods Enzymol 1955; 1:138–146
    [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  27. Komagata K, SuzuKi K-I. Lipid and cell-wall analusis on bacterial systematics. In Colwell RR, Grigorova R. (editors) Methods in Microbiology 19 London: Academic Press; 1987 pp 177–182
    [Google Scholar]
  28. 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]
  29. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
    [Google Scholar]
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