1887

Abstract

Two bacterial strains, designated BT189 and BT664, were isolated from soil sampled in the Republic of Korea. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains BT189 and BT664 belonged to the genus , family (order ). The 16S rRNA genes of the two strains shared a sequence similarity of 93.7 %. The closely related species of strain BT189 were DG7B (97.1 % 16S rRNA similarity) and DG7A (96.7 %). The closest related species to strain BT664 were DG5B (95.3 %) and MIMtkLc17 (95.2 %). The genome sizes of strains BT189 and BT664 were 5 285 287 and 5 475 357 bp, respectively. The genomic DNA G+C contents of strains BT189 and BT664 were 63.2 and 59.3 mol%, respectively. The main fatty acids of strain BT189 were iso-C, anteiso-C and summed feature 3 (C 6/C 7), and those of strain BT664 were iso-C, C 5 and summed feature 3 (C 6/C7). The main polar lipid in both strains was phosphatidylethanolamine and the predominant respiratory quinone was MK-7, supporting the affiliation of these strains with the genus . Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, BT189 (=KCTC 72341=NBRC 114843) and BT664 (KACC 21967=NBRC 114856), are proposed.

Funding
This study was supported by the:
  • Seoul Women’s University (Award 2022)
    • Principle Award Recipient: NotApplicable
  • National Institute of Biological Resources (Award NIBR202002108)
    • Principle Award Recipient: NotApplicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005267
2022-03-01
2024-12-06
Loading full text...

Full text loading...

References

  1. Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B et al. Hymenobacter roseosalivarius gen. nov., sp. nov. from continental antartica soils and sandstone: bacteria of the cytophaga/flavobacterium/bacteroides line of phylogenetic descent. Syst Appl Microbiol 1998; 21:374–383
    [Google Scholar]
  2. Buczolits S, Denner EBM, Kämpfer P, Busse H-J. Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 2006; 56:2723 [View Article]
    [Google Scholar]
  3. Han L, Wu S-J, Qin C-Y, Zhu Y-H, Lu Z-Q et al. Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie van Leeuwenhoek 2014; 105:971–978 [View Article] [PubMed]
    [Google Scholar]
  4. Reddy GS. Phylogenetic analyses of the genus Hymenobacter and description of Siccationidurans gen. nov., and Parahymenobacter gen. nov. J Phylogen Evolution Biol 2013; 01:122 [View Article]
    [Google Scholar]
  5. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  6. Sedláček I, Pantůček R, Zeman M, Holochová P, Šedo O et al. Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica. Int J Syst Evol Microbiol 2020; 70:6364–6372 [View Article] [PubMed]
    [Google Scholar]
  7. Dahal RH, Chaudhary DK, Kim DU, Kim J. Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station. Int J Syst Evol Microbiol 2020; 70:4890–4896 [View Article] [PubMed]
    [Google Scholar]
  8. Jiang F, Danzeng W, Zhang Y, Zhang Y, Jiang L et al. Hymenobacter rubripertinctus sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2018; 68:663–668 [View Article] [PubMed]
    [Google Scholar]
  9. Maeng S, Kim MK, Subramani G. Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island. Antonie van Leeuwenhoek 2020; 113:553–561 [View Article] [PubMed]
    [Google Scholar]
  10. Sedláček I, Pantůček R, Králová S, Mašlaňová I, Holochová P et al. Hymenobacter amundsenii sp. nov. resistant to ultraviolet radiation, isolated from regoliths in Antarctica. Syst Appl Microbiol 2019; 42:284–290 [View Article] [PubMed]
    [Google Scholar]
  11. Kim MK, Kang MS, Srinivasan S, Lee DH, Lee SY et al. Complete genome sequence of Hymenobacter sedentarius DG5BT, a bacterium resistant to gamma radiation. Mol Cell Toxicol 2017; 13:199–205 [View Article]
    [Google Scholar]
  12. Liang Y, Tang K, Wang Y, Yuan B, Tan F et al. Hymenobacter crusticola sp. nov., isolated from biological soil crust. Int J Syst Evol Microbiol 2019; 69:547–551 [View Article] [PubMed]
    [Google Scholar]
  13. Sun J, Xing M, Wang W, Dai F, Liu J et al. Hymenobacter profundi sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2018; 68:947–950 [View Article] [PubMed]
    [Google Scholar]
  14. Kang H, Cha I, Kim H, Joh K. Hymenobacter aquatilis sp. nov., isolated from a mesotrophic artificial lake. Int J Syst Evol Microbiol 2018; 68:2036–2041 [View Article] [PubMed]
    [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  21. 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]
  22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  24. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
    [Google Scholar]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  26. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421 [View Article] [PubMed]
    [Google Scholar]
  30. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  31. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005; 102:2567–2572 [View Article] [PubMed]
    [Google Scholar]
  32. Cox MM, Battista JR. Deinococcus radiodurans - the consummate survivor. Nat Rev Microbiol 2005; 3:882–892 [View Article] [PubMed]
    [Google Scholar]
  33. 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]
  34. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  35. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005267
Loading
/content/journal/ijsem/10.1099/ijsem.0.005267
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error