1887

Abstract

A Gram-stain-negative, motile by gliding, rod-shaped, aerobic bacterium, designated 15J6-3T6, was isolated from a soil sample collected from Jeju Island, South Korea, and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 15J6-3T6 belongs to the family Cytophagaceae and is related to Larkinella harenae 15J9-9 (93.9 % similarity), Larkinella arboricola Z0532 (93.6 %), Larkinella bovis M2TB15 (93.3 %), and Larkinella insperata LMG 22510 (93.3 %). The DNA G+C content of strain 15J6-3T6 was 50.6 mol%. The detection of phosphatidylethanolamine and an unidentified polar lipid as major polar lipids, menaquinone-7 as the predominant quinone, and C16 : 1ω5c, iso-C15 : 0, and iso-C17 : 0 3-OH as the major fatty acids also supports the affiliation of the isolate to the genus Larkinella . Based on its phenotypic properties and phylogenetic distinctiveness, we propose that strain 15J6-3T6 should be classified in the genus Larkinella as a representative of a novel species, for which the name Larkinella knui sp. nov. is proposed. The type strain is 15J6-3T6 (=KCTC 42998=JCM 31989)

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002550
2018-01-04
2019-10-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/2/582.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002550&mimeType=html&fmt=ahah

References

  1. Vancanneyt M, Nedashkovskaya OI, Snauwaert C, Mortier S, Vandemeulebroecke K et al. Larkinella insperata gen. nov., sp. nov., a bacterium of the phylum 'Bacteroidetes' isolated from water of a steam generator. Int J Syst Evol Microbiol 2006; 56: 237– 241 [CrossRef] [PubMed]
    [Google Scholar]
  2. Anandham R, Kwon SW, Weon HY, Kim SJ, Kim YS et al. Larkinella bovis sp. nov., isolated from fermented bovine products, and emended descriptions of the genus Larkinella and of Larkinella insperata Vancanneyt et al. 2006. Int J Syst Evol Microbiol 2011; 61: 30– 34 [CrossRef] [PubMed]
    [Google Scholar]
  3. Park SJ, Lee JJ, Lee SY, Lee DS, Kim MK et al. Larkinella harenae sp. nov., isolated from Korean beach soil. Curr Microbiol 2017; 74: 798– 802 [CrossRef] [PubMed]
    [Google Scholar]
  4. Kulichevskaya IS, Zaichikova MV, Detkova EN, Dedysh SN, Zavarzin GA. Larkinella arboricola sp. nov., a new spiral-shaped bacterium of the phylum Bacteroidetes isolated from the microbial community of decomposing wood. Microbiology 2009; 78: 741– 746 [CrossRef]
    [Google Scholar]
  5. Kim MK, Srinivasan S, Back C-G, Joo ES, Lee S-Y et al. Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol Cell Toxicol 2015; 11: 315– 321 [CrossRef]
    [Google Scholar]
  6. Kwak Y, Park GS, Shin JH. High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium. Stand Genomic Sci 2016; 11: 51 [CrossRef] [PubMed]
    [Google Scholar]
  7. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173: 697– 703 [CrossRef]
    [Google Scholar]
  8. Yoon SH, Sm H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67: 1613– 1617 [Crossref]
    [Google Scholar]
  9. 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 [CrossRef] [PubMed]
    [Google Scholar]
  10. 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]
  11. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  14. 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]
  15. 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 [CrossRef]
    [Google Scholar]
  16. 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 [CrossRef]
    [Google Scholar]
  17. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44: 846– 849 [CrossRef]
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  19. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31: 575– 580
    [Google Scholar]
  20. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50: 1861– 1868 [CrossRef]
    [Google Scholar]
  21. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 9th ed. San Francisco, USA: Benjamin Cummings; 2010
    [Google Scholar]
  22. Wilson K. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman et al. (editors) Current Protocols in Molecular Biology Supplement 27 USA: Jonh Wiley & Sons, Inc; 1997; pp. 2.4.1– 2.4.2
    [Google Scholar]
  23. 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 [CrossRef]
    [Google Scholar]
  24. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19: 161– 205 [Crossref]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002550
Loading
/content/journal/ijsem/10.1099/ijsem.0.002550
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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