1887

Abstract

Using a newly developed culture method for not yet cultured soil bacteria, three Gram-stain-negative, aerobic, non-spore-forming, motile, and rod-shaped bacteria (strain designated J18, J11 and J9) were isolated from forest soil at Kyonggi University, South Korea. Isolates were subjected to a taxonomic study by using a polyphasic approach. According to a phylogenetic tree based on 16S rRNA gene sequences, strains J18, J11 and J9 belonged to the genus and clustered with CCUG 38318 (similarity range: 97.6~98.0 %). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the genomic DNA G+C contents of strains J18, J11 and J9 were 63.4, 68.7 and 64.5 mol%, respectively. The major polyamines were putrescine and 2-hydroxyputescine, which were detected in all three strains. DNA–DNA between the three tested strains and the reference strains much lower than 70 %, the recommended threshold value for the delineation of genomic species. The predominant respiratory quinine was ubiquinone-8 (Q-8) and the major cellular fatty acids were Summed feature 3 (Cω6/C ω7) and C. On the basis of phenotypic and genotypic data and DNA–DNA hybridization results, the three isolates are considered to represent three novel species of the genus , for which the names sp. nov. for type strain J18 (=KEMB 9005-366=JCM 31607), sp. nov. for type strain J11 (=KEMB 9005-360=JCM 31606) and sp. nov. for type strain J9 (=KEMB 9005-359=JCM 31605) are proposed.

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2017-08-01
2024-03-28
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References

  1. La Scola B, Birtles RJ, Mallet MN, Raoult D, Gen M. Massilia timonae gen. nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 1998; 36:2847–2852[PubMed]
    [Google Scholar]
  2. Kämpfer P, Lodders N, Martin K, Falsen E. Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 2011; 61:1528–1533 [View Article][PubMed]
    [Google Scholar]
  3. Altankhuu K, Kim J. Massilia pinisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:3669–3674 [View Article][PubMed]
    [Google Scholar]
  4. Pitcher DG, Saunders NA, Owen RJ. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 1989; 8:151–156 [View Article]
    [Google Scholar]
  5. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester, UK: Wiley; 1991 pp. 115–175
    [Google Scholar]
  6. Yoon SH, Ha SM, 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]
  7. 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][PubMed]
    [Google Scholar]
  8. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [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[PubMed]
    [Google Scholar]
  10. 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]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. 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]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  15. Rohde M. Microscopy. In Rainey F, Oren A. (editors) Methods in Microbiology, 1st ed. vol. 38 Oxford, UK: Academic Press; 2011 pp. 61–100
    [Google Scholar]
  16. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC, USA: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  17. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979; 47:87–95
    [Google Scholar]
  18. Hiraishi A, Ueda Y, Ishihara J. Quinone profiling of bacterial communities in natural and synthetic sewage activated sludge for enhanced phosphate removal. Appl Environ Microbiol 1998; 64:992–998[PubMed]
    [Google Scholar]
  19. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE, USA: MIDI Inc; 1990
    [Google Scholar]
  20. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [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. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
    [Google Scholar]
  23. Weon HY, Yoo SH, Kim SJ, Kim YS, Anandham R et al. Massilia jejuensis sp. nov. and Naxibacter suwonensis sp. nov., isolated from air samples. Int J Syst Evol Microbiol 2010; 60:1938–1943 [View Article][PubMed]
    [Google Scholar]
  24. Orthová I, Kämpfer P, Glaeser SP, Kaden R, Busse HJ et al. Massilia norwichensis sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 2015; 65:56–64 [View Article][PubMed]
    [Google Scholar]
  25. Du Y, Yu X, Wang G. Massilia tieshanensis sp. nov., isolated from mining soil. Int J Syst Evol Microbiol 2012; 62:2356–2362 [View Article][PubMed]
    [Google Scholar]
  26. Zhang YQ, Li WJ, Zhang KY, Tian XP, Jiang Y et al. Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China. Int J Syst Evol Microbiol 2006; 56:459–463 [View Article][PubMed]
    [Google Scholar]
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