1887

Abstract

A novel acid-tolerant and alkalitolerant gammaproteobacterium designated strain RS22 was isolated from Kyonggi University forest soil. Cells were aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, rod-shaped and yellow-pigmented. Flexirubin-type pigments were absent. Strain RS22 was able to assimilate lactic acid, -proline and 3-hydroxybenzoic acid; it tolerated 4 % (w/v) NaCl, fermented glucose and was able to grow at pH 11.0. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RS22 formed a lineage within the class of the phylum that was distinct from various species of the genus , including 2APBS1 (97.7 % sequence similarity), LCS2 (97.5 %), GP18-1 (97.5 %) and DCY45 (97.2 %). The predominant respiratory quinone was Q-8. The major polar lipids of strain RS22 were phosphatidylethanolamine, phosphatidyl--methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids were summed feature 9 (iso-Cω9 and/or C 10-methyl), iso-C, iso-C, iso-C, anteiso-C and C. The DNA G+C content of strain RS22 was 63.2 mol%. DNA–DNA hybridization between strain RS22 and other closest members of the genus revealed relatedness values from 28 to 51 %. On the basis of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain RS22 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RS22 (=KEMB 9005-480=KACC 19048=NBRC 112473).

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2017-05-01
2024-03-28
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References

  1. Nalin R, Simonet P, Vogel TM, Normand P. Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 1999; 49:19–23 [View Article][PubMed]
    [Google Scholar]
  2. Lee CS, Kim KK, Aslam Z, Lee ST. Rhodanobacter thiooxydans sp. nov., isolated from a biofilm on sulfur particles used in an autotrophic denitrification process. Int J Syst Evol Microbiol 2007; 57:1775–1779 [View Article][PubMed]
    [Google Scholar]
  3. Weon HY, Kim BY, Hong SB, Jeon YA, Kwon SW et al. Rhodanobacter ginsengisoli sp. nov. and Rhodanobacter terrae sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2007; 57:2810–2813 [View Article][PubMed]
    [Google Scholar]
  4. Bui TP, Kim YJ, Kim H, Yang DC. Rhodanobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:2935–2939 [View Article][PubMed]
    [Google Scholar]
  5. Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A, Watson DB et al. Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer. Int J Syst Evol Microbiol 2012; 62:2457–2462 [View Article][PubMed]
    [Google Scholar]
  6. Koh HW, Hong H, Min UG, Kang MS, Kim SG et al. Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater. Int J Syst Evol Microbiol 2015; 65:4574–4579 [View Article][PubMed]
    [Google Scholar]
  7. Dahal RH, Kim J. Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. Int J Syst Evol Microbiol 2016; 66:2205–2211 [View Article][PubMed]
    [Google Scholar]
  8. Wilson K. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology NY: John Wiley and Sons, Inc; 1997 pp. 2.4.1–2.4.2
    [Google Scholar]
  9. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
    [Google Scholar]
  10. 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][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [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[PubMed]
    [Google Scholar]
  20. 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]
  21. Reichenbach H. The order Cytophagales. In Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al. (editors) The Prokaryotes, 2nd ed. vol. 4 New York: Springer; 1992 pp. 3631–3675 [CrossRef]
    [Google Scholar]
  22. Breznak JA, Costilow RN. Physicochemical factors in growth. In Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: American Society for Microbiology; 2007 pp. 309–329
    [Google Scholar]
  23. 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]
  24. 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 et al. (editors) Methods for General and Molecular Bacteriology, 3rd ed. Washington, DC: ASM Press; 2007 pp 330–393
    [Google Scholar]
  25. Chaudhary DK, Kim J. Arvibacter flaviflagrans gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:4347–4354 [View Article][PubMed]
    [Google Scholar]
  26. Macfaddin JF. Bacterial Tests for Identification of Medical Bacteria, 2nd ed. Baltimore MD: Williams and Wilkins; 1980 pp. 162–218
    [Google Scholar]
  27. Mormak DL, Casida LE. Study of Bacillus subtilis endospores in soil by use of a modified endospore stain. Appl Environ Microbiol 1985; 59:1356–1360
    [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  29. 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]
  30. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [CrossRef]
    [Google Scholar]
  31. 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]
  32. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric DNA-DNA hybridization in microdilution wells as an alternative to member filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989; 39:224–229
    [Google Scholar]
  33. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Brenner DJ, Grimont PAD et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
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