1887

Abstract

A bacterial isolate, designated G-5-5, was isolated from forest soil at Kyonggi University. Strain G-5-5 was acid-tolerant and alkali-tolerant. Cells were strictly aerobic, Gram-stain-negative, catalase- and oxidase-positive, non-motile, non-spore-forming, rod-shaped, and yellow-coloured. Strain G-5-5 hydrolysed DNA and tyrosine; assimilated d-glucose, maltose, N-acetyl-glucosamine and l-fucose; and tolerated only 0.5 % NaCl (w/v). Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-5-5 formed a lineage within the family Rhodanobacteraceae and that it grouped with but was distinct from various members of the genus Rhodanobacter . The closest member was Rhodanobacter umsongensis GR24-2 (97.8 % sequence similarity). The sole respiratory quinone was Q-8. The major polar lipids of strain G-5-5 were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major cellular fatty acids were summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 0, iso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. The DNA G+C content of strain G-5-5 was 64.1 mol%. DNA–DNA hybridization relatedness between strain G-5-5 and other close members of the genus Rhodanobacter ranged from 19 % to 45 %. On the basis of the polyphasic characterization and phylogenetic analyses, strain G-5-5 represents a novel species of the genus Rhodanobacter , for which the name Rhodanobacter hydrolyticus sp. nov. is proposed. The type strain is G-5-5 (=KEMB 9005-533=KACC 19113=NBRC 112685).

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2018-06-28
2022-01-19
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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. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE et al. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2015; 107:467–485 [View Article][PubMed]
    [Google Scholar]
  3. Cho GY, Lee JC, Whang KS. Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere. Int J Syst Evol Microbiol 2017; 67:1387–1392 [View Article][PubMed]
    [Google Scholar]
  4. 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]
  5. An DS, Lee HG, Lee ST, Im WT. Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea. Int J Syst Evol Microbiol 2009; 59:691–694 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Wang L, An DS, Kim SG, Jin FX, Lee ST et al. Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2011; 61:3028–3032 [View Article][PubMed]
    [Google Scholar]
  8. Kim YS, Kim SJ, Anandham R, Weon HY, Kwon SW. Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field. J Microbiol 2013; 51:258–261 [View Article][PubMed]
    [Google Scholar]
  9. Dahal RH, Kim J. Rhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:1185–1190 [View Article][PubMed]
    [Google Scholar]
  10. 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]
  11. Prakash O, Green SJ, Jasrotia P, Overholt WA, Canion A 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]
  12. 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]
  13. Dahal RH, Kim J. Microvirga soli sp. nov., an alphaproteobacterium isolated from soil. Int J Syst Evol Microbiol 2017; 67:127–132 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  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. 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]
  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. 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]
  21. 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]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  25. Chen MH, Xia F, Lv YY, Zhou XY, Qiu LH. Dyella acidisoli sp. nov., D. flagellata sp. nov. and D. nitratireducens sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:736–743 [View Article][PubMed]
    [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  29. 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]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc.; 1990
    [Google Scholar]
  31. 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]
  32. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203
    [Google Scholar]
  33. 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]
  34. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric DNA–DNA hybridization in microdilution wells as an alternative to member folter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Microbiol 1989; 39:224–229
    [Google Scholar]
  35. 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 [View Article]
    [Google Scholar]
  36. Won K, Singh H, Ngo HT, Son H, Kook M et al. Rhodanobacter koreensis sp. nov., a bacterium isolated from tomato rhizosphere. Int J Syst Evol Microbiol 2015; 65:1180–1185 [View Article][PubMed]
    [Google Scholar]
  37. Madhaiyan M, Poonguzhali S, Saravanan VS, Kwon SW. Rhodanobacter glycinis sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean. Int J Syst Evol Microbiol 2014; 64:2023–2028 [View Article][PubMed]
    [Google Scholar]
  38. Xie CH, Yokota A. Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil. Int J Syst Evol Microbiol 2005; 55:753–756 [View Article][PubMed]
    [Google Scholar]
  39. An DS, Im WT, Yang HC, Yang DC, Lee ST. Dyella koreensis sp. nov., a β-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2005; 55:1625–1628 [View Article][PubMed]
    [Google Scholar]
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