1887

Abstract

A novel -proteobacterium, designated strain S-54, was isolated from forest soil sampled at Kyonggi University and subjected to polyphasic study. 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 S-54 assimilated lactic acid, -glucose and 4-hydroxybenzoic acid. Strain S-54 tolerated 4 % NaCl (w/v), and grew optimally at 45 °C and pH 10.5. Phylogenetic analysis based on 16S rRNA gene sequence data revealed that strain S-54 formed a lineage within the class of the phylum that was distinct from various members of the genus , including JCM 17037 (96.8 % sequence similarity), S3-63 (96.6 %), KCTC 22672 (96.5 %) and C9-11 (96.5 %). Q-10 was the sole isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and sphingoglycolipid. The major cellular fatty acids were Cω7, C and C18 : 1ω7 11-methyl. The DNA G+C content of strain S-54 was 64.2 mol%. On the basis of the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analysis, strain S-54 represents a novel species in the genus , for which the name sp. nov. is proposed. The type strain of is S-54 (=KEMB 9005-542=KACC 19119=NBRC 112676).

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2018-05-01
2024-04-19
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References

  1. Kwon KK, Woo JH, Yang SH, Kang JH, Kang SG et al. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol 2007; 57:2207–2211 [View Article][PubMed]
    [Google Scholar]
  2. Lee KB, Liu CT, Anzai Y, Kim H, Aono T et al. The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005; 55:467–486 [View Article][PubMed]
    [Google Scholar]
  3. Liao H, Li Y, Zhang M, Lin X, Lai Q et al. Altererythrobacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2017; 67:4851–4856 [View Article][PubMed]
    [Google Scholar]
  4. Yan ZF, Lin P, Won KH, Yang JE, Li CT et al. Altererythrobacter deserti sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2017; 67:3806–3811 [View Article][PubMed]
    [Google Scholar]
  5. Yuan N, Zeng Y, Feng H, Yu Z, Huang Y. Altererythrobacter xixiisoli sp. nov., isolated from wetland soil. Int J Syst Evol Microbiol 2017; 67:3655–3659 [View Article][PubMed]
    [Google Scholar]
  6. Jung YT, Park S, Lee JS, Yoon JH. Altererythrobacter aquiaggeris sp. nov., isolated from water of an estuary bank. Int J Syst Evol Microbiol 2017; 67:3410–3416 [View Article][PubMed]
    [Google Scholar]
  7. Park S, Jung YT, Choi SJ, Yoon JH. Altererythrobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2017; 67:3446–3451 [View Article][PubMed]
    [Google Scholar]
  8. Fidalgo C, Rocha J, Martins R, Proença DN, Morais PV et al. Altererythrobacter halimionae sp. nov. and Altererythrobacter endophyticus sp. nov., two endophytes from the salt marsh plant Halimione portulacoides . Int J Syst Evol Microbiol 2017; 67:3057–3062 [View Article][PubMed]
    [Google Scholar]
  9. Liang X, Lin H, Wang K, Liao Y, Lai Q et al. Altererythrobacter salegens sp. nov., a slightly halophilic bacterium isolated from surface sediment. Int J Syst Evol Microbiol 2017; 67:909–913 [View Article][PubMed]
    [Google Scholar]
  10. Nedashkovskaya OI, Cho SH, Joung Y, Joh K, Kim MN et al. Altererythrobacter troitsensis sp. nov., isolated from the sea urchin Strongylocentrotus intermedius . Int J Syst Evol Microbiol 2013; 63:93–97 [View Article][PubMed]
    [Google Scholar]
  11. Xue H, Piao CG, Guo MW, Wang LF, Fang W et al. Description of Altererythrobacter aerius sp. nov., isolated from air, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2016; 66:4543–4548 [View Article][PubMed]
    [Google Scholar]
  12. Xue X, Zhang K, Cai F, Dai J, Wang Y et al. Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter . Int J Syst Evol Microbiol 2012; 62:28–32 [View Article][PubMed]
    [Google Scholar]
  13. Fan ZY, Xiao YP, Hui W, Tian GR, Lee JS et al. Altererythrobacter dongtanensis sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2011; 61:2035–2039 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Dahal RH, Kim J. Rhabdobacter roseus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 2016; 66:308–314 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251 [View Article][PubMed]
    [Google Scholar]
  33. Knapp JS, Holmes KK. Modified oxidation-fermentation medium for detection of acid production from carbohydrates by Neisseria spp. and Branhamella catarrhalis . J Clin Microbiol 1983; 18:56–62[PubMed]
    [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  35. 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]
  36. Komagata K, Suzuki K. Lipids and cell wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–203 [Crossref]
    [Google Scholar]
  37. 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]
  38. 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 [View Article]
    [Google Scholar]
  39. Xu XW, Wu YH, Wang CS, Wang XG, Oren A et al. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae . Int J Syst Evol Microbiol 2009; 59:2247–2253 [View Article][PubMed]
    [Google Scholar]
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