1887

Abstract

A Gram-stain-negative, aerobic, non-motile, rod-shaped, catalase-positive and oxidase-positive bacteria (THG-T61), was isolated from rhizosphere of . Growth occurred at 10–37 °C (optimum 25–30 °C), at pH 5.0–9.0 (optimum 7.0) and in the presence of 0–2.0 % NaCl (optimum without NaCl supplement). Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T61 were identified as KCTC 12630 (97.9 %), DSM 18422 (97.8 %), NBRC 102146 (97.4 %), KCTC 12629 (97.2 %), ‘’ KCTC 12336 (97.1 %) and KCTC 23718 (96.9 %). The isoprenoid quinone was ubiquinone-10 (Q-10). The major fatty acids were C, C 6, summed feature 4 (-C 2-OH and/or Cω7) and summed feature 7 (C 7, C 9 and/or C 12). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, one unidentified lipid, one unidentified phospholipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The polyamine was homospermidine. The DNA G+C content of strain THG-T61 was 65.6 mol%. The DNA–DNA relatedness values between strain THG-T61 and its closest reference strains were less than 49.2 %, which is lower than the threshold value of 70 %. Therefore, strain THG-T61 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is THG-T61 (=KACC 19189=CCTCC AB 2016245).

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2018-02-01
2024-11-04
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References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas . Microbiol Immunol 1990; 34:99–119 [View Article][PubMed]
    [Google Scholar]
  2. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article][PubMed]
    [Google Scholar]
  3. Yabuuchi E, Kosako Y, Fujiwara N, Naka T, Matsunaga I et al. Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola . Int J Syst Evol Microbiol 2002; 52:1485–1496 [View Article][PubMed]
    [Google Scholar]
  4. Busse HJ, Denner EB, Buczolits S, Salkinoja-Salonen M, Bennasar A et al. Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas . Int J Syst Evol Microbiol 2003; 53:1253–1260 [View Article][PubMed]
    [Google Scholar]
  5. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
    [Google Scholar]
  6. An DS, Liu QM, Lee HG, Jung MS, Kim SC et al. Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov. Int J Syst Evol Microbiol 2013; 63:496–501 [View Article][PubMed]
    [Google Scholar]
  7. Asker D, Beppu T, Ueda K. Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan. Int J Syst Evol Microbiol 2007; 57:1435–1441 [View Article][PubMed]
    [Google Scholar]
  8. Huy H, Jin L, Lee KC, Kim SG, Lee JS et al. Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 2014; 64:1412–1418 [View Article][PubMed]
    [Google Scholar]
  9. Srinivasan S, Lee JJ, Kim MK. Sphingomonas rosea sp. nov. and Sphingomonas swuensis sp. nov., rosy colored β-glucosidase- producing bacteria isolated from soil. J Microbiol 2011; 49:610–616 [View Article][PubMed]
    [Google Scholar]
  10. Asker D, Beppu T, Ueda K. Sphingomonas astaxanthinifaciens sp. nov., a novel astaxanthin-producing bacterium of the family Sphingomonadaceae isolated from Misasa, Tottori, Japan. FEMS Microbiol Lett 2007; 273:140–148 [View Article][PubMed]
    [Google Scholar]
  11. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. Kimura M. The Neutral Theory of Molecular Evolution UK: Cambridge University Press; 1984
    [Google Scholar]
  16. 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]
  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. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Biol 1969; 18:1–32 [View Article]
    [Google Scholar]
  19. 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]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  21. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
    [Google Scholar]
  22. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703 [View Article][PubMed]
    [Google Scholar]
  23. Yan ZF, Trinh H, Moya G, Lin P, Li CT et al. Lysobacter rhizophilus sp. nov., isolated from rhizosphere soil of mugunghwa, the national flower of South Korea. Int J Syst Evol Microbiol 2016; 66:4754–4759 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A et al. Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 2008; 56:625–636 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
    [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. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  32. Hu HY, Lim BR, Goto N, Fujie K. Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 2001; 47:17–24[PubMed] [Crossref]
    [Google Scholar]
  33. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  34. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
    [Google Scholar]
  35. Taibi G, Schiavo MR, Gueli MC, Rindina PC, Muratore R et al. Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B Biomed Sci Appl 2000; 745:431–437 [View Article][PubMed]
    [Google Scholar]
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