1887

Abstract

A Gram-stain-negative, single polar flagellum bacterium, WZY27, was isolated from rhizospheric soil of plants. The results of phylogenetic analysis based on 16S rRNA gene sequences showed that this strain is closely related to DSM 7418 (97.2 % similarity), KCTC 2883 (97.1 %) and JCM 17074 (97.0 %). The genomic average nucleotide identity values between strain WZY27 and the above three strains were 75.3, 73.2 and 75.4 %, and the DNA–DNA hybridization values were 19.1 , 20.1 and 20.9 %, respectively. The major fatty acids (>5 %) of strain WZY27 were summed feature 8 (C 7/C 6), C, C 2-OH and C 7 11-methyl. The predominant respiratory quinone and polyamine were ubiquinone Q-10 and homospermidine, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospholipids, glycolipids, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 68.4 mol%. Based on the results of genotypic, chemotaxonomic and phenotypic characterization, strain WZY27 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is WZY27 (=KCTC 62523=CCTCC AB 2018056).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003477
2019-10-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/2972.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003477&mimeType=html&fmt=ahah

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. Busse HJ, Kämpfer P, Denner EB. Chemotaxonomic characterisation of Sphingomonas . J Ind Microbiol Biotechnol 1999; 23:242–251 [View Article][PubMed]
    [Google Scholar]
  3. Wittich RM, Busse HJ, Kämpfer P, Macedo AJ, Tiirola M et al. Sphingomonas fennica sp. nov. and Sphingomonas haloaromaticamans sp. nov., outliers of the genus Sphingomonas . Int J Syst Evol Microbiol 2007; 57:1740–1746 [View Article][PubMed]
    [Google Scholar]
  4. Liu L, Hui N, Liang L, Zhang X, Sun Q et al. Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil. Int J Syst Evol Microbiol 2019; 69:441–446 [View Article][PubMed]
    [Google Scholar]
  5. 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]
  6. Fan H, Su C, Wang Y, Yao J, Zhao K et al. Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China. J Appl Microbiol 2008; 105:529–539 [View Article][PubMed]
    [Google Scholar]
  7. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990; 28:1942–1946[PubMed]
    [Google Scholar]
  8. 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]
  9. 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]
  10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  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. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  16. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  17. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article][PubMed]
    [Google Scholar]
  18. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  19. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article][PubMed]
    [Google Scholar]
  20. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  21. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485[PubMed]
    [Google Scholar]
  22. Ryu E. A simple method of differentiation between Gram-positive and Gram-negative organisms without staining. Kitasato ArchExp Med 1940; 17:58–63
    [Google Scholar]
  23. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology, 1st ed. Beijing: Scientific Press; 2001
    [Google Scholar]
  24. Breznak JA, Costilow RN. Physicochemical factors in growth. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 137–154
    [Google Scholar]
  25. Smibert RM, Krieg NR. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Phenotypic characterization. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  26. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26[PubMed]
    [Google Scholar]
  27. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  28. 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]
  29. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  30. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  31. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322[PubMed]
    [Google Scholar]
  32. Lee JS, Shin YK, Yoon JH, Takeuchi M, Pyun YR et al. Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol 2001; 51:1491–1498 [View Article][PubMed]
    [Google Scholar]
  33. Choi TE, Liu QM, Yang JE, Sun S, Kim SY et al. Sphingomonas ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2010; 48:760–766 [View Article][PubMed]
    [Google Scholar]
  34. Singh P, Kim YJ, Hoang VA, Farh M-A, Yang DC. Sphingomonas panacis sp. nov., isolated from rhizosphere of rusty ginseng. Antonie van Leeuwenhoek 2015; 108:711–720 [View Article][PubMed]
    [Google Scholar]
  35. Zhu L, Si M, Li C, Xin K, Chen C et al. Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum . Int J Syst Evol Microbiol 2015; 65:1160–1166 [View Article][PubMed]
    [Google Scholar]
  36. Feng GD, Yang SZ, Zhu HH, Li HP. Emended descriptions of the species Sphingomonas adhaesiva Yabuuchi et al. 1990 and Sphingomonas ginsenosidimutans Choi et al. 2011. Int J Syst Evol Microbiol 2018; 68:970–973 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003477
Loading
/content/journal/ijsem/10.1099/ijsem.0.003477
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error