1887

Abstract

A Gram-stain-negative, strictly aerobic, motile by one single flagellum, dark-orange pigmented and rod-shaped bacterial strain, designated CAU 1457, was isolated from marine sediment in the Republic of Korea and its taxonomic position was investigated by using a polyphasic approach. The isolate grew optimally at 30 °C, at pH 6.0 and in the presence of 2 % (w/v) NaCl. Based on 16S rRNA gene sequences similarity, strain CAU 1457 belonged to the genus Sphingomicrobium and was related most closely to Sphingomicrobium astaxanthinifaciens JCM 18551 (98.2 % similarity). Strain CAU 1457 contained ubiquinone-10 as the predominant isoprenoid quinone and 11-methyl C18 : 1ω7c and summed feature 8 (C18 : 1ω7c/ω6c) as the major cellular fatty acids. Triamine sym-homospermidine was detected as the major compound in the polyamine pattern. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, four unidentified glycolipids, one unidentified aminophospholipid, two unidentified phospholipids, one unidentified aminolipid and one unidentified lipid. DNA–DNA relatedness between strain CAU 1457 and the closely related strains, Sphingomicrobium astaxanthinifaciens JCM 18551 and Sphingomicrobium aestuariivivum KCTC 42286 were 32.7 and 28.4 %, respectively. The DNA G+C content of strain was 68.8 mol%. The phenotypic, chemotaxonomic and phylogenetic data indicated that strain CAU 1457 represents a novel species of the genus Sphingomicrobium , for which the name Sphingomicrobium arenosum sp. nov. is proposed. The type strain is CAU 1457 (=KCTC 62233=NBRC 113094).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002875
2018-06-22
2019-08-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/8/2551.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002875&mimeType=html&fmt=ahah

References

  1. Kämpfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J et al. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 2012;62:1326–1330 [CrossRef][PubMed]
    [Google Scholar]
  2. Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC et al. Sphingomicrobium astaxanthinifaciens sp. nov., an astaxanthin-producing glycolipid-rich bacterium isolated from surface seawater and emended description of the genus Sphingomicrobium. Int J Syst Evol Microbiol 2013;63:3415–3422 [CrossRef][PubMed]
    [Google Scholar]
  3. Shahina M, Hameed A, Lin SY, Hsu YH, Liu YC et al. Sphingomicrobium marinum sp. nov. and Sphingomicrobium flavum sp. nov., isolated from surface seawater, and emended description of the genus Sphingomicrobium. Int J Syst Evol Microbiol 2013;63:4469–4476 [CrossRef][PubMed]
    [Google Scholar]
  4. Park S, Park JM, Sun Joo E, Won SM, Kyum Kim M et al. Sphingomicrobium aestuariivivum sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2015;65:2678–2683 [CrossRef][PubMed]
    [Google Scholar]
  5. Gordon RE, Mihm JM. Identification of Nocardia caviae (Erikson) nov. comb. Ann N Y Acad Sci 1962;98:628–636 [CrossRef]
    [Google Scholar]
  6. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991; pp.115–175
    [Google Scholar]
  7. 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 [CrossRef][PubMed]
    [Google Scholar]
  8. 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 [CrossRef][PubMed]
    [Google Scholar]
  9. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HH. (editor) Mammalian Protein Metabolism New York: Academic Press; 1969; pp.21–132
    [Google Scholar]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  11. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][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 [CrossRef]
    [Google Scholar]
  13. Sudhir K, Glen S, Koichiro T. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2017;33:1870–1874
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef]
    [Google Scholar]
  16. Goris J, Suzuki K-Ichiro, Vos PD, Nakase T, Kersters K. Evaluation of a microplate DNA–DNA hybridization method compared with the initial renaturation method. Can J Microbiol 1998;44:1148–1153 [CrossRef]
    [Google Scholar]
  17. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984;25:125–128 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. Nicholson WL, Setlow P. Sporulation, germination and outgrowth. In Harwood CR, Cutting SM. (editors) Molecular Biological Methods for Bacillus Chichester: Wiley; 1990; pp.391–450
    [Google Scholar]
  20. Conn HJ, Bartholomew JW, Jennison MW. Staining methods. In The Society of American Bacteriologists (editor) Manual of Microbial Methods New York: McGraw-Hill; 1957; pp.30–36
    [Google Scholar]
  21. Bernardet JF, Nakagawa Y, Holmes B.Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002;52:1049–1070 [CrossRef][PubMed]
    [Google Scholar]
  22. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960
    [Google Scholar]
  23. Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Characteristics of the heterotrophic bacterial populations in hypersaline environments of different salt concentrations. Microb Ecol 1981;7:235–243 [CrossRef][PubMed]
    [Google Scholar]
  24. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th ed. Menlo Park, CA: Benjamin/Cummings; 2002
    [Google Scholar]
  25. 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]
  26. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980;188:221–233 [CrossRef]
    [Google Scholar]
  27. 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 [CrossRef]
    [Google Scholar]
  28. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef]
    [Google Scholar]
  30. 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 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002875
Loading
/content/journal/ijsem/10.1099/ijsem.0.002875
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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