Skip to main content
SpringerLink
Log in

Joostella atrarenae sp. nov., a novel member of the Flavobacteriaceae originating from the black sea sand of Jeju Island

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Strain M1-2T was isolated from the black sand from the seashore of Jeju Island, Republic of Korea and was classified using a polyphasic taxonomic approach. Strain M1-2T appeared as Gram-negative, motile rods that could grow in the presence of 1–10% (w/v) NaCl and at temperatures ranging from 4 to 37°C. This isolate has catalase and oxidase activity and hydrolyses aesculin, DNA and l-tyrosine. Based on phylogenetic analysis using 16S rRNA gene sequences, strain M1-2T belongs to the genus Joostella and is clearly distinct from the other described species of this genus, Joostella marina (type strain En5T). The 16S rRNA gene sequence similarity level between M1-2T and J. marina En5T is 97.2%, and the DNA–DNA relatedness value between the two strains is 23.9%. Strain M1-2T contains MK-6 as the major menaquinone and iso-C15:0, summed feature 3 (C16:1 ω7c and/or iso-C15:0 2OH) and iso-C17:0 3OH as major cellular fatty acids. The DNA G + C content is 32.3 mol%. These data suggest that strain M1-2T should be classified as a novel species, for which the name Joostella atrarenae sp. nov. is proposed. The type strain for the novel species is M1-2T (= KCTC 23194T = NCAIM B.002413T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Abell GC, Bowman JP (2005) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51:265–277

    Article  CAS  PubMed  Google Scholar 

  2. Barrow GI, Feltham RKA (1993) Cowan and Steel’s Manual for the identification of medical bacteria, 3rd edn. Cambridge University Press, Cambridge

    Book  Google Scholar 

  3. Baumann P, Baumann L (1981) The marine Gram-negative eubacteria; genera Photobacterium, Beneckea, Alteromonas, Pseudomonas, and Alcaligenes. In: Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG (eds) The prokaryotes, a handbook on habitats, isolation, and identification of bacteria. Springer, Berlin, pp 1302–1330

    Google Scholar 

  4. Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070

    Article  CAS  PubMed  Google Scholar 

  5. Bowman JP, Nichols DS (2005) Novel members of the family Flavobacteriaceae from Antarctic maritime habitats including Subsaximicrobium wynnwilliamsii gen. nov., sp. nov., Subsaximicrobium saxinquilinus sp. nov., Subsaxibacter broadyi gen. nov., sp. nov., Lacinutrix copepodicola gen. nov., sp. nov., and novel species of the genera Bizionia, Gelidibacter and Gillisia. Int J Syst Evol Microbiol 55:1471–1486

    Article  CAS  PubMed  Google Scholar 

  6. Chang SC, Wu MC, Chen WM, Tsai YH, Lee TM (2009) Chitinilyticum litopenaei sp. nov., isolated from a freshwater shrimp pond, and emended description of the genus Chitinilyticum. Int J Syst Evol Microbiol 59:2651–2655

    Article  CAS  PubMed  Google Scholar 

  7. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW (2007) EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 57:2259–2261

    Article  CAS  PubMed  Google Scholar 

  8. Collins MD, Jones D (1981) A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Bacteriol 51:129–134

    CAS  PubMed  Google Scholar 

  9. Ezaki T, Hashimoto Y, Yabuuchi E (1989) 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 39:224–229

    Article  Google Scholar 

  10. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  12. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package), version 3.6. Distributed by the author, Department of Genome Sciences. University of Washington, Seattle, USA

    Google Scholar 

  13. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  14. Jooste PJ (1985) The taxonomy and significance of Flavobacterium–Cytophaga strains from dairy sources. Thesis, University of the Orange Free State, Bloemfontein, South Africa

  15. Komagata K, Suzuki K (1987) Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–203

    Article  CAS  Google Scholar 

  16. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  17. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  18. Quan ZX, Xiao YP, Roh SW, Nam YD, Chang HW, Shin KS, Rhee SK, Park YH, Bae JW (2008) Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea. Int J Syst Evol Microbiol 58:1388–1392

    Article  CAS  PubMed  Google Scholar 

  19. Reichenbach H (1989) Order I. Cytophagales Leadbetter 1974. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 3. Williams & Wilkins, Baltimore, pp 2011–2013

    Google Scholar 

  20. Reichenbach H (1992) Flavobacteriaceae fam. nov. in validation of the publication of new names and new combinations previously effectively published outside the IJSB, List no. 41. Int J Syst Bacteriol 42:327–329

    Article  Google Scholar 

  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  22. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, New York

    Google Scholar 

  23. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, Technical Note 101. MIDI Inc., Newark, DE

    Google Scholar 

  24. Shieh WY, Chen AL, Chiu HH (2000) Vibrio aerogenes sp. nov., a facultatively anaerobic marine bacterium that ferments glucose with gas production. Int J Syst Evol Microbiol 50:321–329

    CAS  PubMed  Google Scholar 

  25. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed  Google Scholar 

  26. Wayne LG, Brenner DJ, Colwell RR et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

Download references

Acknowledgments

We thank Dr. Hans Georg Trüper for his advice on the Latin naming of the organism. This work was supported by the Mid-career Researcher Program through an NRF Grant funded by the MEST (No. 2009-0083557), Grant NMC0301039 and a Grant from the KRIBB Research Initiative Program.

Author information

Authors and Affiliations

  1. Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Korea

    Byung-Chun Kim, Kang Hyun Lee, Mi Na Kim, Min Young Jung, Young-Hyo Chang & Kee-Sun Shin

  2. Product Technology Part, Central Research Institute, Korea Ginseng Corp., Daejeon, Korea

    Jongtae Lee

Authors
  1. Byung-Chun Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kang Hyun Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mi Na Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Min Young Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Young-Hyo Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jongtae Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kee-Sun Shin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kee-Sun Shin.

Additional information

The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of the strain M1-2T is GQ872420.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, BC., Lee, K.H., Kim, M.N. et al. Joostella atrarenae sp. nov., a novel member of the Flavobacteriaceae originating from the black sea sand of Jeju Island. Curr Microbiol 62, 606–611 (2011). https://doi.org/10.1007/s00284-010-9750-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-010-9750-y

Keywords

Search

Navigation