Skip to main content
SpringerLink
Log in

Dankookia rubra gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream

  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

WS-10T–a Gram-negative, non-motile, and aerobic bacterial strain–was isolated from the sediment of a shallow stream in Korea. The optimum ranges of temperature and pH for growth were 20–40°C (optimum 28°C) and pH 6.0–8.0 (optimum pH 7.0), respectively. The DNA G+C content of strain WS-10T was 72.7 mol%. The major fatty acids (>5%) were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, and C18:1 2-OH. The major polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminolipids. Q-10 was the predominant respiratory quinone. The highest similarities in the 16S rRNA gene sequence were shown with Paracraurococcus ruber (95.3%), Belnapia soli (95.3%), B. moabensis (95.1%), and B. rosea (95.0%). A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain WS-10T formed a distinct line within a clade containing the genera Paracraurococcus, Craurococcus, and Belnapia in the family Acetobacteraceae. On the basis of polyphasic evidence, strain WS-10T represents a novel species of a new genus in the family Acetobacteraceae, for which the name Dankookia rubra gen. nov., sp. nov. is proposed. The type strain of the type species is WS-10T (= KACC 18533T = JCM 30602T).

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.

Similar content being viewed by others

References

  • Alarico, S., Rainey, F.A., Empadinhas, N., Schumann, P., Nobre, M.F., and da Costa, M.S. 2002. Rubritepida flocculans gen. nov., sp. nov., a new slightly thermophilic member of the alpha-1 subclass of the Proteobacteria. Syst. Appl. Microbiol. 25, 198–206.

    Article  CAS  PubMed  Google Scholar 

  • Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403–410.

    Article  CAS  PubMed  Google Scholar 

  • Bernardet, J.F., Nakagawa, Y., and 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.

    CAS  PubMed  Google Scholar 

  • Collins, M.D. 1985. Analysis of isoprenoid quinone. In Gottschalk, G. (ed.), Methods in Microbiology, Vol. 18, pp. 329–366. Academic Press, London, UK.

    Google Scholar 

  • Furuhata, K., Miyamoto, H., Goto, K., Kato, Y., Hara, M., and Fukuyama, M. 2008. Roseomonas stagni sp. nov., isolated from pond water in Japan. J. Gen. Appl. Microbiol. 54, 167–171.

    Article  CAS  PubMed  Google Scholar 

  • Gillis, M. 1978. Intra- and intergeneric similarities of the rRNA cistrons of Acetobacter and Gluconobacter. Antonie van Leeuwenhoek 44, 117–118.

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez, J.M. and Saiz-Jimenez, C. 2002. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ. Microbiol. 4, 770–773.

    Article  CAS  PubMed  Google Scholar 

  • Han, X.Y., Pham, A.S., Tarrand, J.J., Rolston, K.V., Helsel, L.O., and Levett, P.N. 2003. Bacteriologic characterization of 36 strains of Roseomonas species and proposal of Roseomonas mucosa sp nov and Roseomonas gilardii subsp rosea subsp nov. Am. J. Clin. Pathol. 120, 256–264.

    Article  PubMed  Google Scholar 

  • Jin, L., Lee, H.G., No, K.J., Ko, S.R., Kim, H.S., Ahn, C.Y., and Oh, H.M. 2013. Belnapia soli sp. nov., a proteobacterium isolated from grass soil. Int. J. Syst. Evol. Microbiol. 63, 1955–1959.

    Article  CAS  PubMed  Google Scholar 

  • Jin, R., Su, J., Liu, H.Y., Wei, Y.Z., Li, Q.P., Zhang, Y.Q., and Yu, L.Y. 2012. Description of Belnapia rosea sp. nov. and emended description of the genus Belnapia Reddy et al. 2006. Int. J. Syst. Evol. Microbiol. 62, 705–709.

    Article  CAS  PubMed  Google Scholar 

  • Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee J.H., Yi, H., et al. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721.

    Article  CAS  PubMed  Google Scholar 

  • Kim, W.H., Lee, S., and Ahn, T.Y. 2014. Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream. Int. J. Syst. Evol. Microbiol. 64, 3235–3239.

    Article  CAS  PubMed  Google Scholar 

  • Kolde, R. 2012. pheatmap: Pretty Heatmaps. R package version 061.

    Google Scholar 

  • Lane, D.J. 1991. 16S/23S rRNA sequencing. Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. In Stackebrandt, E. and Goodfellow, M. (eds.), Wiley, Chichester, UK.

    Google Scholar 

  • Lee, S., Weon, H.Y., Han, K., and Ahn, T.Y. 2012. Flavobacterium dankookense sp. nov., isolated from a freshwater reservoir, and emended descriptions of Flavobacterium cheonanense, F. chungnamense, F. koreense and F. aquatile. Int. J. Syst. Evol. Microbiol. 62, 2378–2382.

    Article  CAS  PubMed  Google Scholar 

  • Minnikin, D.E., O’Donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.

    Article  CAS  Google Scholar 

  • Nawrocki, E.P., Kolbe, D.L., and Eddy, S.R. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25, 1335–1337.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perry, L.B. 1973. Gliding motility in some non-spreading flexibacteria. J. Appl. Bacteriol. 36, 227–232.

    Article  CAS  PubMed  Google Scholar 

  • Reddy, G.S., Nagy, M., and Garcia-Pichel, F. 2006. Belnapia moabensis gen. nov., sp. nov., an alphaproteobacterium from biological soil crusts in the Colorado Plateau, USA. Int. J. Syst. Evol. Microbiol. 56, 51–58.

    Article  CAS  PubMed  Google Scholar 

  • Rihs, J.D., Brenner, D.J., Weaver, R.E., Steigerwalt, A.G., Hollis, D.G., and Yu, V.L. 1993. Roseomonas, a new genus associated with bacteremia and other human infections. J. Clin. Microbiol. 42, 121–140.

    Google Scholar 

  • Saitoh, S., Suzuki, T., and Nishimura, Y. 1998. Proposal of Craurococcus roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil. Int. J. Syst. Bacteriol. 48, 1043–1047.

    Article  PubMed  Google Scholar 

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

    Google Scholar 

  • Skerman, V.B.D. 1967. A guide to the identification of the genera of bacteria, with methods and digests of generic characteristics. 2d edn. Williams & Wilkins Co., Baltimore, USA.

    Google Scholar 

  • Smibert, R.M. and Krieg, N.R. 1994. Phenotypic characterization. In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.), Methods for General and Molecular Bacteriology, pp. 607–654. American Society for Microbiology, Washington DC, USA.

    Google Scholar 

  • Tamura, K., Dudley, J., Nei, M., and Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599.

    Article  CAS  PubMed  Google Scholar 

  • Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yurkov, V., Stackebrandt, E., Holmes, A., Fuerst, J.A., Hugenholtz, P., Golecki, J., Gad’on, N., Gorlenko, V.M., Kompantseva, E.I., and Drews, G. 1994. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int. J. Syst. Bacteriol. 44, 427–434.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, 31116, Republic of Korea

    Wan-Hoe Kim, Do-hak Kim, Keunsoo Kang & Tae-Young Ahn

Authors
  1. Wan-Hoe Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Do-hak Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Keunsoo Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tae-Young Ahn
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tae-Young Ahn.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kim, WH., Kim, Dh., Kang, K. et al. Dankookia rubra gen. nov., sp. nov., an alphaproteobacterium isolated from sediment of a shallow stream. J Microbiol. 54, 420–425 (2016). https://doi.org/10.1007/s12275-016-6054-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-016-6054-3

Keywords

Search

Navigation