Skip to main content
SpringerLink
Log in

Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment

  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

A Gram-stain-positive, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium, designated strain CHu64-6-1T, was isolated from a 67-cm-long sediment core collected from the Daechung Reservoir at a water depth of 17-m in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies placed the new isolate in the class Sphingobacteriia, and the isolate is notably most closely related to Flavihumibacter sediminis CJ663T (98.1% similarity), Flavihumibacter solisilvae 3-3T (97.8%), Flavihumibacter petaseus T41T (97.5%), Flavihumibacter cheonanensis WS16T (97.4%), and Flavihumibacter stibioxidans YS-17T (97.2%). The cells of strain CHu64-6-1T formed yellow colonies on R2A agar and contained MK-7 as the only menaquinone, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified aminolipids as the major polar lipids, and C15:0 iso, C17:0 iso 3-OH, C15:1 iso G, and C16:1ω5c as the major fatty acids (> 5%). The DNA G + C content of the genome was determined to be 46.5 mol%. The DNA-DNA hybridization values of strain CHu64-6-1T with F. sediminis CJ663T, F. solisilvae 3-3T, F. petaseus T41T, F. cheonanensis WS16T, and F. stibioxidans YS-17T were 12.4–33.2%. Based on the combined genotypic and phenotypic data, we propose that strain CHu64-6-1T represents a novel species of the genus Flavihumibacter, for which the name Flavihumibacter profundi sp. nov. is proposed. The type strain is CHu64-6-1T (= KCTC 62290T = CCTCC AB 2018060T).

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

Similar content being viewed by others

References

  • Ezaki, T., Hashimoto, Y., and 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 

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

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein, J. 1985 Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783–791

    Article  PubMed  Google Scholar 

  • Fitch, W.M. 1971 Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416

    Article  Google Scholar 

  • Hall, T.A. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41, 95–98

    CAS  Google Scholar 

  • Han, Y., Zhang, F., Wang, Q., Zheng, S., Guo, W., Feng, L., and Wang, G. 2016 Flavihumibacter stibioxidans sp. nov., an antimony-oxidizing bacterium isolated from antimony mine soil. Int. J. Syst. Evol. Microbiol. 66, 4676–4680

    PubMed  Google Scholar 

  • Jin, L., Ko, S.R., Ahn, C.Y, Lee, H.G., and Oh, H.M. 2016 Rhizobacter profundi sp. nov., isolated from freshwater sediment. Int. J. Syst. Evol. Microbiol. 66, 1926–1931

    Article  PubMed  CAS  Google Scholar 

  • Jin, L., Lee, C.S., Ahn, C.Y., Lee, H.G., Lee, S., Shin, H.H., Lim, D., and Oh, H.M. 2017 Abundant iron and sulfur oxidizers in the stratified sediment of a eutrophic freshwater reservoir with annual cyanobacterial blooms. Sci. Rep. 7, 43814

    Article  PubMed  PubMed Central  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

    PubMed  CAS  Google Scholar 

  • Komagata, K. and Suzuki, K.I. 1987 Lipid and cell wall analysis in bacterial systematics. Methods Microbiol. 19, 161–207

    Article  CAS  Google Scholar 

  • Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115–176 In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic acid techniques in bacterial systematics. Wiley, Chichester, UK.

    Google Scholar 

  • Lee, D.H. and Cha, C.J. 2016 Flavihumibacter sediminis sp. nov., isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 66, 4310–4314

    PubMed  Google Scholar 

  • Lee, H.J., Jeong, S.E., Cho, M.S., Kim, S., Lee, S.S., Lee, B.H., and Jeon, C.O. 2014 Flavihumibacter solisilvae sp. nov., isolated from forest soil. Int. J. Syst. Evol. Microbiol. 64, 2897–2901

    Article  PubMed  CAS  Google Scholar 

  • Saitou, N. and Nei, M. 1987 The neighbor-joining method; a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425

    PubMed  CAS  Google Scholar 

  • Tamaoka, J. and Komagata, K. 1984 Determination of DNA base composition by reverse-phased high-performance liquid chromatography. FEMS Microbiol. Lett. 125, 125–128

    Article  Google Scholar 

  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. mega6: molecular evolutionary genetics analysis version 6.0 Mol. Biol. Evol. 30, 2725–2729

    Article  CAS  Google Scholar 

  • Tarrand, J.J. and Groschel, D.H.M. 1982 Rapid, modified oxidase test for oxidase-variable bacterial isolates. J. Clin. Microbiol. 16, 772–774

    PubMed  PubMed Central  CAS  Google Scholar 

  • Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997 The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876–4882

    Article  Google Scholar 

  • Tindall, B.J. 1990 A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst. Appl. Microbiol. 13, 128–130

    Article  CAS  Google Scholar 

  • Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., et al. 1987 International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463–464

    Google Scholar 

  • Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017 Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang, N.N., Qu, J.H., Yuan, H.L., Sun, Y.M., and Yang, J.S. 2010 Flavihumibacter petaseus gen. nov., sp. nov., isolated from soil of a subtropical rainforest. Int. J. Syst. Evol. Microbiol. 60, 1609–1612

    PubMed  CAS  Google Scholar 

Download references

Author information

Author notes

  1. These authors contributed equally to this work.

Authors and Affiliations

  1. College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, P. R. China

    Ting-Ting Ren, Feng-Jie Jin, Taihua Li & Long Jin

  2. Industrial Biomaterial Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea

    Chun-Zhi Jin & Chang-Jin Kim

  3. Department of Bio-Molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea

    Chun-Zhi Jin & Chang-Jin Kim

  4. Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea

    Hee-Mock Oh & Hyung-Gwan Lee

Authors
  1. Ting-Ting Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chun-Zhi Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Feng-Jie Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Taihua Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chang-Jin Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hee-Mock Oh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hyung-Gwan Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Long Jin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Long Jin.

Additional information

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strain CHu64-6-1T is MF770247.

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

Electronic supplementary material

12275_2018_7567_MOESM1_ESM.pdf

Maximum-Parsimony (A) and Maximum-Likelihood (B) trees based on 16S rRNA gene sequences showing positions of strain CHu64-6-1T and related taxa. Only bootstrap values (expressed as percentages of 1,000 replications) greater than 50% are indicated at nodes.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ren, TT., Jin, CZ., Jin, FJ. et al. Flavihumibacter profundi sp. nov., isolated from eutrophic freshwater sediment. J Microbiol. 56, 467–471 (2018). https://doi.org/10.1007/s12275-018-7567-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-018-7567-8

Keywords

Search

Navigation