Skip to main content
Springer Nature Link
Log in

Hymenobacter busanensis sp. nov., radiation-resistant species isolated from soil in South Korea

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

Two bacterial strains designated as MA3T and BT182 were isolated from a soil sample in South Korea. Cells of the two strains were Gram-stain-negative, non-motile, rod-shaped and formed red colonies on R2A agar at 25 °C. The 16S rRNA genes of the two strains shared a sequence similarity of 99.8%. Both strains shared the highest 16S rRNA gene similarity of 96.8% with Hymenobacter edaphi NLT, followed by Hymenobacter paludis KBP-30T (96.3%), Hymenobacter coalescens WW84T (96.3%) and Hymenobacter gummosus ANT-18T (96.3%). Growth was observed at 15–37 °C (optimum 30 °C), pH 6–8 (optimum pH 7) and in the presence up to 1% NaCl. The genome size of strains MA3T and BT182 is 4.9 Mb and 4.8 Mb, respectively. The genomic G + C content of both strains is 62.0 mol%. The main polar lipid of the strains was phosphatidylethanolamine, the only respiratory quinone detected was menaquinone-7 and the major fatty acids were anteiso-C15:0, iso-C15:0, summed feature 4 (iso-C17:1 I/anteiso-C17:1 B) and summed feature 3 (C16:1 ω6c/C16:1 ω7c), supporting the affiliation of these strains with the genus Hymenobacter. Based on the phylogenetic, genotypic, phenotypic and chemotaxonomic data, strains MA3T and BT182 represent a novel species of the genus Hymenobacter, for which the name Hymenobacter busanensis is proposed. The type strain is MA3T (= KCTC 72631T = NBRC 114193T).

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Explore related subjects

Discover the latest articles and news from researchers in related subjects, suggested using machine learning.

References

  • Buczolits S, Denner EB, Kämpfer P, Busse HJ (2006) Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999. Int J Syst Evol Microbiol 56:2189–2192

    Article  Google Scholar 

  • Chen W, Chen W, Young C, Sheu S (2017) Hymenobacter gummosus sp. nov., isolated from a spring. Int J Syst Evol Microbiol 67:4728–4735

    Article  CAS  PubMed  Google Scholar 

  • Chen W, Chen Z, Young C, Sheu S (2016) Hymenobacter paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 66:1546–1553

    Article  CAS  PubMed  Google Scholar 

  • Chin C, Alexander DH, Marks P, Klammer AA, Drake J et al (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–596

    Article  CAS  PubMed  Google Scholar 

  • Dai J, Wang Y, Zhang L, Tang Y, Luo X et al (2009) Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai-Tibet plateau. Syst Appl Microbiol 32:543–548

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Han L, Wu S, Qin C, Zhu Y, Lu Z et al (2014) Hymenobacter qilianensis sp. nov., isolated from a subsurface sandstone sediment in the permafrost region of Qilian Mountains, China and emended description of the genus Hymenobacter. Antonie Van Leeuwenhoek 105:971–978

    Article  CAS  PubMed  Google Scholar 

  • Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469

    Article  CAS  Google Scholar 

  • Hirsch P, Ludwig W, Hethke C, Sittig M, Hoffmann B (1998) Hymenobacter roseosalivarius gen. nov., sp. nov. from continental Antartica soils and sandstone: bacteria of the Cytophaga/Flavobacterium/Bacteroides line of phylogenetic descent. Syst Appl Microbiol 21:374–383

    Article  CAS  PubMed  Google Scholar 

  • Kang JW, Bai KS, Im W, Seong CN (2016) Hymenobacter coalescens sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 66:3546–3551

    Article  CAS  PubMed  Google Scholar 

  • Kang JY, Chun J, Choi A, Moon SH, Cho J et al (2013) Hymenobacter koreensis sp. nov. and Hymenobacter saemangeumensis sp. nov., isolated from estuarine water. Int J Syst Evol Microbiol 63:4568–4573

    Article  CAS  PubMed  Google Scholar 

  • Kim KH, Im WT, Lee ST (2008) Hymenobacter soli sp. nov., isolated from grass soil. Int J Syst Evol Microbiol 58:941–945

    Article  CAS  PubMed  Google Scholar 

  • Kim MK, Kang M, Srinivasan S, Lee DH, Lee S et al (2017) Complete genome sequence of Hymenobacter sedentarius DG5BT, a bacterium resistant to gamma radiation. Mol Cell Toxicol 13:199–205

    Article  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205

    Article  CAS  Google Scholar 

  • Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–3294

    Article  CAS  PubMed  Google Scholar 

  • Lee I, Kim YO, Park CJ (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    Article  CAS  PubMed  Google Scholar 

  • Lee JJ, Park SJ, Lee YH, Lee SY, Ten LN et al (2017) Hymenobacter aquaticus sp. nov., a radiation-resistant bacterium isolated from a river. Int J Syst Evol Microbiol 67:1206–1211

    Article  CAS  PubMed  Google Scholar 

  • Lee JJ, Srinivasan S, Lim S, Joe M, Lee SH et al (2014) Hymenobacter swuensis sp. nov., a gamma-radiation-resistant bacteria isolated from mountain soil. Curr Microbiol 68:305–310

    Article  CAS  PubMed  Google Scholar 

  • Maeng S, Kim MK, Subramani G (2019) Hymenobacterjejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island. Antonie Van Leeuwenhoek 113:553. https://doi.org/10.1007/s10482-019-01363-8

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformat 14:60

    Article  Google Scholar 

  • Minnikin DE, O’donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Munoz R, Rosselló-Móra R, Amann R (2016) Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 39:281–296

    Article  PubMed  Google Scholar 

  • Nie L, Fan X, Xiang D, Liao S, Wang G (2019) Hymenobacter edaphi sp. nov., isolated from abandoned arsenic-contaminated farmland soil. Int J Syst Evol Microbiol 69:2921–2927

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Srinivasan S, Lee S, Kim MK, Jung H (2017) Complete genome sequence of Hymenobacter sp. DG25A, a gamma radiation-resistant bacterium isolated from soil. Mol Cell Toxicol 13:65–72

    Article  CAS  Google Scholar 

  • Srinivasan S, Joo ES, Lee JJ, Kim MK (2015) Hymenobacter humi sp. nov., a bacterium isolated from soil. Antonie Van Leeuwenhoek 107:1411–1419

    Article  CAS  PubMed  Google Scholar 

  • Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  • Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki PE et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoon S, Ha S, Kwon S, Lim J, Kim Y et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Liu C, Tang Y, Zhou G, Shen P et al (2007) Hymenobacter xinjiangensis sp. nov., a radiation-resistant bacterium isolated from the desert of Xinjiang, China. Int J Syst Evol Microbiol 57:1752–1756

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This study was supported by a research grant from the Seoul Women’s University (2020) and by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201902111). We are grateful to Dr. Aharon Oren (The Hebrew University of Jerusalem, Israel) for helping with the etymology.

Author information

Author notes

  1. Sang Eun Lee and Leonid N. Ten contributed equally to this work.

Authors and Affiliations

  1. Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 139-774, Republic of Korea

    Sang Eun Lee, Yuna Park, Soohyun Maeng & Myung Kyum Kim

  2. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Leonid N. Ten & Hee ‑ Young Jung

  3. Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea

    Jing Zhang & Min-Kyu Kim

  4. National Institute of Biological Resources, Hwangyeong-ro 42, Seo-gu, Incheon, 22689, Republic of Korea

    In-Tae Cha, Ki-Eun Lee & Byoung-Hee Lee

  5. Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea

    Hee ‑ Young Jung

Authors
  1. Sang Eun Lee
    View author publications

    Search author on:PubMed Google Scholar

  2. Leonid N. Ten
    View author publications

    Search author on:PubMed Google Scholar

  3. Yuna Park
    View author publications

    Search author on:PubMed Google Scholar

  4. Soohyun Maeng
    View author publications

    Search author on:PubMed Google Scholar

  5. Jing Zhang
    View author publications

    Search author on:PubMed Google Scholar

  6. Min-Kyu Kim
    View author publications

    Search author on:PubMed Google Scholar

  7. In-Tae Cha
    View author publications

    Search author on:PubMed Google Scholar

  8. Ki-Eun Lee
    View author publications

    Search author on:PubMed Google Scholar

  9. Byoung-Hee Lee
    View author publications

    Search author on:PubMed Google Scholar

  10. Hee ‑ Young Jung
    View author publications

    Search author on:PubMed Google Scholar

  11. Myung Kyum Kim
    View author publications

    Search author on:PubMed Google Scholar

Corresponding authors

Correspondence to Hee ‑ Young Jung or Myung Kyum Kim.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Additional information

Communicated by Erko stackebrandt.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The GenBank accession numbers for the 16S rRNA gene sequences of strain MA3T and strain BT182 are MN396447 and MN555344, respectively. The whole-genome sequences of strain MA3T and strain BT182 have been deposited into DDBJ/EMBL/GenBank under the accession numbers VTWU00000000 and CP047647, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 2274 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lee, S.E., Ten, L.N., Park, Y. et al. Hymenobacter busanensis sp. nov., radiation-resistant species isolated from soil in South Korea. Arch Microbiol 203, 755–762 (2021). https://doi.org/10.1007/s00203-020-02080-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-020-02080-x

Keywords