Skip to main content

Advertisement

SpringerLink
Log in

Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A gamma radiation-resistant, Gram-stain negative, oxidase and catalase positive, aerobic, flagellated, rod-shaped, methylotrophic and pink-pigmented bacterial strain designated 17SD2-17 T was isolated from gamma-ray-irradiated soil collected in Korea. The 16S rRNA gene sequence analysis showed that strain 17SD2-17 T is phylogenetically related to Methylobacterium organophilum DSM 760 T (97.6%), Methylobacterium oxalidis 35aT (97.4%) and Methylobacterium soli YIM 48816 T (97.0%). The G+C content calculated based on the draft genome sequence is 68.7 mol%. The DNA–DNA hybridisation between 17SD2-17 T and its close relatives was found to be less than 40%. The predominant fatty acid was identified as summed feature 8 (C18:1ω7c and/or C18:1ω6c) and the major respiratory quinone as Q-10. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of the data from phenotypic tests and genotypic differences between strain 17SD2-17 T and its close phylogenetic relatives, strain 17SD2-17 T is concluded to represent a new species belonging to the genus Methylobacterium, for which the name Methylobacterium durans sp. nov. (= KCTC 52908 T = NBRC 112876 T) is proposed.

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
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Steven R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Beck DA, McTaggart TL, Setboonsarng U, Vorobev A, Goodwin L, Shapiro N, Woyke T, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L (2015) Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environ Microbiol 17:547–554

    Article  CAS  PubMed  Google Scholar 

  • Cao YR, Wang Q, Jin RX, Tang SK, Jiang Y, He WX, Lai HX, Xu LH, Jiang CL (2011) Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil. Antonie Van Leeuwenhoek 99:629–634

    Article  CAS  PubMed  Google Scholar 

  • Chen W, Cai C, Li Z,Young C, Sheu S (2019) Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field. https://doi.org/10.1099/ijsem.0.003693

    Article  PubMed  Google Scholar 

  • Chhetri G, Yang D, Choi J, Kim H, Seo T (2018) Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea. Antonie Van Leeuwenhoek 111:2385–2392

    Article  CAS  PubMed  Google Scholar 

  • Chhetri G, Yang D, Choi J, Kim H, Seo T (2019) Flavobacterium edaphi sp. nov., isolated from soil from Jeju Island. Korea Arch Microbiol 201:539–545

    Article  CAS  PubMed  Google Scholar 

  • Chistoserdova L (2011) Modularity of methylotrophy, revisited. Environ Microbiol 13:2603–2622

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cox MM, Battista JR (2005) Deinococcus radiodurans—the consummate survivor. Nat Rev Microbiol 3:882–892

    Article  CAS  PubMed  Google Scholar 

  • 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 Evol Microbiol 39:224–229

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Gallego V, Garcia MT, Ventosa A (2005) Methylobacterium hispanicum sp. Nov. and Methylobacterium aquaticum sp. Nov., isolated from drinking water. Int J Syst Evol Microbiol 55:281–287

    Article  CAS  PubMed  Google Scholar 

  • Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Green PN (1992) The genus Methylobacterium. In: The prokaryotes, 2nd edn. Springer, New York, pp 2342–2349

  • Green PN, Ardley JK (2018) Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov. Int J Syst Evol Microbiol 68:2727–2748

    Article  CAS  PubMed  Google Scholar 

  • Green PN, Bousfield IJ (1983) Emendation of Methylobacterium Patt, Cole, and Hanson 1976; Methylobacterium rhodinum (Heumann 1962) comb. nov. corrig.; Methylobacterium radiotolerans (Ito and Iizuka 1971) comb. nov. corrig.; and Methylobacterium mesophilicum (Austin and Goodfellow 1979) comb. nov. Int J Syst Evol Microbiol 33:875–877

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Hornei B, Lüneberg E, Schmidt-Rotte H, Maass M, Weber K, Heits F, Frosch M, Solbach W (1999) Systemic infection of an immunocompromised patient with Methylobacterium zatmanii. J Clin Microbiol 37:248–250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ito H, Iizuka H (1971) Taxonomic studies on a radio-resistant Pseudomonas. Part XII. Studies on the microorganisms of cereal grain. Agric Biol Chem 35:1566–1571

    Google Scholar 

  • Kang MS, Srinivasan S (2018) Complete genome sequence of Methylobacterium sp. 17Sr1-43, a radiation-resistant bacterium. Mol Cell Toxicol 14:453–457

    Article  CAS  Google Scholar 

  • Kim I, Choi J, Chhetri G, Seo T (2019a) Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea. Antonie Van Leeuwenhoek 112:1253–1262

    Article  CAS  PubMed  Google Scholar 

  • Kim J, Chhetri G, Kim I, Kim H, Kim MK, Seo T (2019b) Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol 57:1–8. https://doi.org/10.1007/s12275-019-9007-9

    Article  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitution 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 

  • 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 

  • Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361

    CAS  Google Scholar 

  • Lee I, Kim YO, Park SC, Chun J (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 

  • Madhaiyan M, Poonguzhali S (2014) Methylobacterium pseudosasicola sp. nov. and Methylobacterium phyllostachyos sp. nov., isolated from bamboo leaf surfaces. Int J Syst Evol Microbiol 64:2376–2384

    Article  CAS  PubMed  Google Scholar 

  • Madhaiyan M, Poonguzhali S, Senthilkumar M, Lee JS, Lee KC (2012) Methylobacterium gossipiicola sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the cotton phyllosphere. Int J Syst Evol Microbiol 62:162–167

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Patt TE, Cole GC, Hanson RS (1976) Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int J Syst Evol Microbiol 26:226–229

    CAS  Google Scholar 

  • Raja P, Balachandar D, Sundaram SP (2008) Genetic diversity and phylogeny of pink-pigmented facultative methylotrophic bacteria isolated from the phyllosphere of tropical crop plants. Biol Fertil Soils 45:45–53

    Article  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 106:19126–19131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 9:945–967

    CAS  Google Scholar 

  • 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 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI, Inc, Newark

  • Schauer S, Kämpfer P, Wellner S, Spröer C, Kutschera U (2011) Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. Int J Syst Evol Microbiol 61:870–876

    Article  CAS  PubMed  Google Scholar 

  • Srinivasan S, Lee SY, Kim MK, Jung HY (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 

  • Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539

    Article  CAS  PubMed  Google Scholar 

  • Tani A, Sahin N, Kimbara K (2012) Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata. Int J Syst Bacteriol 62:1647–1652

    Article  CAS  Google Scholar 

  • 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  PubMed Central  Google Scholar 

  • Tindall BJ, Sikorski J, Smibert RM, Kreig NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology, 3rd edn. American Society for Microbiology, Washington, DC, pp 330–393

    Google Scholar 

  • Truant AL, Gulati R, Giger O, Satishchandran V, Caya JG (1998) Methylobacterium species: an increasingly important opportunistic pathogen. Lab Med 29:704–710

    Article  Google Scholar 

  • Wellner S, Lodders N, Kämpfer P (2012) Methylobacterium cerastii sp. nov., isolated from the leaf surface of Cerastium holosteoides. Int J Sys Evol Microbiol 62:917–924

    Article  CAS  Google Scholar 

  • Wellner S, Lodders N, Glaeser SP, Kämpfer P (2013) Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces. Int J Syst Evol Microbiol 63:2690–2699

    Article  CAS  PubMed  Google Scholar 

  • Weon HY, Kim BY, Joa JH, Son JA, Song MH, Kwon SW, Go SJ, Yoon SH (2008) Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 58:93–96

    Article  CAS  PubMed  Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, 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  CAS  PubMed  PubMed Central  Google Scholar 

  • Zimmerman JM, Battista JR (2006) 32 Measuring survival in microbial populations following exposure to ionizing radiation. Methods Microbiol 35:745–754

    Article  Google Scholar 

Download references

Acknowledgements

This work was supported by a research grant from Seoul Women’s University (2018), and the project on the survey of indigenous species of Korea, of the National Institute of Biological Resources (NIBR) funded by the Ministry of Environment (MOE).

Author information

Authors and Affiliations

  1. Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea

    Jiyoun Kim, Geeta Chhetri, Inhyup Kim & Taegun Seo

  2. Department of Bio and Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 01797, South Korea

    Myung Kyum Kim

Authors
  1. Jiyoun Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Geeta Chhetri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Inhyup Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Myung Kyum Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Taegun Seo
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

GC isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, wrote the original draft; JK, HK and IK helped the analysis of taxonomic data; MKK and TS designed and supervised the study, edited the original draft.

Corresponding author

Correspondence to Taegun Seo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 4210 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kim, J., Chhetri, G., Kim, I. et al. Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. Antonie van Leeuwenhoek 113, 211–220 (2020). https://doi.org/10.1007/s10482-019-01331-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-019-01331-2

Keywords

Search

Navigation