Skip to main content
SpringerLink
Log in

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

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

An Erratum to this article was published on 02 January 2020

This article has been updated

Abstract

A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7–90.4% and 22–39.6%, respectively. The major fatty acids of strain 17Sr1-28T were summed feature 8 (C18:1ω7c and/or C18:1ω6c), and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) 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

Similar content being viewed by others

Change history

  • 02 January 2020

    In the article by Kim <Emphasis Type="Italic">et al.</Emphasis> published in Journal of Microbiology 2019; 57, 959–966, The NBRC accession number NBRC 112879<Superscript>T</Superscript> on 33<Superscript>th</Superscript> line of 2<Superscript>nd</Superscript> paragraph in the section of ‘Description of <Emphasis Type="Italic">Methylobacterium terrae</Emphasis> sp. nov.’ on page 964 should be corrected in NBRC 112873<Superscript>T</Superscript>.

    The sentence in abstract should have read: The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genome sequences of the type strain 17Sr1-28T (= KCTC 52904T = NBRC 112873T) are KY939566 and CP029553, respectively.

    We apologize for any inconvenience that this may have caused.

References

  • Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M., Kubal, M., et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics9, 75.

    PubMed  PubMed Central  Google Scholar 

  • Beck, D.A., McTaggart, T.L., Setboonsarng, U., Vorobev, A., Goodwin, L., Shapiro, N., Woyke, T., Kalyuzhnaya, M.G., Lidstrom, M.E., and Chistoserdova, L. 2015. Multiphyletic origins of methylotrophy in Alphaproteobacteria, exemplified by comparative genomics of Lake Washington isolates. Environ. Microbiol.17, 547–554.

    CAS  PubMed  Google Scholar 

  • Breznak, J.A. and Costilow, R.N. 2007. Physicochemical factors in growth. In Beveridge, T.J., Breznak, J.A., Marzluf, G.A., Schmidt, T.M., and Snyder, L.R. (eds.), Methods for general and molecular bacteriology, 3rd edn., pp. 309–329. American Society for Microbiology, Washington, D.C., USA.

    Google Scholar 

  • Buck, J.D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol.44, 992–993.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cao, Y.R., Wang, Q., Jin, R.X., Tang, S.K., Jiang, Y., He, W.X., Lai, H.X., Xu, L.H., and Jiang, C.L. 2011. Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil. Antonie van Leeuwenhoek99, 629–634.

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Chistoserdova, L. and Lidstrom, M.E. 2013. Aerobic methylotrophic prokaryotes. In Rosenberg, E., DeLong, E.F., Thompson, F., Lory, S., Stackebrandt, E., et al. (eds.). The Prokaryotes, pp. 267–285. Springer, Berlin, Heidelberg, German.

    Google Scholar 

  • Collins, M.D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev.45, 316–354.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cox, M.M. and Battista, J.R. 2005. Deinococcus radiodurans—he consummate survivor. Nat. Rev. Microbiol.3, 882–892.

    CAS  PubMed  Google Scholar 

  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution39, 783–791.

    PubMed  Google Scholar 

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

    Google Scholar 

  • Gallego, V., García, M.T., and Ventosa, A. 2005. Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water.Int. J. Syst. Evol. Microbiol.55, 281–287.

    CAS  PubMed  Google Scholar 

  • Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol.57, 81–91.

    CAS  PubMed  Google Scholar 

  • Green, P.N. 1992. The genus Methylobacterium. In The Prokaryotes, 2nd edn, pp. 2342–2349. Springer. New York, N.Y., USA.

    Google Scholar 

  • Green, P.N. and Ardley, J.K. 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.

    CAS  PubMed  Google Scholar 

  • Green, P.N. and Bousfield, I.J. 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. Bacteriol.33, 875–877.

    Google Scholar 

  • Hiraishi, A., Ueda, Y., Ishihara, J., and 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.

    CAS  Google Scholar 

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

    Google Scholar 

  • Kang, Y.S., Kim, J., Shin, H.D., Nam, Y.D., Bae, J.W., Jeon, C.O., and Park, W. 2007. Methylobacterium platani sp. nov., isolated from a leaf of the tree Platanus orientalis. Int. J. Syst. Evol. Microbiol.57, 2849–2853.

    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., Jeon, Y.S., et al. 2012. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbial.62, 716–721.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  • Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol.33, 1870–1874.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kuykendall, L.D., Roy, M.A., O’Neill, J.J., and Devine, T.E. 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, Y. and Jeon, C.O. 2018. Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system. Int. J. Syst. Evol. Microbiol.68, 299–304.

    CAS  PubMed  Google Scholar 

  • Lee, I., Kim, Y.O., Park, S.C., and Chun, J. 2016. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol.66, 1100–1103.

    CAS  PubMed  Google Scholar 

  • Madhaiyan, M. and 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.

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Göker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics14, 60.

    PubMed  PubMed Central  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. Methods2, 233–241.

    CAS  Google Scholar 

  • Park, C., Lee, Y.S., Park, S., and Park, W. 2018. Methylobacterium currus sp. nov., isolated from a car air conditioning system. Int. J. Syst. Evol. Microbiol.68, 3621–3626.

    CAS  PubMed  Google Scholar 

  • Patt, T.E., Cole, G.C., Bland, J., and Hanson, R.S. 1974. Isolation and characterization of bacteria that grow on methane and organic compounds as sole sources of carbon and energy. J. Bacteriol.120, 955–964.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Patt, T.E., Cole, G.C., and Hanson, R.S. 1976. Methylobacterium, a new genus of facultatively methylotrophic bacteria. Int. J. Syst. Evol. Microbiol.26, 226–229.

    CAS  Google Scholar 

  • Raja, P., Balachandar, D., and Sundaram, S.P. 2008. Genetic diversity and phylogeny of pink-pigmented facultative methylotrophic bacteria isolated from the phyllosphere of tropical crop plants. Biol. Fertil. Soils45, 5–53.

    Google Scholar 

  • Richter, M. and Rosselló-Móra, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA106, 19126–19131.

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Schauer, S., Kämpfer, P., Wellner, S., Spröer, C., and 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.

    CAS  PubMed  Google Scholar 

  • Stothard, P. and Wishart, D.S. 2005. Circular genome visualization and exploration using CGView. Bioinformatics21, 537–539.

    CAS  PubMed  Google Scholar 

  • Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol.10, 512–526.

    CAS  PubMed  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.25, 4876–4882.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Trotsenko, Y.A., Ivanova, E.G., and Doronina, N.V. 2001. Aerobic methylotrophic bacteria as photosymbionts. Microbiology (English translation of Mikrobiologiya)70, 725–736.

    Google Scholar 

  • Ultee, A., Souvatzi, N., Maniadi, K., and Konig, H. 2004. Identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Germany. J. Appl. Microbiol.96, 560–568.

    CAS  PubMed  Google Scholar 

  • Veyisoglu, A., Camas, M., Tatar, D., Guven, K., Sazak, A., and Sahin, N. 2013. Methylobacterium tarhaniae sp. nov., isolated from arid soil. Int. J. Syst. Evol. Microbiol.63, 2823–2828.

    CAS  PubMed  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol.173, 697–703.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wellner, S., Lodders, N., Glaeser, S.P., and 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.

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Weon, H.Y., Kim, B.Y., Joa, J.H., Son, J.A., Song, M.H., Kwon, S.W., Go, S.J., and Yoon, S.H. 2008. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int. J. Syst. Evol. Microbiol.58, 93–96.

    CAS  PubMed  Google Scholar 

  • Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., and Chun, J. 2017. A largescale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek110, 1281–1286.

    CAS  PubMed  Google Scholar 

  • Zimmerman, J.M. and Battista, J.R. 2006. 32 Measuring survival in microbial populations following exposure to ionizing radiation. Methods Microbiol.35, 745–754.

    Google Scholar 

Download references

Acknowledgements

This work was supported by a research grant from the Seoul Women’s University (2018), a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR2017-01107), and a National Research Foundation of Korea (NRF) grant by the Korean government (MIST) (NRF-2017R1A-2B4009448).

Author information

Authors and Affiliations

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

    Jiyoun Kim, Geeta Chhetri, Inhyup Kim, Hyungdong Kim & Taegun Seo

  2. Department of Bio & Environmental Technology, College of Natural Science, Seoul Women’s University, Seoul, 01797, Republic of 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. Hyungdong Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Myung Kyum Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Taegun Seo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Taegun Seo.

Ethics declarations

The authors declare that they have no conflicts of interest.

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, J., Chhetri, G., Kim, I. et al. Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil. J Microbiol. 57, 959–966 (2019). https://doi.org/10.1007/s12275-019-9007-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-019-9007-9

Keywords

Search

Navigation