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Spirosoma migulaei sp. nov., isolated from soil

  • Microbial Systematics and Evolutionary Microbiology
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Abstract

A Gram-stain-negative, non-motile, non-spore-forming, rod-shaped, aerobic bacterium, designated 15J9-8T, was isolated from soil on Jeju Island, Republic of Korea. The isolate was able to grow between 10 and 30°C, pH 6.5–8.5, and in presence of 0–1% (w/v) NaCl. The results of comparative 16S rRNA gene sequence analysis indicated that strain 15J9-8T represented a member of the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to Spirosoma aerophilum 5516J-17T (96.1% similarity), Spirosoma pulveris JSH5-14T (95.6%), and Spirosoma linguale DSM 74T (95.2%). The G + C content of the genomic DNA of the isolate was 47.0 mol%. Strain 15J9-8T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and iso-C15:0 as the major fatty acids, phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, and menaquinone MK-7 as the predominant respiratory quinone. On the basis of its phenotypic and genotypic properties, and phylogenetic distinctiveness, strain 15J9-8T should be classified as a representative of a novel species of the genus Spirosoma, for which the name Spirosoma migulaei sp. nov. is proposed. The type strain is 15J9-8T (=KCTC 52028T =JCM 31996T).

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References

  • Ahn, J.H., Weon, H.Y., Kim, S.J., Hong, S.B., Seok, S.J., and Kwon, S.W. 2014. Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma. Int. J. Syst. Evol. Microbiol. 64, 3230–3234.

    Article  CAS  PubMed  Google Scholar 

  • Baik, K.S., Kim, M.S., Park, S.C., Lee, D.W., Lee, S.D., Ka, J.O., Choi, S.K., and Seong, C.N. 2007. Spirosoma rigui sp. nov., isolated from fresh water. Int. J. Syst. Evol. Microbiol. 57, 2870–2873.

    Article  CAS  PubMed  Google Scholar 

  • Cappuccino, J.G. and Sherman, N. 2010. Microbiology: A laboratory manual, 9th edn. Benjamin Cummings, San Francisco, USA.

    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 

  • Finster, K.W., Herbert, R.A., and Lomstein, B.A. 2009. Spirosoma spitsbergense sp. nov. and Spirosoma luteum sp. nov., isolated from a high Arctic permafrost soil, and emended description of the genus Spirosoma. Int. J. Syst. Evol. Microbiol. 59, 839–844.

    Article  CAS  PubMed  Google Scholar 

  • Fries, J., Pfeiffer, S., Kuffner, M., and Sessitsch, A. 2013. Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea. Int. J. Syst. Evol. Microbiol. 63, 4586–4590.

    Article  CAS  PubMed  PubMed Central  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 

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

  • Joo, E.S., Kim, E.B., Jeon, S.H., Srinivasan, S., and Kim, M.K. 2017. Spirosoma swuense sp. nov., a bacterium isolated from wet soil. Int. J. Syst. Evol. Microbiol. 67, 532–536.

    Article  PubMed  Google Scholar 

  • Joo, E.S., Lee, J.J., Cha, S., Jheong, W., Seo, T., Lim, S., Jeong, S.W., and Srinivasan, S. 2015. Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J. Microbiol. 53, 750–755.

    Article  CAS  PubMed  Google Scholar 

  • Kim, S.J., Ahn, J.H., Weon, H.Y., Hong, S.B., Seok, S.J., Kim, J.S., and Kwon, S.W. 2016. Spirosoma aerophilum sp. nov., isolated from an air sample. Int. J. Syst. Evol. Microbiol. 66, 2342–2346.

    Article  CAS  PubMed  Google Scholar 

  • Kim, D.U., Lee, H., Kim, S.G., Ahn, J.H., Park, S.Y., and Ka, J.O. 2015a. Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system. Int. J. Syst. Evol. Microbiol. 65, 4003–4007.

    Article  CAS  PubMed  Google Scholar 

  • Kim, M., Srinivasan, S., Back, C.G., Joo, E., Lee, S.Y., and Jung, H.Y. 2015b. Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol. Cell. Toxicol. 11, 315–321.

    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. and Suzuki, K. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 1–207.

    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.

    Article  CAS  PubMed  Google Scholar 

  • Kwak, Y., Li, Q.X., and Shin, J.H. 2016. Draft genome sequence of Mycobacterium rufum JS14T, a polycyclic-aromatic hydrocarbon- degrading bacterium from petroleum-contaminated soil in Hawaii. Stand. Genomic Sci. 11, 47.

    Article  PubMed  PubMed Central  Google Scholar 

  • Lail, K., Sikorski, J., Saunders, E., Lapidus, A., Glavina del Rio, T., Copeland, A., Tice, H., Cheng, J.F., Lucas, S., Nolan, M., et al. 2010. Complete genome sequence of Spirosoma linguale type strain (1T). Stand. Genomic Sci. 2, 176–185.

    Article  PubMed  PubMed Central  Google Scholar 

  • Larkin, J.M. and Borrall, R. 1984. Family I. Spirosomaceae larkin and borrall 1978, 595AL, pp. 125–126. In Krieg, N.R. and Holt, J.G. (eds.), Bergey’s Manual of Systematic Bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, Maryland, USA.

  • Lee, J.J., Kang, M.S., Joo, E.S., Kim, M.K., Im, W.T., Jung, H.Y., and Srinivasan, S. 2015. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J. Microbiol. 53, 429–434.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J.J., Lee, Y.H., Park, S.J., Lee, S.Y., Kim, B.O., Ten, L.N., Kim, M.K., and Jung, H.Y. 2017a. Spirosoma knui sp. nov., a radiationresistant bacterium isolated from the Han River. Int. J. Syst. Evol. Microbiol. 67, 1359–1365.

    Article  PubMed  Google Scholar 

  • Lee, J.J., Lee, Y.H., Park, S.J., Lim, S., Jeong, S.W., Lee, S.Y., Cho, Y.J., Kim, M.K., and Jung, H.Y. 2016. Spirosoma fluminis sp. nov., a gamma–radiation resistant bacterium isolated from sediment of the Han River in South Korea. Curr. Microbiol. 73, 689–695.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J.J., Park, S.J., Lee, Y.H., Lee, S.Y., Park, S., Cho, Y.J., Kim, M.K., Ten, L.N., and Jung, H.Y. 2017b. Spirosoma luteolum sp. nov. isolated water. J. Microbiol. 55, 247–252.

    Article  CAS  PubMed  Google Scholar 

  • Lee, J.J., Srinivasan, S., Lim, S., Joe, M., Im, S., Bae, S.I., Park, K.R., Han, J.H., Park, S.H., Joo, B.M., et al. 2014. Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. Curr. Microbiol. 69, 286–291.

    Article  CAS  PubMed  Google Scholar 

  • Li, Y., Ai, M.J., Sun, Y., Zhang, Y.Q., and Zhang, J.Q. 2017. Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a fresh water reservoir. Int. J. Syst. Evol. Microbiol. 67, 3144–3149.

    Article  PubMed  Google Scholar 

  • Liu, Q.M., Ten, L.N., Yu, H.S., Jin, F.X., Im, W.T., and Lee, S.T. 2008. Emticicia ginsengisoli sp. nov., a species of the family ‘Flexibacteraceae’ isolated from soil of a ginseng field. Int. J. Syst. Evol. Microbiol. 58, 1100–1105.

    Article  CAS  PubMed  Google Scholar 

  • Mesbah, M., Premachandran, U., and Whitman, W.B. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39, 159–167.

    Article  CAS  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 

  • Oren, A. and Garrity, G.M. 2017a. List of novel names and novel combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol. 67, 1095–1098.

    Article  PubMed  Google Scholar 

  • Oren, A. and Garrity, G.M. 2017b. List of novel names and novel combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol. 67, 2075–2078.

    Article  PubMed  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 

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

    Google Scholar 

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

  • Stackebrandt, E. and Goebel, B.M. 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 

  • Ten, L.N., Xu, J.L., Jin, F.X., Im, W.T., Oh, H.M., and Lee, S.T. 2009. Spirosoma panaciterrae sp. nov., isolated from soil. Int. J. Syst. Evol. Microbiol. 59, 331–335.

    Article  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. 24, 4876–4882.

    Article  Google Scholar 

  • Tittsler, R.P. and Sandholzer, L.A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575–580.

    CAS  PubMed  PubMed Central  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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson, K. 1997. Preparation of genomic DNA from bacteria. In Ausubel., F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. (eds.), Current Protocols in Molecular Biology, InterScience, 2.4.1–2.4.5, Supplement 27. John Wiley & Sons, Inc., USA.

  • 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 

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Authors and Affiliations

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

    Joseph Okiria, Leonid N. Ten, Su-Jin Park, Seung-Yeol Lee & Hee-Young Jung

  2. Planning and Coordination Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, Republic of Korea

    Dong Hoon Lee

  3. Department of Horticultural Science, Kyungpook National University, Daegu, 41566, Republic of Korea

    In-Kyu Kang

  4. Department of Environmental Engineering, Kyungpook National University, Daegu, 41566, Republic of Korea

    Dae Sung Lee

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

    Hee-Young Jung

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  1. Joseph Okiria
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Correspondence to Hee-Young Jung.

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Okiria, J., Ten, L.N., Park, SJ. et al. Spirosoma migulaei sp. nov., isolated from soil. J Microbiol. 55, 927–932 (2017). https://doi.org/10.1007/s12275-017-7377-4

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  • DOI: https://doi.org/10.1007/s12275-017-7377-4

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