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Spirosoma jeollabukense sp. nov., isolated from soil

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Abstract

A Gram-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S2-3-6T, was isolated from soil in Jeollabuk-do province, South Korea, and was characterized taxonomically using a polyphasic approach. According to a comparative 16S rRNA gene sequence analysis, strain S2-3-6T belonged to the family Cytophagaceae and was most closely related to Spirosoma endophyticum EX36T (98.2%), Spirosoma fluviale MSd3T (96.0%), and Spirosoma linguale DSM 74T (95.7%). Strain S2-3-6T contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, and C16:0 N alcohol as major cellular fatty acids, MK-7 as the predominant respiratory quinone, and phosphatidylethanolamine as the main polar lipid. The DNA G+C content of strain S2-3-6T was 47.8%. Phenotypic and chemotaxonomic data supported the affiliation of strain S2-3-6T to the genus Spirosoma. However, the DNA–DNA relatedness between strain S2-3-6T and Spirosoma endophyticum KACC 17920T was 27%, clearly showing that the isolate constitutes a new genospecies. Strain S2-3-6T could be clearly differentiated from its closest neighbors based on its phenotypic, genotypic, and chemotaxonomic features. Therefore, strain S2-3-6T represents a novel species of the genus Spirosoma, for which the name Spirosoma jeollabukense sp. nov. is proposed. The type strain is S2-3-6T (= KCTC 52725T = JCM 32129T).

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References

  • Agarwal S, Hunnicutt DW, McBride MJ (1997) Cloning and characterization of the Flavobacterium johnsoniae (Cytophaga johnsonae) gliding motility gene, gldA. Proc Natl Acad Sci USA 94:12139–12144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ahn JH, Weon HY, Kim SJ, Hong SB, Seok SJ, Kwon SW (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 KS, Kim MS, Park SC, Lee DW, Lee SD, Ka JO, Choi SK, Seong CN (2007) Spirosoma rigui sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 57:2870–2873

    Article  CAS  PubMed  Google Scholar 

  • Cappuccino JG, Sherman N (2010) Microbiology: a Laboratory Manual, 9th edn. Benjamin Cummings, San Francisco

    Google Scholar 

  • Chang X, Jiang F, Wang T, Kan W, Qu Z, Ren L, Fang C, Peng F (2014) Spirosoma arcticum sp. nov., isolated from high arctic glacial till. Int J Syst Evol Microbiol 64:3230–3234

    Article  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

    Article  CAS  PubMed  Google Scholar 

  • Finster KW, Herbert RA, Lomstein BA (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 

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

    Article  Google Scholar 

  • Fries J, Pfeiffer S, Kuffner M, 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 TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Hatayama K, Kuno T (2015) Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 65:3447–3450

    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 

  • Joo ES, Kim EB, Jeon SH, Srinivasan S, Kim MK (2017) Spirosoma swuense sp. nov., a bacterium isolated from wet soil. Int J Syst Evol Microbiol 67:532–536

    Article  PubMed  Google Scholar 

  • Kim DU, Lee H, Kim SG, Ahn JH, Park SY, Ka JO (2015) 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 SJ, Ahn JH, Weon HY, Hong SB, Seok SJ, Kim JS, Kwon SW (2016) Spirosoma aerophilum sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 66:2342–2346

    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  Google Scholar 

  • Kwak Y, Li QX, Shin JH (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 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 JM, Borrall R (1984) Family I. Spirosomaceae Larkin and Borrall 1978, 595AL. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 1. Williams & Wilkins, Baltimore, pp 125–126

    Google Scholar 

  • Lee JJ, Srinivasan S, Lim S, Joe M, Im S, Bae SI, Park KR, Han JH, Park SH, Joo BM, Park SJ, Kim MK (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 

  • Lee JJ, Kang MS, Joo ES, Kim MK, Im WT, Jung HY, 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 JJ, Lee YH, Park SJ, Lim S, Jeong SW, Lee SY, Cho YJ, Kim MK, Jung HY (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 JJ, Lee YH, Park SJ, Lee SY, Kim BO, Ten LN, Kim MK, Jung HY (2017a) Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 67:1359–1365

    Article  PubMed  Google Scholar 

  • Lee JJ, Park SJ, Lee YH, Lee SY, Park S, Cho YJ, Kim MK, Ten LN, Jung HY (2017b) Spirosoma luteolum sp. nov. isolated water. J Microbiol 55:247–252

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Ai MJ, Sun Y, Zhang YQ, Zhang JQ (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 QM, Ten LN, Yu HS, Jin FX, Im WT, Lee ST (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, Whitman WB (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 DE, O’Donnella AG, Goodfellowb M, Aldersonb G, Athalyeb M, Schaala 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 

  • Oren A, Garrity GM (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, Garrity GM (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, 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

    Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  • Srinivasan S, Kim M, Joo E, Lee SY, Lee DS, Jung HY (2015) Complete genome sequence of Rufibacter sp. DG31D, a bacterium resistant to gamma and UV radiation toxicity. Mol Cell Toxicol 11:415–421

    Article  CAS  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 

  • Ten LN, Xu JL, Jin FX, Im WT, Oh HM, Lee ST (2009) Spirosoma panaciterrae sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:331–335

    Article  CAS  PubMed  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 

  • Tittsler RP, Sandholzer LA (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 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 

  • Wilson K (1997) Preparation of genomic DNA from bacteria. In: Ausubel FM et al (eds). Current protocols in molecular biology. Wiley, New York.2.4.1–2.4.5.

    Google Scholar 

  • Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2016) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Google Scholar 

Download references

Acknowledgements

This work was supported by a Cooperative Research Program for Agriculture Science and Technology Development Rural Development Administration, Republic of Korea and the Brain Pool Program of 2016 through the Korean Federation of Science and Technology Societies (KOFST) funded by the Ministry of Science, ICT and Future Planning, Republic of Korea.

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Authors and Affiliations

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

    Weilan Li, Leonid N. Ten, 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. Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea

    Hee-Young Jung

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  1. Weilan Li
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Correspondence to Hee-Young Jung.

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Communicated by Erko Stackebrandt.

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Li, W., Ten, L.N., Lee, SY. et al. Spirosoma jeollabukense sp. nov., isolated from soil. Arch Microbiol 200, 431–438 (2018). https://doi.org/10.1007/s00203-017-1453-3

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  • DOI: https://doi.org/10.1007/s00203-017-1453-3

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