Current Microbiology

, Volume 75, Issue 3, pp 328–335 | Cite as

Spirosoma humi sp. nov., Isolated from Soil in South Korea

  • Li Weilan
  • Jae-Jin Lee
  • Seung-Yeol Lee
  • Sangkyu Park
  • Leonid N. Ten
  • Hee-Young Jung
Article
  • 36 Downloads

Abstract

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated S7-4-1T, was isolated from soil in Gyeongsangnam-do, South Korea and characterized using a polyphasic approach to determine its taxonomic position. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain S7-4-1T belonged to the family Cytophagaceae and was most closely related to Spirosoma fluviale MSd3T (96.2%), ‘Spirosoma radiotolerans’ DG5A (96.0%), Spirosoma pulveris JSH5-14T (95.9%), and Spirosoma linguale DSM 74T (95.8%). The G+C content of the genomic DNA of the isolate was 49.0 mol%. The strain contained summed feature 3 (C16:1 ω7c/C16:1 ω6c; 41.0%), C16:1 ω5c (24.9%), and C15:0 iso (9.3%) as the major fatty acids, menaquinone MK-7 as the predominant respiratory quinone, and phosphatidylethanolamine and an unidentified aminophospholipid as the main polar lipids, which supported its affiliation with the genus Spirosoma. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of the isolate from recognized Spirosoma species. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain S7-4-1T represents a novel species of the genus Spirosoma, for which the name Spirosoma humi sp. nov. is proposed. The type strain is S7-4-1T (= KCTC 52729T = JCM 32132T).

Notes

Acknowledgements

This work was supported by a Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ011631042017) Rural Development Administration, Republic of Korea, and the Brain Pool Program of 2016 (Grant 162S-4-3-1727) through the Korean Federation of Science and Technology Societies (KOFST) funded by the Ministry of Science, ICT and Future Planning, Republic of Korea.

Compliance with Ethical Standards

Conflict of interest

The authors declare that there are no conflicts of interest.

Supplementary material

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References

  1. 1.
    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 94:12139–12144CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    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 64:3230–3234CrossRefPubMedGoogle Scholar
  3. 3.
    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 57:2870–2873CrossRefPubMedGoogle Scholar
  4. 4.
    Cappuccino JG, Sherman N (2010) Microbiology: a laboratory manual, 9th edn. Benjamin Cummings, San FranciscoGoogle Scholar
  5. 5.
    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 64:3230–3234CrossRefGoogle Scholar
  6. 6.
    Eldariny N, Ten LN, Lee JJ, Lee YH, Park SJ, Cho YJ, Kim MK, Jung HY (2017) Spirosoma daeguensis sp. nov., isolated from beach soil. J Microbiol 55:678–683CrossRefGoogle Scholar
  7. 7.
    Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  8. 8.
    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 59:839–844CrossRefPubMedGoogle Scholar
  9. 9.
    Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  10. 10.
    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 63:4586–4590CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  12. 12.
    Hatayama K, Kuno T (2015) Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 65:3447–3450CrossRefPubMedGoogle Scholar
  13. 13.
    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 42:457–469CrossRefGoogle Scholar
  14. 14.
    Joo ES, Lee JJ, Cha S, Jheong W, Seo T, Lim S, Jeong SW, Srinivasan S (2015) Spirosoma pulveris sp.nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J Microbiol 53:750–755CrossRefPubMedGoogle Scholar
  15. 15.
    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 67:532–536CrossRefPubMedGoogle Scholar
  16. 16.
    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 65:4003–4007CrossRefPubMedGoogle Scholar
  17. 17.
    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 66:2342–2346CrossRefPubMedGoogle Scholar
  18. 18.
    Kim M, Srinivasan S, Back CG, Joo E, Lee SY, Jung HY (2015) Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol Cell Toxicol 11:315–321CrossRefGoogle Scholar
  19. 19.
    Kwak Y, Park GS, Shin JH (2016) (2016) High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium. Stand Genom Sci 11:51CrossRefGoogle Scholar
  20. 20.
    Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  21. 21.
    Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
  22. 22.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  23. 23.
    Lail K, Sikorski J, Saunders E, Lapidus A et al (2010) Complete genome sequence of Spirosoma linguale type strain (1T). Stand Genom Sci 2:176–185CrossRefGoogle Scholar
  24. 24.
    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, MD, pp 125–126Google Scholar
  25. 25.
    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 69:286–291CrossRefPubMedGoogle Scholar
  26. 26.
    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 73:689–695CrossRefPubMedGoogle Scholar
  27. 27.
    Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO, Ten LN, Kim MK, Jung HY (2017) Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 67:1359–1365CrossRefPubMedGoogle Scholar
  28. 28.
    Lee JJ, Park SJ, Lee YH, Lee SY, Park S, Cho YJ, Kim MK, Ten LN, Jung HY (2017) Spirosoma luteolum sp. nov. isolated from water. J Microbiol 55:247–252CrossRefPubMedGoogle Scholar
  29. 29.
    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 67:3144–3149CrossRefPubMedGoogle Scholar
  30. 30.
    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 39:159–167CrossRefGoogle Scholar
  31. 31.
    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 2:233–241CrossRefGoogle Scholar
  32. 32.
    Oren A, Garrity GM (2017) List of novel names and novel combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 67:2075–2078CrossRefPubMedGoogle Scholar
  33. 33.
    Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  34. 34.
    Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  35. 35.
    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 607–654Google Scholar
  36. 36.
    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 44:846–849CrossRefGoogle Scholar
  37. 37.
    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 59:331–335CrossRefPubMedGoogle Scholar
  38. 38.
    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 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Tittsler RP, Sandholzer LA (1936) The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580PubMedPubMedCentralGoogle Scholar
  40. 40.
    Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  41. 41.
    Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Wilson K (1997)Preparation of genomic DNA from bacteria. In: Ausubel FM et al (ed) Current protocols in molecular biology, Wiley, Hoboken, 2.4.1–2.4.5, Supplement 17Google Scholar
  43. 43.
    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 67:1613–1617CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  • Li Weilan
    • 1
  • Jae-Jin Lee
    • 1
  • Seung-Yeol Lee
    • 1
  • Sangkyu Park
    • 1
  • Leonid N. Ten
    • 1
  • Hee-Young Jung
    • 1
    • 2
  1. 1.School of Applied BiosciencesKyungpook National UniversityDaeguRepublic of Korea
  2. 2.Institute of Plant MedicineKyungpook National UniversityDaeguRepublic of Korea

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