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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 3

sp. nov., isolated from apple orchard soil Free

Abstract

A Gram-negative, motile by gliding, rod-shaped, aerobic bacterium, designated S7-3-19, was isolated from apple orchard soil in Gyeongsangnam-do Province, Republic of Korea, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain S7-3-19 belonged to the family and was most closely related to DSM 74 (96.38 %), MSd3 (96.38 %), JSH5-14 (96.35 %) and DG5A (96.24 %). Chemotaxonomic characteristics supported the classification of strain S7-3-19 within the genus . Summed feature 3 (C 7/C 6; 46.7 %) and Cω5 (23.8 %) were the major fatty acids. Phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified phospholipid and two unidentified lipids were the major polar lipids. Menaquinone with seven isoprene units was the predominant respiratory quinone. The G+C content of the genomic DNA of strain S7-3-19 was 48.6 mol%. On the basis of its phenotypic properties, genotypic distinctiveness and chemotaxonomic features, strain S7-3-19 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is S7-3-19 (=KCTC 52728=JCM 32131).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , soil bacteria and Spirosoma
© 2018 IUMS
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2018-03-01
2024-04-19
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References

  1. Larkin JM, Borrall R. Family I. Spirosomaceae Larkin and Borrall 1978, 595AL . In Krieg NR, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 1 Baltimore: Williams & Wilkins; 1984 pp. 125–126
     [Google Scholar]
  2. Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO et al. Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 2017; 67:1359–1365 [View Article][PubMed]
     [Google Scholar]
  3. Li Y, Ai MJ, Sun Y, Zhang YQ, Zhang JQ. Spirosoma lacussanchae sp. nov., a phosphate-solubilizing bacterium isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2017; 67:3144–3149 [View Article][PubMed]
     [Google Scholar]
  4. Lee JJ, Park SJ, Lee YH, Lee SY, Park S et al. Spirosoma luteolum sp. nov. isolated from water. J Microbiol 2017; 55:247–252 [View Article][PubMed]
     [Google Scholar]
  5. Oren A, Garrity GM. List of novel names and novel combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:2075–2078 [View Article][PubMed]
     [Google Scholar]
  6. Joo ES, Kim EB, Jeon SH, Srinivasan S, Kim MK. Spirosoma swuense sp. nov., isolated from wet soil. Int J Syst Evol Microbiol 2017; 67:532–536 [View Article][PubMed]
     [Google Scholar]
  7. Lee JJ, Lee YH, Park SJ, Lim S, Jeong SW et al. Spirosoma fluminis sp. nov., a gamma-radiation resistant bacterium isolated from sediment of the Han river in South Korea. Curr Microbiol 2016; 73:689–695 [View Article][PubMed]
     [Google Scholar]
  8. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:1095–1098 [View Article][PubMed]
     [Google Scholar]
  9. Lee JJ, Kang MS, Joo ES, Kim MK, Im WT et al. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J Microbiol 2015; 53:429–434 [View Article][PubMed]
     [Google Scholar]
  10. Lee JJ, Srinivasan S, Lim S, Joe M, Im S et al. Spirosoma radiotolerans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil. Curr Microbiol 2014; 69:286–291 [View Article][PubMed]
     [Google Scholar]
  11. Ahn JH, Weon HY, Kim SJ, Hong SB, Seok SJ et al. Spirosoma oryzae sp. nov., isolated from rice soil and emended description of the genus Spirosoma . Int J Syst Evol Microbiol 2014; 64:3230–3234 [View Article][PubMed]
     [Google Scholar]
  12. Fries J, Pfeiffer S, Kuffner M, Sessitsch A. Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea . Int J Syst Evol Microbiol 2013; 63:4586–4590 [View Article][PubMed]
     [Google Scholar]
  13. Kim MK, Srinivasan S, Back C-G, Joo ES, Lee S-Y et al. Complete genome sequence of Deinococcus swuensis, a bacterium resistant to radiation toxicity. Mol Cell Toxicol 2015; 11:315–321 [View Article]
     [Google Scholar]
  14. Kwak Y, Park GS, Shin JH. High quality draft genome sequence of the type strain of Pseudomonas lutea OK2T, a phosphate-solubilizing rhizospheric bacterium. Stand Genomic Sci 2016; 11:51 [View Article][PubMed]
     [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  16. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  19. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  23. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article][PubMed]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  25. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  26. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
     [Google Scholar]
  27. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580[PubMed]
     [Google Scholar]
  28. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 9th ed. San Francisco, USA: Benjamin Cummings; 2010
     [Google Scholar]
  29. Ten LN, Baek SH, Im WT, Lee M, Oh HW et al. Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea. Int J Syst Evol Microbiol 2006; 56:2677–2681 [View Article][PubMed]
     [Google Scholar]
  30. Wilson K. Preparation of genomic DNA from bacteria. In Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology New York: John Wiley & Sons, Inc; 1997 pp. 2.4.1–2.4.2
     [Google Scholar]
  31. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  32. Ten LN, Jung HM, Im WT, Yoo SA, Lee ST. Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 2008; 46:519–524 [View Article][PubMed]
     [Google Scholar]
  33. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  34. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  35. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  36. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–205 [Crossref]
     [Google Scholar]
  37. Chang X, Jiang F, Wang T, Kan W, Qu Z et al. Spirosoma arcticum sp. nov., isolated from high Arctic glacial till. Int J Syst Evol Microbiol 2014; 64:2233–2237 [View Article][PubMed]
     [Google Scholar]
  38. Lail K, Sikorski J, Saunders E, Lapidus A, Glavina del Rio T et al. Complete genome sequence of Spirosoma linguale type strain (1T). Stand Genomic Sci 2010; 2:176–184 [View Article][PubMed]
     [Google Scholar]
  39. Hatayama K, Kuno T. Spirosoma fluviale sp. nov., isolated from river water. Int J Syst Evol Microbiol 2015; 65:3447–3450 [View Article][PubMed]
     [Google Scholar]
  40. Joo ES, Lee JJ, Cha S, Jheong W, Seo T et al. Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J Microbiol 2015; 53:750–755 [View Article][PubMed]
     [Google Scholar]
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Spirosoma horti sp. nov., isolated from apple orchard soil
Int J Syst Evol Microbiol 68, 930 (2018); https://doi.org/10.1099/ijsem.0.002614
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