Antonie van Leeuwenhoek

, Volume 107, Issue 6, pp 1437–1444 | Cite as

Lysobacter fragariae sp. nov. and Lysobacterrhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant

  • Hina Singh
  • Juan Du
  • Hien T. T. Ngo
  • KyungHwa Won
  • Jung-Eun Yang
  • Ki-Young Kim
  • Tae-Hoo Yi
Original Paper


Two bacterial strains, designated THG-DN8.7T and THG-DN8.3T, were isolated from the rhizosphere of a strawberry plant in Gyeryong Mountain, South Korea. Cells of both isolates were observed to be Gram-negative, yellow-coloured and rod-shaped. Comparative 16S rRNA gene sequence analysis showed that strain THG-DN8.7T had highest sequence similarities to Lysobacter yangpyeongensis KACC 11407T (97.2 %), Lysobacter niabensis KACC 11587T (97.0 %) and Lysobacter oryzae KCTC 22249T (96.9 %), while strain THG-DN8.3T had closely similarity with L. niabensis KACC 11587T (98.1 %), L. oryzae KCTC 22249T (97.1 %) and L. yangpyeongensis KACC 11407T (96.1 %). DNA–DNA relatedness values between strains THG-DN8.7T and THG-DN8.3T and their closest phylogenetically neighbours were below 30.0 %, which indicates that strains THG-DN8.7T and THG-DN8.3T represent distinct species within the genus Lysobacter. Both strains were found to contain iso-C15:0, iso-C16:0 and iso-C17:1ω9c as predominant fatty acids and ubiquinone-8 as major isoprenoid quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strains THG-DN8.7T and THG-DN8.3T were determined to be 66.9 and 67.8 mol%, respectively. These data are consistent with the affiliation of the two new species represented by THG-DN8.7T and THG-DN8.3T to the genus Lysobacter. The names Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. are proposed for these species with the type strains THG-DN8.7T (=KCTC 42236T = JCM 30322T) and THG-DN8.3T (=KCTC 42237T = JCM 30321T), respectively.


Lysobacter fragariae Lysobacter rhizosphaerae Gram-negative 16S rRNA Ubiquinone-8 



This work was conducted under the industrial infrastructure program (No. N0000888) for fundamental technologies which is funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

Supplementary material

10482_2015_439_MOESM1_ESM.pdf (20 kb)
Supplementary material 1 (PDF 20 kb)
10482_2015_439_MOESM2_ESM.pdf (102 kb)
Supplementary material 2 (PDF 102 kb)
10482_2015_439_MOESM3_ESM.pdf (151 kb)
Supplementary material 3 (PDF 151 kb)


  1. Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393CrossRefGoogle Scholar
  2. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354PubMedCentralPubMedGoogle Scholar
  3. 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 Bacteriol 39:224–229CrossRefGoogle Scholar
  4. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  5. Hall TA (1999). BioEdit: a user–friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series 41: 95–98Google Scholar
  6. 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
  7. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon–e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  8. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  9. Lee JW, Im WT, Kim MK, Yang DC (2006) Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 56:231–235CrossRefPubMedGoogle Scholar
  10. Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Lai WA, Young CC (2015) Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie van Leeuwenhoek. doi:10.1007/s10482-015-0419-1
  11. 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
  12. Minnikin DE, O’Donnel AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parleet JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinines and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  13. Moore DD, Dowhan D (1995) Preparation and Analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11Google Scholar
  14. Ngo HTT, Won K, Du J, Son HM, Park Y, MooChang K, Kim KY, Jin FX, Yi TH (2014) Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.067397-0 Google Scholar
  15. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR (2008) Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. 341. Int J Syst Evol Microbiol 58:387–392CrossRefPubMedGoogle Scholar
  16. Saitou N, Nei M (1987) The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425Google Scholar
  17. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark: MIDI IncGoogle Scholar
  18. Skerman VBD (1967) A Guide to the Identification of the Genera of Bacteria, 2nd edn. Williams and Wilkins, BaltimoreGoogle Scholar
  19. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A, Boero F, Alifano P (2008) Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 56:625–636CrossRefPubMedGoogle Scholar
  20. 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 Evol Microbiol 44:846–849Google Scholar
  21. Tamaoka J, Katayama-Fujiruma A, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacieriol 54:31–36CrossRefGoogle Scholar
  22. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefPubMedCentralPubMedGoogle Scholar
  23. 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 25:4876–4882CrossRefPubMedCentralPubMedGoogle Scholar
  24. Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202CrossRefGoogle Scholar
  25. Wei DQ, Yu TT, Yao JC, Zhou EM, Song ZQ (2012) Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south–west China. Antonie Van Leeuwenhoek 102:643–651CrossRefPubMedGoogle Scholar
  26. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedCentralPubMedGoogle Scholar
  27. Yang SZ, Feng GD, Zhu HH, Wang YH (2014) Lysobacter mobilis sp. nov., isolated from abandoned lead–zinc ore. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.000026 Google Scholar
  28. Ye XM, Chu CW, Shi C, Zhu JC, He Q, He J (2014) Lysobacter caeni sp. nov., isolated from the sludge of pesticide manufacturing factory. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.000026 Google Scholar
  29. Yu TT, Zhou EM, Yin YR, Yao JC, Ming H, Dong L, Li S, Nie GX, Li WJ et al (2013) Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilumcomb. nov. Antonie Van Leeuwenhoek 104:369–376CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Hina Singh
    • 1
  • Juan Du
    • 1
  • Hien T. T. Ngo
    • 1
  • KyungHwa Won
    • 1
  • Jung-Eun Yang
    • 1
  • Ki-Young Kim
    • 2
  • Tae-Hoo Yi
    • 1
  1. 1.Department of Oriental Medicine Biotechnology, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea
  2. 2.Department of Genetic Engineering, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea

Personalised recommendations