Abstract
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-C17:1 ω9c 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.
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References
Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354
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 39:224–229
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Hall TA (1999). BioEdit: a user–friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic acids symposium series 41: 95–98
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
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 62:716–721
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Lee JW, Im WT, Kim MK, Yang DC (2006) Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 56:231–235
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
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
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 2:233–241
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 2–11
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
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 58:387–392
Saitou N, Nei M (1987) The neighbor–joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark: MIDI Inc
Skerman VBD (1967) A Guide to the Identification of the Genera of Bacteria, 2nd edn. Williams and Wilkins, Baltimore
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 56:625–636
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 44:846–849
Tamaoka J, Katayama-Fujiruma A, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacieriol 54:31–36
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 28:2731–2739
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
Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202
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 102:643–651
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
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
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
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 104:369–376
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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).
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Hina Singh and Juan Du have equally contributed to this work.
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Singh, H., Du, J., Ngo, H.T.T. et al. Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. Antonie van Leeuwenhoek 107, 1437–1444 (2015). https://doi.org/10.1007/s10482-015-0439-x
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DOI: https://doi.org/10.1007/s10482-015-0439-x