1887

Abstract

A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain C8-1, was isolated from the rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10–40 °C, at pH 6.0–8.0 and in the presence of up to 1 % (w/v) NaCl, with optimal growth at 30 °C and pH 7.0. The predominant isoprenoid quinone was Q-8. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. The genomic DNA G+C content was 70.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C8-1 should be assigned to the genus Lysobacter . 16S rRNA gene sequence similarity analysis showed that strain C8-1 was closely related to Lysobacter cavernae YIM C01544 (98.6 %), Lysobacter soli DCY21 (97.6 %), Lysobacter panacisoli CJ29 (97.3 %), Lysobacter firmicutimachus PB-6250 (97.3 %), Lysobacter niastensis GH41-7 (97.3 %) and Lysobacter gummosus KCTC 12132 (97.1 %). DNA–DNA hybridization data indicated that the isolate may represent a novel genomic species belonging to the genus Lysobacter . Polyphasic taxonomic characteristics indicated that strain C8-1 represents a novel species of the genus Lysobacter , for which the name Lysobacter tabacisoli sp. nov. is proposed. The type strain is C8-1 (=KCTC 62034=CGMCC 1.16271) .

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2018-12-12
2024-03-29
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References

  1. Christensen P, Cook FD. Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 1978; 28:367–393 [View Article]
    [Google Scholar]
  2. Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW et al. Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 2006; 56:947–951 [View Article][PubMed]
    [Google Scholar]
  3. Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ et al. Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:1543–1547 [View Article][PubMed]
    [Google Scholar]
  4. Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW et al. Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 2007; 57:548–551 [View Article][PubMed]
    [Google Scholar]
  5. Wei DQ, Yu TT, Yao JC, Zhou EM, Song ZQ et al. Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. Antonie van Leeuwenhoek 2012; 102:643–651 [View Article][PubMed]
    [Google Scholar]
  6. Chen W, Zhao YL, Cheng J, Zhou XK, Salam N et al. Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample. Antonie van Leeuwenhoek 2016; 109:1047–1053 [View Article][PubMed]
    [Google Scholar]
  7. Choi JH, Seok JH, Cha JH, Cha CJ. Lysobacter panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 2014; 64:2193–2197 [View Article][PubMed]
    [Google Scholar]
  8. Miess H, van Trappen S, Cleenwerck I, de Vos P, Gross H. Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov. Int J Syst Evol Microbiol 2016; 66:4162–4166 [View Article][PubMed]
    [Google Scholar]
  9. Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H et al. Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 2013; 63:3313–3318 [View Article][PubMed]
    [Google Scholar]
  10. Siddiqi MZ, Im WT. Lysobacter hankyongensis sp. nov., isolated from activated sludge and Lysobacter sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2016; 66:212–218 [View Article][PubMed]
    [Google Scholar]
  11. Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH et al. Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum . Antonie van Leeuwenhoek 2015; 107:1261–1270 [View Article][PubMed]
    [Google Scholar]
  12. Ahmed K, Chohnan S, Ohashi H, Hirata T, Masaki T et al. Purification, bacteriolytic activity, and specificity of beta-lytic protease from Lysobacter sp. IB-9374. J Biosci Bioeng 2003; 95:27–34 [View Article][PubMed]
    [Google Scholar]
  13. Folman LB, de Klein M, Postma J, van Veen JA. Production of antifungal compounds by Lysobacter enzymogenesisolate 3.1T8 under different conditions in relation to its efficacyas a biocontrol agent of Pythium aphanidermatum in cucumber. BiolControl 2004; 31:145–154
    [Google Scholar]
  14. de Bruijn I, Cheng X, de Jager V, Expósito RG, Watrous J et al. Comparative genomics and metabolic profiling of the genus Lysobacter . BMC Genomics 2015; 16:991 [View Article][PubMed]
    [Google Scholar]
  15. Ryazanova LP, Stepnaya OA, Suzina NE, Kulaev IS. Antifungal action of the lytic enzyme complex from Lysobacter sp. XL1. Process Biochem 2005; 40:557–564 [View Article]
    [Google Scholar]
  16. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  17. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams; 1967
    [Google Scholar]
  18. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  19. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  20. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp. 607–655
    [Google Scholar]
  21. Puopolo G, Tomada S, Sonego P, Moretto M, Engelen K et al. The Lysobacter capsici AZ78 Genome Has a Gene Pool Enabling it to Interact Successfully with Phytopathogenic Microorganisms and Environmental Factors. Front Microbiol 2016; 7:96 [View Article][PubMed]
    [Google Scholar]
  22. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  23. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newwark, DE: MIDI Inc; 1990
    [Google Scholar]
  26. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiol 2017; 57:1424–1428
    [Google Scholar]
  27. 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; 67:1613–1618 [View Article][PubMed]
    [Google Scholar]
  28. 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]
  29. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  34. Ezaki T, Hashimoto Y, Yabuuchi E. 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 1989; 39:224–229 [View Article]
    [Google Scholar]
  35. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M. DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 2000; 50:1095–1102 [View Article][PubMed]
    [Google Scholar]
  36. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article][PubMed]
    [Google Scholar]
  37. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 1999; 27:4636–4641 [View Article][PubMed]
    [Google Scholar]
  38. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler OK et al. International committee on systematic bacteriology. report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacterio 1987; l37:463–464
    [Google Scholar]
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