1887

Abstract

A Gram-staining-negative, aerobic, motile, rod-shaped, catalase- and oxidase-negative strain with one polar flagellum, designated THG-YS3.6, was isolated from rhizosphere soil of a mugunghwa flower collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10–37 °C (optimum 25–30 °C), at pH 6–8 (optimum 7.0) and with 0–2.0 % NaCl (optimum 1 %). The isoprenoid quinone was ubiquinone-8 (Q–8). The major cellular fatty acids were iso-C11: 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C16 : 0, C16 : 1ω7c alcohol, C16 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unknown phospholipid, one unknown lipid and three unknown aminolipids. The DNA G+C content of strain THG-YS3.6 was 65.3 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-YS3.6 were identified as Lysobacter yangpyeongensis KACC 11407 (98.7 %), Lysobacter oryzae KCTC 22249 (98.0 %), Lysobacter niabensis KACC 11587 (97.6 %) and Lysobacter terrae KACC 17646 (97.1 %). The DNA–DNA relatedness values between strain THG-YS3.6 and L. yangpyeongensis KACC 11407, L. oryzae KCTC 22249, L. niabensis KACC 11587 and L. terrae KACC 17646 were 53.8±1.0 %, 12.9±1.2 %, 10.9±0.6 % and 7.0±1.9 %, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA–DNA hybridization data, strain THG-YS3.6 represents a novel species of the genus Lysobacter , for which the name Lysobacter rhizophilus sp. nov. is proposed. The type strain is THG-YS3.6 (=KCTC 52082=CCTCC AB 2015358).

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2016-11-01
2019-10-17
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References

  1. Aslam Z., Yasir M., Jeon C. O., Chung Y. R..( 2009;). Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.). . Int J Syst Evol Microbiol59:675–680. [CrossRef][PubMed]
    [Google Scholar]
  2. Buck J. D..( 1982;). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. . Appl Environ Microbiol44:992–993.[PubMed]
    [Google Scholar]
  3. Chen W. M., Lin Y. S., Sheu D. S., Sheu S. Y..( 2012;). Delftia litopenaei sp. nov., a poly-β-hydroxybutyrate-accumulating bacterium isolated from a freshwater shrimp culture pond. . Int J Syst Evol Microbiol62:2315–2321. [CrossRef][PubMed]
    [Google Scholar]
  4. Christensen P., Cook F. D..( 1978;). Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. . Int J Syst Evol Microbiol28:367–393. [CrossRef]
    [Google Scholar]
  5. Collins M. D., Jones D..( 1980;). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. . J Appl Bacteriol48:459–470. [CrossRef]
    [Google Scholar]
  6. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E..( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol100:221–230. [CrossRef][PubMed]
    [Google Scholar]
  7. 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 Bacteriol39:224–229. [CrossRef]
    [Google Scholar]
  8. Felsenstein J..( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol17:368–376. [CrossRef][PubMed]
    [Google Scholar]
  9. Felsenstein J..( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution39:783–791. [CrossRef]
    [Google Scholar]
  10. Hall T. A..( 1999;). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser41:95–98.
    [Google Scholar]
  11. Hu H. Y., Lim B. R., Goto N., Fujie K..( 2001;). Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. . J Microbiol Methods47:17–24. [CrossRef][PubMed]
    [Google Scholar]
  12. Jørgensen N. O., Brandt K. K., Nybroe O., Hansen M..( 2009;). Delftia lacustris sp. nov., a peptidoglycan-degrading bacterium from fresh water, and emended description of Delftia tsuruhatensis as a peptidoglycan-degrading bacterium. . Int J Syst Evol Microbiol59:2195–2199. [CrossRef][PubMed]
    [Google Scholar]
  13. Kim O.-S., Cho Y.-J., Lee K., Yoon S.-H., Kim M., Na H., Park S.-C., Jeon Y. S., Lee J.-H. et al.( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol62:716–721. [CrossRef][PubMed]
    [Google Scholar]
  14. Kimura M..( 1984;). The Neutral Theory of Molecular Evolution. Cambridge:: Cambridge University Press;.
    [Google Scholar]
  15. Kluge A. G., Farris J. S..( 1969;). Quantitative phyletics and the evolution of anurans. . Syst Biol18:1–32.[CrossRef]
    [Google Scholar]
  16. Kovacs N..( 1956;). Identification of Pseudomonas pyocyanea by the oxidase reaction. . Nature178:703. [CrossRef][PubMed]
    [Google Scholar]
  17. Kroppenstedt R. M..( 1982;). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. . J Liq Chromatogr5:2359–2367. [CrossRef]
    [Google Scholar]
  18. Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A. et al.( 2007;). clustal w and clustal x version 2.0. . Bioinformatics23:2947–2948. [CrossRef][PubMed]
    [Google Scholar]
  19. Lee J. W., Im W. T., Kim M. K., Yang D. C..( 2006;). Lysobacter koreensis sp. nov., isolated from a ginseng field. . Int J Syst Evol Microbiol56:231–235. [CrossRef][PubMed]
    [Google Scholar]
  20. Mesbah M., Premachandran U., Whitman W. B..( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol39:159–167. [CrossRef]
    [Google Scholar]
  21. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H..( 1984;). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods2:233–241. [CrossRef]
    [Google Scholar]
  22. Ngo H. T., Won K., Du J., Son H. M., Park Y., Kook M., Kim K. Y., Jin F. X., Yi T. H..( 2015;). Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. . Int J Syst Evol Microbiol65:587–592. [CrossRef][PubMed]
    [Google Scholar]
  23. Park J. H., Kim R., Aslam Z., Jeon C. O., Chung Y. R..( 2008;). Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. . Int J Syst Evol Microbiol58:387–392. [CrossRef][PubMed]
    [Google Scholar]
  24. Saitou N., Nei M..( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol4:406–425.[PubMed]
    [Google Scholar]
  25. Sasser M..( 1990;). Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, , MIDI Technical Note 101.. Newark, DE:: MIDI Inc;.
    [Google Scholar]
  26. Shigematsu T., Yumihara K., Ueda Y., Numaguchi M., Morimura S., Kida K..( 2003;). Delftia tsuruhatensis sp. nov., a terephthalate-assimilating bacterium isolated from activated sludge. . Int J Syst Evol Microbiol53:1479–1483. [CrossRef][PubMed]
    [Google Scholar]
  27. Singh H., Du J., Ngo H. T. T., Won K. H., Yang J. E., Kim K. Y., Yi T. H..( 2015;). Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. . Antonie van Leeuwenhoek107:1437–1444.[CrossRef]
    [Google Scholar]
  28. Skerman V. B. D..( 1967;). A Guide to the Identification of the Genera of Bacteria, , 2nd edn.. Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  29. Stabili L., Gravili C., Tredici S. M., Piraino S., Talà A., Boero F., Alifano P..( 2008;). Epibiotic Vibrio luminous bacteria isolated from some Hydrozoa and Bryozoa species. . Microb Ecol56:625–636. [CrossRef][PubMed]
    [Google Scholar]
  30. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S..( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol30:2725–2729. [CrossRef][PubMed]
    [Google Scholar]
  31. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. et al.( 1987;). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol37:463–464.[CrossRef]
    [Google Scholar]
  32. Wei D. Q., Yu T. T., Yao J. C., Zhou E. M., Song Z. Q., Yin Y. R., Ming H., Tang S. K., Li W. J..( 2012;). Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. . Antonie van Leeuwenhoek102:643–651. [CrossRef][PubMed]
    [Google Scholar]
  33. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J..( 1991;). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol173: 697–703.[PubMed][CrossRef]
    [Google Scholar]
  34. Weon H. Y., Kim B. Y., Baek Y. K., Yoo S. H., Kwon S. W., Stackebrandt E., Go S. J..( 2006;). Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. . Int J Syst Evol Microbiol56:947–951. [CrossRef][PubMed]
    [Google Scholar]
  35. Weon H. Y., Kim B. Y., Kim M. K., Yoo S. H., Kwon S. W., Go S. J., Stackebrandt E..( 2007;). Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. . Int J Syst Evol Microbiol57:548–551. [CrossRef][PubMed]
    [Google Scholar]
  36. Yan Z. F., Lin P., Chu X., Kook M., Li C. T., Yi T. H..( 2016;). Aeromicrobium halotolerans sp. nov., isolated from desert soil sample. . Arch Microbiol198:423–427. [CrossRef][PubMed]
    [Google Scholar]
  37. Yu T. T., Zhou E. M., Yin Y. R., Yao J. C., Ming H., Dong L., Li S., Nie G., Li W. J..( 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 thermophilum comb. nov. . Antonie van Leeuwenhoek104:369–376. [CrossRef][PubMed]
    [Google Scholar]
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