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Lysobacter terrigena sp. nov., isolated from a Korean soil sample

  • Weilan Li
  • Nabil Salah Elderiny
  • Leonid N. Ten
  • Seung-Yeol Lee
  • Myung Kyum Kim
  • Hee-Young JungEmail author
Original Paper
  • 34 Downloads

Abstract

A bacterial strain isolated from a soil collected in Jeju Island, designated as 17J7-1T, was Gram-negative, rod-shaped, yellow colored, and motile by gliding. This strain was able to grow at temperature range from 10 to 42 °C, pH 7–9, and tolerated up to 1% NaCl. Analysis of 16S rRNA sequence identified strain 17J7-1T as a member of the genus Lysobacter with close sequence similarity with Lysobacter mobilis 9NM-14T (97.4%), Lysobacter xinjiangensis RCML-52T (97.0%), and Lysobacter humi FJY8T (96.9%). The genomic DNA G + C content of the isolate was 67.9 mol%. DNA–DNA relatedness between strain 17J7-1T and L. mobilis, L. humi, and L. xinjiangensis were 42.3%, 39.5%, and 35.8%, respectively, clearly showing that the isolate is distinct from its closest phylogenetic neighbors in the genus Lysobacter. Average nucleotide identity (ANI) and digital DNA–DNAhybridization (dDDH) values between strain 17J7-1T and L. enzymogenes ATCC 29487T, the type species of this genus, and several other close Lysobacter species were less than 77% and 22%, respectively. Major fatty acids were C16:0 iso (29.8%), summed feature 9 (C17:1 iso ω9c/C16:0 10-methyl; 20.1%), and C15:0 iso (17.7%). The predominant respiratory quinone was ubiquinone Q-8 and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. In the light of the polyphasic evidence accumulated in this study, strain 17J7-1T is considered to represent a novel species in the genus Lysobacter, for which name Lysobacter terrigena sp. nov. is proposed. The type strain is 17J7-1T (= KCTC 62217T = JCM 33057T).

Keywords

Lysobacter Lysobacteraceae Soil bacteria 

Notes

Acknowledgements

This research was supported by Kyungpook National University Development Project Research Fund, 2018.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

203_2019_1776_MOESM1_ESM.docx (4.5 mb)
Supplementary file1 (DOCX 4573 kb)

References

  1. Agarwal S, Hunnicutt DW, McBride MJ (1997) Cloning and characterization of the Flavobacterium johnsoniae (Cytophaga johnsonae) gliding motility gene, gldA. Proc Natl Acad Sci USA 94:12139–12144CrossRefGoogle Scholar
  2. Aslam Z, Im WT, Ten LN, Lee MJ, Kim KH, Lee ST (2006) Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea. Int J Syst Evol Microbiol 56:2209–2213CrossRefGoogle Scholar
  3. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC genomics 9:75CrossRefGoogle Scholar
  4. Cappuccino JG, Sherman N (2010) Microbiology: a laboratory manual, 9th edn. Benjamin Cummings, San FranciscoGoogle Scholar
  5. Chen W, Zhao YL, Cheng J, Zhou XK, Salam N, Fang BZ, Li QQ, Hozzein WN, Li WJ (2016) Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample. Antonie Van Leeuwenhoek 109:1047–1053CrossRefGoogle Scholar
  6. Christensen P (2005) Genus IV Lysobacter Christensen and Cook 1978 372AL. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, pp 95–101.Google Scholar
  7. Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Evol Microbial 28:367–393Google Scholar
  8. 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 Evol Microbiol 39:224–229Google Scholar
  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
  10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  12. 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 App Microbiol 42:457–469CrossRefGoogle Scholar
  13. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
  14. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567–2572CrossRefGoogle Scholar
  15. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  16. La HJ, Im WT, Ten LN, Kang MS, Shin DY, Lee ST (2005) Paracoccus koreensis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket (UASB) reactor. Int J Syst Evol Microbiol 55:1657–1660CrossRefGoogle Scholar
  17. Lee D, Jang JH, Cha S, Seo T (2017a) Lysobacter humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 67:951–955CrossRefGoogle Scholar
  18. Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO, Ten LN, Kim MK, Jung HY (2017b) Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 67:1359–1365CrossRefGoogle Scholar
  19. Li J, Han Y, Guo W, Wang Q, Liao S, Wang G (2018) Lysobacter tongrenensis sp. nov., isolated from soil of a manganese factory. Arch Microbiol 200:439–444CrossRefGoogle Scholar
  20. Liu M, Liu Y, Wang Y, Luo X, Dai J, Fang C (2011) Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample. Int J Syst Evol Microbiol 61:433–437CrossRefGoogle Scholar
  21. Margesin R, Zhang DC, Albuquerque L, Froufe HJ, Egas C, da Costa MS (2018) Lysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov. Int J Syst Evol Microbiol 68:1571–1577CrossRefGoogle Scholar
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf 14:60CrossRefGoogle Scholar
  23. Minnikin DE, O’Donnella AG, Goodfellowb M, Aldersonb G, Athalyeb M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
  24. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  25. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical note 101. MIDI Inc, Newark, DE, USAGoogle Scholar
  26. Siddiqi MZ, Im WT (2016) Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. Arch Microbiol 198:551–557CrossRefGoogle Scholar
  27. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
  28. 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 Bacteriol 44:846–849CrossRefGoogle Scholar
  29. Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol 9:678–687PubMedGoogle Scholar
  30. Ten LN, Baek SH, Im WT, Lee M, Oh HW, Lee ST (2006) Paenibacillus panacisoli sp. nov., a xylanolytic bacterium isolated from soil in a ginseng field in South Korea. Int J Syst Evol Microbiol 56:2677–2681CrossRefGoogle Scholar
  31. Ten LN, Jung HM, Yoo SA, Im WT, Lee ST (2008) Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea. J Microbiol 46:519–524CrossRefGoogle Scholar
  32. 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 25:4876–4882CrossRefGoogle Scholar
  33. Tittsler RP, Sandholzer LA (1936) The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 31:575–580PubMedCentralGoogle Scholar
  34. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky I, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464CrossRefGoogle Scholar
  35. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefGoogle Scholar
  36. Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R (2016) Lysobacter chengduensis sp. nov. isolated from the air of captive Ailuropoda melanoleuca enclosures in Chengdu, China. Curr Microbiol 72:88–93CrossRefGoogle Scholar
  37. Wilson K (1997) Preparation of genomic DNA from bacteria. In: Ausubel FM, et al. (eds) Current protocols in molecular biology. Wiley, New York, pp 241–245Google Scholar
  38. Yang SZ, Feng GD, Zhu HH, Wang YH (2015) Lysobacter mobilis sp. Nov., isolated from abandoned lead-zinc ore. Int J Syst Evol Microbial 65:833–837CrossRefGoogle Scholar
  39. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBio-Cloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefGoogle Scholar
  40. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286CrossRefGoogle Scholar
  41. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669–2677CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Weilan Li
    • 1
  • Nabil Salah Elderiny
    • 1
  • Leonid N. Ten
    • 1
  • Seung-Yeol Lee
    • 1
  • Myung Kyum Kim
    • 2
  • Hee-Young Jung
    • 1
    • 3
    Email author
  1. 1.School of Applied BiosciencesKyungpook National UniversityDaeguRepublic of Korea
  2. 2.Department of Bio and Environmental TechnologySeoul Women’s UniversitySeoulRepublic of Korea
  3. 3.Institute of Plant MedicineKyungpook National UniversityDaeguRepublic of Korea

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