Skip to main content
SpringerLink
Log in

Lysobacter segetis sp. nov., Isolated from Soil

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

A Gram-negative, aerobic, motile by gliding, rod-shaped bacterium, strain 17J68-2T, was isolated from a soil sample taken from Jeju Island, Republic of Korea. The isolate displayed high 16S rRNA gene sequence similarity to the members of the genus Lysobacter in the family Lysobacteraceae, with Lysobacter humi FJY8T (98.4% similarity), Lysobacter xinjiangensis RCML-52T (98.3%), and Lysobacter mobilis 9NM-14T (98.1%) as closest phylogenetic neighbors. Growth of strain 17J68-2T occurred at 15–42 °C, pH 7–8, and in the presence of 0–1.0% NaCl. Draft genome was 2.94 Mb in size with G+C content of 70.5 mol%. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. Ubiquinone Q-8 was the predominant respiratory quinone and the major fatty acids were C16:0 iso (39.4%), summed feature 3 (C16:1ω7c/C16:1ω6c) (6.6%), C11:0 iso 3–OH (6.4%), C15:0 iso (6.4%), and C16:1 iso H (6.2%). The DNA–DNA relatedness between strain 17J68-2T and L. humi, L. xinjiangensis, and L. mobilis were 39.9, 39.4, and 25.3%, respectively. From these results, it is concluded that the novel isolate possesses sufficient characteristics to differentiate it from the most closely affiliated Lysobacter species, and strain 17J68-2T represents a novel species of the genus Lysobacter, for which the name Lysobacter segetis sp. nov. (=KCTC 62237T = JCM 33058T) is proposed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

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 94:12139–12144

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 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 Genom 9:75

    PubMed  PubMed Central  Google Scholar 

  3. Cappuccino JG, Sherman N (2010) Microbiology: a laboratory manual, 9th edn. Benjamin Cummings, San Francisco

    Google Scholar 

  4. 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 109:1047–1053

    CAS  PubMed  Google Scholar 

  5. Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Evol Microbiol 28:367–393

    Google 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

  7. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Hana Y, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466

    CAS  PubMed  Google Scholar 

  8. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric DNA–DNA 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

    Google Scholar 

  9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  PubMed  Google Scholar 

  10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Google Scholar 

  11. Fukuda W, Kimura T, Araki S, Miyoshi Y, Atomi H, Imanaka T (2013) Lysobacter oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica. Int J Syst Evol Microbiol 63:3313–3318

    CAS  PubMed  Google Scholar 

  12. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al (2018) RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 46(D1):D851–D860

    CAS  PubMed  Google Scholar 

  13. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  14. 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

    CAS  Google Scholar 

  15. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  PubMed  Google Scholar 

  16. Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205

    CAS  Google Scholar 

  17. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    CAS  PubMed  Google Scholar 

  19. Lee M, Woo SG, Chae M, Shin MC, Jung HM, Ten LN (2011) Stenotrophomonas daejeonensis sp. nov., isolated from sewage. Int J Syst Evol Microbiol 61:598–604

    CAS  PubMed  Google Scholar 

  20. Lee I, Kim YO, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103

    CAS  PubMed  Google Scholar 

  21. Lee JJ, Lee YH, Park SJ, Lee SY, Kim BO, Ten LN, Kim MK, Jung HY (2017) Spirosoma knui sp. nov., a radiation-resistant bacterium isolated from the Han River. Int J Syst Evol Microbiol 67:1359–1365

    CAS  PubMed  Google Scholar 

  22. Lee D, Jang JH, Cha S, Seo T (2017) Lysobacter humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 67:951–955

    CAS  PubMed  Google Scholar 

  23. 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 200:439–444

    CAS  PubMed  Google Scholar 

  24. 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 61:433–437

    CAS  PubMed  Google Scholar 

  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Google Scholar 

  26. Meier-Kolthoff JP, Klenk HP, Göker M (2014) Taxonomic use of DNA G+ C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356

    CAS  PubMed  Google Scholar 

  27. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Google Scholar 

  28. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  30. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc, Newark

  31. Siddiqi MZ, Im WT (2016) Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. Arch Microbiol 198:551–557

    CAS  PubMed  Google Scholar 

  32. 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 607–654

    Google Scholar 

  33. 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 44:846–849

    CAS  Google Scholar 

  34. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155

    Google Scholar 

  35. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44:6614–6624

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 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 46:519–524

    CAS  PubMed  Google Scholar 

  37. Ten LN, Jung HM, Im WT, Yoo SA, Oh HM, Lee ST (2009) Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 59:958–963

    CAS  PubMed  Google Scholar 

  38. Tindall BJ (2014) The family name Solimonadaceae Losey et al. 2013 is illegitimate, proposals to create the names ‘Sinobacter soli’comb. nov. and ‘Sinobacter variicoloris’ contravene the Code, the family name Xanthomonadaceae Saddler and Bradbury 2005 and the order name Xanthomonadales Saddler and Bradbury 2005 are illegitimate and notes on the application of the family names Solibacteraceae Zhou et al. 2008, Nevskiaceae Henrici and Johnson 1935 (Approved Lists 1980) and Lysobacteraceae Christensen and Cook 1978 (Approved Lists 1980) and order name Lysobacteriales Christensen and Cook 1978 (Approved Lists 1980) with respect to the classification of the corresponding type genera Solibacter Zhou et al. 2008, Nevskia Famintzin 1892 (Approved Lists 1980) and Lysobacter Christensen and Cook 1978 (Approved Lists 1980) and importance of accurately expressing the link between a taxonomic name, its authors and the corresponding description/circumscription/emendation. Int J Syst Evol Microbiol 64 293–297

  39. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Google Scholar 

  40. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Wen C, Xi L, She R, Zhao S, Hao Z, Luo L, Liao H, Chen Z, Han G, Cao S, Wu R, Yan Q, Hou R (2016) Lysobacter chengduensis sp. nov. isolated from the air of captive Ailuropoda melanoleuca enclosures in Chengdu China. Curr Microbiol 72:88–93

    CAS  PubMed  Google Scholar 

  42. Wilson K (1997) Preparation of genomic DNA from bacteria. In: Ausubel FM et al (eds) Current protocols in molecular biology, no. supplement 27. Wiley, New York, pp. 2.4.1–2.4.5

    Google Scholar 

  43. Yang SZ, Feng GD, Zhu HH, Wang YH (2015) Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore. Int. J. Syst. Evol. Microbiol. 65:833–837

    CAS  PubMed  Google Scholar 

  44. Yoon J (2016) Polyphasic characterization of Lysobacter maris sp. nov., a bacterium isolated from seawater. Curr Microbiol 72:282–287

    CAS  PubMed  Google Scholar 

  45. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Zhang XF, Wang HH, Sun XY, Pan CM (2017) Lysobacter zhanggongensis sp. nov. isolated from a pit mud. Curr Microbiol 74:1389–1393

    CAS  PubMed  Google Scholar 

  47. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669–2677

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by the Brain Pool Program (Grant No. 2019H1D3A2A01061406) through the National Research Foundation (NRF) funded by the Ministry of Science and ICT, Republic of Korea.

Author information

Authors and Affiliations

  1. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Leonid N. Ten, Jongguen Jeon, Nabil Salah Elderiny, Seung-Yeol Lee & Hee-Young Jung

  2. Department of Bio and Environmental Technology, Seoul Women’s University, Seoul, 01797, Republic of Korea

    Myung Kyum Kim

  3. Institute of Plant Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea

    Seung-Yeol Lee & Hee-Young Jung

Authors
  1. Leonid N. Ten
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jongguen Jeon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nabil Salah Elderiny
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Myung Kyum Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Seung-Yeol Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hee-Young Jung
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hee-Young Jung.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The 16S rRNA gene sequence of strain 17J68-2T has been deposited in NCBI GenBank/EMBL/DDBJ under the accession number LC434628. The draft genome sequence accession number of the strain in GenBank/EMBL/DDBJ is SMRQ00000000. The Digital Protologue Database (DPD) Taxon Number for strain 17J68-2T is TA00939.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 447 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ten, L.N., Jeon, J., Elderiny, N.S. et al. Lysobacter segetis sp. nov., Isolated from Soil. Curr Microbiol 77, 166–172 (2020). https://doi.org/10.1007/s00284-019-01801-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00284-019-01801-w

Search

Navigation