Skip to main content
SpringerLink
Log in

Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea

Antonie van Leeuwenhoek Aims and scope Submit manuscript

Cite this article

Abstract

Two bacterial strains, designated D10T and U8T, were isolated from soil samples from the Dong-angyeong cave and Geommeolle wharf sea-coast, Udo-Island, Jeju, South Korea. Both novel bacterial strains are yellow-pigmented, Gram-stain negative, motile by means of monotrichous flagella, short rod shaped and strictly aerobic. A phylogenetic tree was reconstructed based on their 16S rRNA gene sequences, which indicated that these two strains belong to the genus Lysobacter within the family Xanthomonadaceae. Strain D10T showed high 16S rRNA gene sequence similarities with Lysobacter humi FJY8T (99.0%), Lysobacter xinjiangensis RCML-52T (98.9%) and Lysobacter mobilis 9NM-14T (97.2%), whereas strain U8T showed high sequence similarities to L. mobilis 9NM-14T (97.9%), L. xinjiangensis RCML-52T (97.8%), L. humi FJY8T (97.5%) and Lysobacter bugurensis ZLD-29T (97.1%). The 16S rRNA gene sequence similarity between D10T and U8T was 97.0%. Strain D10T showed low DNA–DNA relatedness to U8T (57.7 ± 3.4%), L. humi FJY8T (48.8 ± 4.3%), L. xinjiangensis RCML-52T (60.1 ± 2.4%) and L. mobilis 9NM-14T (55.9 ± 1.9%). The level of DNA–DNA relatedness for strain U8T with respect to D10T, L. mobilis 9NM-14T, L. xinjiangensis RCML-52T, L. humi FJY8T, and L. bugurensis ZLD-29T was 55.5 ± 0.5%, 54.5 ± 2.1%, 58.1 ± 0.8%, and 51.9 ± 3.4%, respectively. The major polar lipids for both strains were identified as diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major cellular fatty acids for both strains were identified as iso-C15:0, iso-C16:0 and summed feature 9 (iso-C17:1 ω9c/C16:0 10-methyl), and ubiquinone (Q-8) as the only isoprenoid quinone for both strains. The DNA G + C contents of the strains D10T and U8T were determined to be 70.2 mol% and 70.6 mol%. On the basis of phenotypic, genotypic, chemotaxonomic, and phylogenetic analysis, both strains D10T and U8T represent a novel species in the genus Lysobacter, for which the names Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov. are proposed, respectively. The type strain of L. helvus is D10T (= KCTC 62111T = JCM 32364T) and the type strain of L. xanthus is U8T (= KCTC 62112T = JCM 32365T).

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

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman J (eds) (1995) Short protocols in molecular biology: a compendium of methods from current protocols in molecular biology, 3rd edn. Wiley, New York

    Google Scholar 

  • Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993

    CAS  PubMed  PubMed Central  Google Scholar 

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

    Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142

    Article  PubMed  Google Scholar 

  • Fautz E, Reichenbach H (1980) A simple test for flexirubin type pigments. FEMS Microbiol Lett 8:87–91

    Article  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Gillis M, Ley JD, Cleene MD (1970) The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12:143–153

    Article  CAS  PubMed  Google Scholar 

  • Gonzalez JM, Saiz-Jimenez C (2002) A fluorimetric method for the estimation of G + C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 4:770–773

    Article  CAS  PubMed  Google Scholar 

  • Hall T (1997) BioEdit. Biological sequence alignment editor for Win 95/98/NT/2 K/XP. Ibis Therapeutics, Carlsbad

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Jeong SE, Lee HJ, Jeon CO (2016) Lysobacter aestuarii sp. nov., isolated from estuary sediment. Int J Syst Evol Microbiol 66:1346

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361

    CAS  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Lai WA, Young CC (2014) Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie Van Leeuwenhoek 107:1261–1270

    Article  CAS  Google Scholar 

  • Loveland-Curtze J, Miteva VI, Brenchley JE, Vanya IM, Jean EB (2011) Evaluation of a new fluorimetric DNA–DNA hybridization method. Can J Microbiol 57:250–255

    Article  CAS  PubMed  Google Scholar 

  • Luo Y, Dong H, Zhou M, Huang Y, Zhang H, He W, Sheng H, An L (2019) Lysobacter psychrotolerans sp. nov., isolated from soil in the Tianshan Mountains, Xinjiang. China. Int J Syst Evol Microbiol 2019:69

    Google Scholar 

  • Margesin R, Zhang DC, Albuquerque L, Froufe HJC, 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 68:1571–1577

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Ngo HT, Won K, Du J, Son HM, Park Y, Kook M, Kim KY, Jin FX, Yi TH (2015) Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol 65:587

    Article  CAS  PubMed  Google Scholar 

  • Reichenbach H (2006) The Genus Lysobacter. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes. Springer, New York

    Google Scholar 

  • Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 40:121–122

    Article  PubMed  Google Scholar 

  • 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 

  • Siddiqi MZ, Im WT (2016) Lysobacter hankyongensis sp. nov., isolated from activated sludge and Lysobacter sediminicola sp. nov., isolated from fresh water sediment. Int J Syst Evol Microbiol 66:212

    Article  CAS  PubMed  Google Scholar 

  • Singh H, Du J, Ngo HT, Won K, Yang JE, Kim KY, Yi TH (2015a) Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. Antonie Van Leeuwenhoek 107:1437–1444

    Article  CAS  PubMed  Google Scholar 

  • Singh H, Won K, Du J, Yang J-E, Akter S, Kim K-Y, Yi T-H (2015b) Lysobacter agri sp. nov., a bacterium isolated from soil. Antonie Van Leeuwenhoek 108:553–561

    Article  CAS  PubMed  Google Scholar 

  • Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC (2010) Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60:1543–1547

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao M, Xing KZ, Xing C, Yan QD, Dalal HMA, Wan TI, Wael NH, Wei C, Wen JL (2018) Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L. Int J Syst Evol Microbiol 2018:68

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CX (2011) Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:2259–2265

    Article  CAS  PubMed  Google Scholar 

  • Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HH (2018) Lysobacter silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 69:93–98

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was supported by a National Research Foundation of Korea (NRF) grant by the Korean government (MIST) (NRF-2017R1A2B4009448).

Author information

Authors and Affiliations

  1. Department of Life Science, Dongguk University-Seoul, Goyang, 10326, South Korea

    Inhyup Kim, Jiwon Choi, Geeta Chhetri & Taegun Seo

Authors
  1. Inhyup Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiwon Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Geeta Chhetri
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Taegun Seo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Taegun Seo.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Publisher's Note

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

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 283 kb)

Supplementary material 2 (PPTX 45 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kim, I., Choi, J., Chhetri, G. et al. Lysobacter helvus sp. nov. and Lysobacter xanthus sp. nov., isolated from Soil in South Korea. Antonie van Leeuwenhoek 112, 1253–1262 (2019). https://doi.org/10.1007/s10482-019-01256-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-019-01256-w

Keywords

search

Navigation