Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample

We’re sorry, something doesn't seem to be working properly.

Please try refreshing the page. If that doesn't work, please contact support so we can address the problem.

Abstract

A Gram-staining negative, aerobic, rod-shaped bacterium, designated YIM C01544T, was isolated from a soil sample collected from Sigangli Cave, Yunnan province, South-West China. The strain was able to grow over a range of temperatures (4–30 °C), pH (6.0–10.0) and NaCl concentration (0–2 %, w/v). Comparative 16S rRNA gene sequence analysis revealed that strain YIM C01544T should be a member of the genus Lysobacter. The strain is closely related to Lysobacter niastensis GH41-7T (97.6 %), Lysobacter soli DCY21T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.3 %), Lysobacter antibioticus DSM 2044T (97.1 %) and Lysobacter panacisoli CJ29T (97.1 %). The genomic DNA relatedness values (<47 %) as indicated by DNA–DNA hybridization studies were below the threshold limit for characterization of new bacterial species. The chemotaxonomic features of the new isolate include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and two unidentified polar lipids as its characteristic polar lipids and Q-8 as the only quinone. The major fatty acids detected were iso-C15:0 and iso-C17:1 ω9c. The DNA G + C content of the strain was determined to be 64.9 mol %. Based on the data from phenotypic, chemotaxonomic and molecular studies, strain YIM C01544T merits recognition as novel species in the genus Lysobacter for which the name Lysobacter cavernae sp. nov. is proposed. The type strain of Lysobacter cavernae is YIM C01544T (= KCTC 42875T = DSM 101561T = CPCC 100816T).

This is a preview of subscription content, access via your institution.

Fig. 1

References

  1. Allpress JD, Mountain Gowland PC (2002) Production, purification and characterization of an extracellular keratinase from Lysobacter NCIMB 9497. Lett Appl Microbiol 34:337–342

    CAS  Article  PubMed  Google Scholar 

  2. Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122

    CAS  Article  Google Scholar 

  3. Chohnan S, Shiraki K, Yokota K, Ohshima M, Kuroiwa N, Ahmed K, Masaki T, Sakiyama F (2004) A second lysine-specific serine protease from Lysobacter sp. strain IB-9374. J Bacteriol 186:5093–5100

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Choi JH, Seok JH, Cha JH, Cha CJ (2014) Lysobacter panacioli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 64:2193–2197

    CAS  Article  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 Bacteriol 28:367–393

    Article  Google Scholar 

  6. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (2000) DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102

    CAS  Article  PubMed  Google Scholar 

  7. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. Appl Bacteriol 48:459–470

    CAS  Article  Google Scholar 

  8. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  Article  PubMed  Google Scholar 

  9. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP, Xu LH, Jiang CL (2001) Streptomonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363

    CAS  Article  PubMed  Google Scholar 

  10. 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 39:224–229

    Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

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

    Article  Google Scholar 

  14. 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  Article  PubMed  Google Scholar 

  15. Hashizume H, Hattori S, Igarashi M, Akamatsu Y (2004) Tripropeptin E, a new tripropeptin group antibiotic produced by Lysobacter sp. BMK333–48F3. J Antibiot (Tokyo) 57:394–399

    CAS  Article  Google Scholar 

  16. Hayakawa M, Nonomura H (1987) Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65:501–509

    CAS  Article  Google Scholar 

  17. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  Article  PubMed  Google Scholar 

  18. 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  Article  PubMed  Google Scholar 

  19. Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703

    CAS  Article  PubMed  Google Scholar 

  20. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP 18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatograph 5:2359–2387

    CAS  Article  Google Scholar 

  21. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) 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 57:1424–1428

    Article  PubMed  Google Scholar 

  22. Luo G, Shi Z, Wang G (2012) Lysobacter arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from iron-mined soil. Int J Syst Evol Microbiol 62:1659–1665

    CAS  Article  PubMed  Google Scholar 

  23. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  24. Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    CAS  Article  Google Scholar 

  25. Ogura J, Toyoda A, Kurosawa T, Chong AL, Chohnan S, Masaki T (2006) Purification, characterization, and gene analysis of cellulose (Cel8A) from Lysobacter sp. IB-9374. Biosci Biotechnol Biochem 70:2420–2428

    CAS  Article  PubMed  Google Scholar 

  26. Park JH, Kim R, Aslam Z, Jeon CO, Chung YR (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 Microbiol 58:387–392

  27. Puopolo G, Tomada S, Sonego P, Moretto M, Engelen K, Perazzolli M, Pertot I (2016) The Lysobacter capsici AZ78 genome has a gene pool enabling it to interact successfully with phytopathogenic microorganisms and environmental factors. Front Microbiol 7:96. doi:10.3389/fmicb.2016.00096

    Article  PubMed  PubMed Central  Google Scholar 

  28. Saddler GS, Bradbury JF (2005) Family I. Xanthomonadaceae fam. nov. In: Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 2, pp. 63–122. Edited by DJ Brenner, NR Krieg, JT Staley, GM Garrity. New York: Springer

  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

    Google Scholar 

  31. 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

    CAS  Article  PubMed  Google Scholar 

  32. 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  Article  Google Scholar 

  33. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. 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 25:4876–4882

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  35. Tishchenko S, Gabdulkhakov A, Meinik B, Kudryakova I, Latypov O, Vasilyeva N, Leontievsky A (2016) Structural studies of component of lysoamidase bacteriolytic complex from Lysobacter sp. XL1. Protein J 35:44–50

    CAS  Article  PubMed  Google Scholar 

  36. Wei DQ, Yu TT, Yao JC, Zhou EM, Song ZQ, Yin YR, Ming H, Tang SK, Li WJ (2012) Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. Antonie Van Leeuwenhoek 102:643–651

    CAS  Article  PubMed  Google Scholar 

  37. Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW, Stackebrandt E, Go SJ (2006) Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 56:947–951

    CAS  Article  PubMed  Google Scholar 

  38. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors are grateful to Soon-Wo Kwon (KACC, Korea), Miss Sang-Mi Lee (KCTC, Korea) and Dr. Tamura Tomohiko (NBRC, Japan) for providing the reference type strains. This work was funded by projects from China Tobacco Yunnan International Co. Ltd. (Nos. 2015CP01), Key Laboratory of Cigarette Perfumery Industry (2014-334) and Key Discipline Construction Project of Biology in Yunnan province (50097505), Doctoral Scientific Research Foundation of Southwest Forestry University (111441) and the Deanship of Scientific Research at King Saud University through the research group no. PRG-1436-27. Wen-Jun Li was also supported by Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Qing-Qing Li or Wen-Jun Li.

Additional information

Wei Chen and Ying-Liang Zhao contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (RAR 267 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Chen, W., Zhao, YL., Cheng, J. et al. Lysobacter cavernae sp. nov., a novel bacterium isolated from a cave sample. Antonie van Leeuwenhoek 109, 1047–1053 (2016). https://doi.org/10.1007/s10482-016-0704-7

Download citation

Keywords

  • Lysobacter cavernae sp. nov.
  • Sigangli Cave
  • Polyphasic taxonomy