Antonie van Leeuwenhoek

, Volume 108, Issue 3, pp 553–561 | Cite as

Lysobacter agri sp. nov., a bacterium isolated from soil

  • Hina Singh
  • KyungHwa Won
  • Juan Du
  • Jung-Eun Yang
  • Shahina Akter
  • Ki-Young Kim
  • Tae-Hoo YiEmail author
Original Paper


A bacterial strain, designated as THG-SKA3T, was isolated from field soil of Kyung Hee University, South Korea. Cells of the isolate were observed to be Gram-negative, aerobic, rod-shaped and motile by gliding. The strain was found to grow optimally at 28 °C, at pH 7 and in absence of NaCl. Based on 16S rRNA gene sequence comparisons, strain THG-SKA3T shared highest sequence similarity with Lysobacter niastensis KACC 11588T followed by Lysobacter panacisoli KACC 17502T, Lysobacter enzymogenes LMG 8762T and Lysobacter oryzae KCTC 22249T. The G+C content of THG-SKA3T was determined to be 68.9 mol%. The DNA–DNA relatedness values between strain THG-SKA3T and its closest phylogenetic neighbors were below 25.0 %.The major polar lipids of strain THG-SKA3T were determined to be diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was identified as ubiquinone 8 (Q-8). The major cellular fatty acids were identified as branched chain iso-C15:0, iso-C16:0 and unsaturated iso-C17:1 ω9c. On the basis of polyphasic data presented, it is evident that strain THG-SKA3T represents a novel species of the genus Lysobacter, for which the name Lysobacter agri sp. nov. (type strain THG-SKA3T = KACC 18283T = CSCTCC AB 2015126T) is proposed.


Lysobacter agri Polyphasic taxonomy Gram-negative Ubiquinone Q-8 



This work was conducted under the industrial infrastructure program (No. N0000888) for fundamental technologies which is funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

Supplementary material

10482_2015_510_MOESM1_ESM.tif (109 kb)
Supplementary Fig. S1 The maximum-likelihood tree based on 16S rRNA gene sequence analysis showing the phylogenetic relationships between strain THG-SKA3T and members of the genus Lysobacter. Bootstrap values less than 50 % were not indicated. Dyella terrae JS14-6T was used as an out group. Scale bar, 0.05 substitutions per nucleotide position. Supplementary material 1 (TIFF 109 kb)
10482_2015_510_MOESM2_ESM.tif (1.7 mb)
Supplementary Fig. S2. Transmission electron micrograph of Lysobacter agri THG-SKA3T. Bar indicated 0.5 μm. Supplementary material 2 (TIFF 1768 kb)
10482_2015_510_MOESM3_ESM.tif (1.6 mb)
Supplementary Fig. S3. Two-dimensional TLC of the total polar lipids of Lysobacter agri THG-SKA3T (a) and Lysobacter niatensis KACC 11588T (b), stained for total polar lipids with 5 % ethanolic molybdatophosphoric acid. Abbreviations: DPG, diphosphatidylglycerol; PG, phosphatidylglycerol; PE, phosphatidylethanolamine; APL1-2, unidentified aminophospholipid; PL, unidentified phospholipid. Supplementary material 3 (TIFF 1609 kb)


  1. Aslam Z, Yasir M, Jeon CO, Chung YR (2009) Lysobacter oryzae sp. nov., isolated from the rhizosphere of rice (Oryza sativa L.). Int J Syst Evol Microbiol 59:675–680PubMedCrossRefGoogle Scholar
  2. Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070PubMedCrossRefGoogle Scholar
  3. Choi JH, Seok JH, Cha JH, Cha CJ (2014) Lysobacter panacisoli sp. nov., isolated from ginseng soil. Int J Syst Evol Microbiol 64:2193–2197PubMedCrossRefGoogle Scholar
  4. Christensen WB (1946) Urea decomposition as a means of differentiating Proteus and Paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 52:461–466PubMedCentralPubMedGoogle Scholar
  5. Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393CrossRefGoogle Scholar
  6. Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354PubMedCentralPubMedGoogle 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 Bacteriol 39:224–229CrossRefGoogle Scholar
  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle 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. 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 63:3313–3318PubMedCrossRefGoogle Scholar
  12. Gillis M, De Ley J, De Cleene M (1970) The determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12:143–153PubMedCrossRefGoogle 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 41:95–98Google 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 42:457–469CrossRefGoogle Scholar
  15. 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 62:716–721PubMedCrossRefGoogle Scholar
  16. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  17. Lee JW, Im WT, Kim MK, Yang DC (2006) Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol 56:231–235PubMedCrossRefGoogle Scholar
  18. Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Lai WA, Young CC (2015) Lysobacter lycopersici sp. nov., isolated from tomato plant Solanum lycopersicum. Antonie van Leeuwenhoek. doi: 10.1007/s10482-015-0419-1 PubMedCentralGoogle Scholar
  19. 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 61:433–437PubMedCrossRefGoogle Scholar
  20. 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 62:1659–1665PubMedCrossRefGoogle Scholar
  21. McConaughy BL, Laird CD, McCarthy BJ (1969) Nucleic acid reassociation in formamide. Biochemistry 8:3289–3295PubMedCrossRefGoogle Scholar
  22. 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 39:159–167CrossRefGoogle Scholar
  23. Minnikin DE, ODonnell 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 2:233–241CrossRefGoogle Scholar
  24. Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11Google Scholar
  25. Ngo HTT, Won K, Du J, Son HM, Park Y, MooChang K, Kim KY, Jin FX, Yi TH (2014) Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.067397-0 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 58:387–392PubMedCrossRefGoogle Scholar
  27. Reichenbach H (1992) The order Cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH (eds) The prokaryotes, a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, vol 4, 2nd edn. Springer, New York, pp 3631–3675Google Scholar
  28. Romanenko LA, Uchino M, Tanaka N, Frolova GM, Mikhailov VV (2008) Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge. Int J Syst Evol Microbiol 58:370–374PubMedCrossRefGoogle Scholar
  29. Saddler GS, Bradbury JF (2005) Family I. Xanthomonadaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, pp 63–122CrossRefGoogle Scholar
  30. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  31. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  32. Schmidt K, Connor A, Britton G (1994) Analysis of pigments: carotenoids and related polyenes. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 403–461Google Scholar
  33. Singh H, Du J, Ngo HT, Won K, Yang JE, Kim KY, Yi TH (2015) Lysobacter fragariae sp. nov. and Lysobacter rhizosphaerae sp. nov. isolated from rhizosphere of strawberry plant. Antonie van Leeuwenhoek. doi: 10.1007/s10482-015-0439-x Google Scholar
  34. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, BaltimoreGoogle Scholar
  35. 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 60:1543–1547PubMedCrossRefGoogle Scholar
  36. Stabili L, Gravili C, Tredici SM, Piraino S, Talà A, Boero F, Alifano P (2008) Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 56:625–636PubMedCrossRefGoogle Scholar
  37. Tamaoka J, Katayama-Fujiruma A, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36CrossRefGoogle Scholar
  38. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729PubMedCentralPubMedCrossRefGoogle Scholar
  39. Ten LN, Jung H, Im WT, Yoo SA, Oh HM, Lee ST (2009) Lysobacter panaciterrae sp. nov., isolated from soil of ginseng field. Int J Syst Evol Microbiol 59:958–963PubMedCrossRefGoogle Scholar
  40. 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 25:4876–4882PubMedCentralPubMedCrossRefGoogle Scholar
  41. Wang Y, Dai J, Zhang L, Luo X, Li Y, Chen G, Tang Y, Meng Y, Fang C (2009) Lysobacter ximonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:786–789PubMedCrossRefGoogle Scholar
  42. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore WEC, Murray RGE et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 37:463–464Google Scholar
  43. Wei DQ, Yu TT, Yao JC, Zhou EM, Song ZQ (2012) Lysobacter thermophilus sp. nov., isolated from a geothermal soil sample in Tengchong, south-west China. Antonie van Leeuwenhoek 102:643–651PubMedCrossRefGoogle Scholar
  44. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedCentralPubMedGoogle Scholar
  45. 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 56:947–951PubMedCrossRefGoogle Scholar
  46. Weon HY, Kim BY, Kim MK, Yoo SH, Kwon SW, Go SJ, Stackebrandt E (2007) Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea. Int J Syst Evol Microbiol 57:548–551PubMedCrossRefGoogle Scholar
  47. Yang SZ, Feng GD, Zhu HH, Wang YH (2014) Lysobacter mobilis sp. nov., isolated from abandoned lead–zinc ore. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.000026 Google Scholar
  48. Ye XM, Chu CW, Shi C, Zhu JC, He Q, He J (2014) Lysobacter caeni sp. nov., isolated from the sludge of pesticide manufacturing factory. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.000026 Google Scholar
  49. Yu TT, Zhou EM, Yin YR, Yao JC, Ming H, Dong L, Li S, Nie GX, Li WJ et al (2013) Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophiles Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov. Antonie Van Leeuwenhoek 104:369–376PubMedCrossRefGoogle Scholar
  50. Zhang L, Bai J, Wang Y, Wu JL, Dai J, Fang CX (2011) Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:2259–2265PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Hina Singh
    • 1
  • KyungHwa Won
    • 1
  • Juan Du
    • 1
  • Jung-Eun Yang
    • 1
  • Shahina Akter
    • 1
  • Ki-Young Kim
    • 2
  • Tae-Hoo Yi
    • 1
    Email author
  1. 1.Department of Oriental Medicine Biotechnology, College of Life ScienceKyung Hee University Global CampusYongin-siRepublic of Korea
  2. 2.Department of Genetic Engineering, College of Life ScienceKyung Hee University Global CampusYongin-siRepublic of Korea

Personalised recommendations