Journal of Microbiology

, Volume 56, Issue 5, pp 324–330 | Cite as

Tardibacter chloracetimidivorans gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from an agricultural soil from Jeju Island in Republic of Korea

  • Hyosun Lee
  • Dong-Uk Kim
  • Sooyeon Park
  • Jung-Hoon Yoon
  • Jae-Hyung Ahn
  • Jong-Ok KaEmail author
Microbial Systematics and Evolutionary Microbiology


A pale yellow bacterial strain, designated JJ-A5T, was isolated form an agricultural soil from Jeju Island in Republic of Korea. Cells of the strain were Gram-stain-negative, motile, flagellated and rod-shaped. The strain grew at 15–30°C, pH 6.0–9.0, and in the presence of 0–1.5% (w/v) NaCl. Growth occurred on R2A, but not on Luria-Bertani agar, nutrient agar, trypticase soy agar and MacConkey agar. The strain utilized alachlor as a sole carbon source for growth. The strain JJ-A5T showed 16S rRNA gene sequence similarities lower than 95.4% with members of the family Sphingomonadaceae. Phylogenetic analysis showed that the strain belongs to the family Sphingomonadaceae and strain JJ-A5T was distinctly separated from established genera of this family. The strain contained Q-10 as dominant ubiquinone and spermidine as major polyamine. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c), 11-methyl C18:1ω7c, C16:0 and C14:0 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, and phosphatidylcholine. The DNA G + C content of the strain was 62.7 mol%. On the basis of the phenotypic, genomic and chemotaxonomic characteristics, strain JJ-A5T is considered to represent a novel genus and species within the family Sphingomonadaceae, for which the name Tardibacter chloracetimidivorans gen. nov., sp. nov. is proposed. The type strain of Tardibacter chloracetimidivorans is JJ-A5T (= KACC 19450T = NBRC 113160T).


Tardibacter Tardibacter chloracetimidivorans novel genus novel species polyphasic taxonomy 


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  1. Baker, G.C., Smith, J.J., and Cowan, D.A. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55, 541–555.CrossRefPubMedGoogle Scholar
  2. Breznak, J.A. and Costilow, R.N. 2007. Physicochemical factors in growth, pp. 309–329. In Beveridge, T.J., Breznak, J.A., Marzluf, G.A., Schmidt, T.M., and Snyder, L.R. (eds.), Methods for general and molecular bacteriology. American Society for Microbiology, Washington, USA.Google Scholar
  3. Chen, C., Zheng, Q., Wang, Y.N., Yan, X.J., Hao, L.K., Du, X., and Jiao, N. 2010. Stakelama pacifica gen. nov., sp. nov., a new member of the family Sphingomonadaceae isolated from the Pacific Ocean. Int. J. Syst. Evol. Microbiol. 60, 2857–2861.CrossRefPubMedGoogle Scholar
  4. De Ley, J. and Swings, J. 1976. Phenotypic description, numerical analysis and a proposal of an improved taxonomy and nomenclature of the genus Zymomonas Kluyver and van Niel 1936. Int. J. Syst. Bacteriol. 26, 146–157.CrossRefGoogle Scholar
  5. Embley, T.M. and Wait, R. 1994. Structural lipids of eubacteria, pp. 121–161. In Goodfellow, M. and O’Donnell, A.G. (eds.), modern microbial methods. chemical methods in prokaryotic systematics, John Wiley & Sons, Chichester, England.Google Scholar
  6. Felföldi, T., Vengring, A., Márialigeti, K., András, J., Schumann, P., and Tóth, E.M. 2014. Hephaestia caeni gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 64, 738–744.CrossRefPubMedGoogle Scholar
  7. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.CrossRefPubMedGoogle Scholar
  8. Felsenstein, J. 1985. Confidence-limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefPubMedGoogle Scholar
  9. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416.CrossRefGoogle Scholar
  10. Francis, I.M., Jochimsen, K.N., De Vos, P., and van Bruggen, A.H.C. 2014. Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol. 64, 1340–1350.CrossRefPubMedGoogle Scholar
  11. Fukuda, W., Chino, Y., Araki, S., Kondo, Y., Imanaka, H., Kanai, T., Atomi, H., and Imanaka, T. 2014. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock. Int. J. Syst. Evol. Microbiol. 64, 2034–2040.CrossRefPubMedGoogle Scholar
  12. Gich, F. and Overmann, J. 2006. Sandarakinorhabdus limnophila gen. nov., sp. nov., a novel bacteriochlorophyll a-containing, ob ligately aerobic bacterium isolated from freshwater lakes. Int. J. Syst. Evol. Microbiol. 56, 847–854.CrossRefPubMedGoogle Scholar
  13. Gonzalez, J.M. and 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.CrossRefPubMedGoogle Scholar
  14. Jogler, M., Chen, H., Simon, J., Rohde, M., Busse, H.J., Klenk, H.P., Tindall, B.J., and Overmann, J. 2013. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int. J. Syst. Evol. Microbiol. 63, 1342–1349.CrossRefPubMedGoogle Scholar
  15. Kämpfer, P., Arun, A.B., Young, C.C., Busse, H.J., Kassmannhuber, J., Rosselló-Móra, R., Geueke, B., Rekha, P.D., and Chen, W.M. 2012. Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int. J. Syst. Evol. Microbiol. 62, 1326–1330.CrossRefPubMedGoogle Scholar
  16. Kim, J.K., Kang, M.S., Park, S.C., Kim, K.M., Choi, K., Yoon, M.H., and Im, W.T. 2015. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J. Microbiol. 53, 435–441.CrossRefPubMedGoogle Scholar
  17. Kim, M., Kang, O., Zhang, Y., Ren, L., Chang, X., Jiang, F., Fang, C., Zheng, C., and Peng, F. 2016. Sphingoaurantiacus polygranulatus gen. nov., sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of the genera Sandarakinorhabdus, Polymorphobacter and Rhizorhabdus and the species Sandarakinorhabdus limnophila, Rhizorhabdus argentea and Sphingomonas wittichii. Int. J. Syst. Evol. Microbiol. 66, 91–100.CrossRefPubMedGoogle 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.CrossRefPubMedGoogle Scholar
  19. Komagata, K. and Suzuki, K.I. 1987. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–207.CrossRefGoogle Scholar
  20. Kosako, Y., Yabuuchi, E., Naka, T., Fujiwara, N., and Kobayashi, K. 2000. Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990. Microbiol. Immunol. 44, 563–575.CrossRefPubMedGoogle Scholar
  21. Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874.CrossRefPubMedGoogle Scholar
  22. Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115–175. In Stackebrandt, E. and Goodfellow, M. (eds.), nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, USA.Google Scholar
  23. Lee, K.B., Liu, C.T., Anzai, Y., Kim, H., Aono, T., and Oyaizu, H. 2005. The hierarchical system of the ‘Alphaproteobacteria’: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 55, 1907–1919.CrossRefPubMedGoogle Scholar
  24. Lee, S., Malone, C., and Kemp, P.F. 1993. Use of multiple 16S rRNAtargeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria. Mar. Ecol. Prog. Ser. 101, 193–201.CrossRefGoogle Scholar
  25. Liu, K., Li, S., Jiao, N., and Tang, K. 2014. Pacificamonas flava gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from the Southeastern Pacific. Curr. Microbiol. 69, 96–101.CrossRefPubMedGoogle Scholar
  26. Maruyama, T., Park, H.D., Ozawa, K., Tanaka, Y., Sumino, T., Hamana, K., Hiraishi, A., and Kato, K. 2006. Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 56, 85–89.CrossRefPubMedGoogle Scholar
  27. Minnikin, D.E., O’donnell, A.G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., and Parlett, J.H. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.CrossRefGoogle Scholar
  28. Pruesse, E., Peplies, J., and Glöckner, F.O. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Ren, L., Chang, X., Jiang, F., Kan, W., Qu, Z., Qiu, X., Fang, C., and Peng, F. 2015. Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till. Int. J. Syst. Evol. Microbiol. 65, 260–266.CrossRefPubMedGoogle Scholar
  30. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.PubMedGoogle Scholar
  31. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI. Inc., Newark, DE, USA.Google Scholar
  32. Schenkel, E., Berlaimont, V., Dubois, J., Helson-Cambier, M., and Hanocq, M. 1995. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J. Chromatogr. B 668, 189–197.CrossRefGoogle Scholar
  33. Sly, L.I. and Cahill, M.M. 1997. Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov. Int. J. Syst. Evol. Microbiol. 47, 566–568.Google Scholar
  34. Smibert, R.M. and Krieg, N.R. 1994. Phenotypic characterization. methods for general and molecular bacteriology, pp. 607–654. In Gerhardt, P., Murray, R.G.E., Costilow, R.N., Nester, E.W., Wood, W.A., and Krieg, N.R. (eds.), American Society for Microbiology, Washington, USA.Google Scholar
  35. Takeuchi, M., Hamana, K., and Hiraishi, A. 2001. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51, 1405–1417.CrossRefPubMedGoogle Scholar
  36. Thawng, C.N., Park, S.J., Cha, J.H., and Cha, C.J. 2013. Stakelama sediminis sp. nov., isolated from tidal flat sediment. Int. J. Syst. Evol. Microbiol. 63, 560–564.CrossRefPubMedGoogle Scholar
  37. Tindall, B.J., Rosselló-Móra, R., Busse, H.J., Ludwig, W., and Kämpfer, P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60, 249–266.CrossRefPubMedGoogle Scholar
  38. Uchida, H., Hamana, K., Miyazaki, M., Yoshida, T., and Nogi, Y. 2012. Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int. J. Syst. Evol. Microbiol. 62, 2224–2228.CrossRefPubMedGoogle Scholar
  39. Yabuuchi, E., Ikuya, Y., Oyaizu, H., Hashimoto, Y., Ezaki, T., and Yamamoto, H. 1990. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34, 99–119.CrossRefPubMedGoogle Scholar
  40. Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017. Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequence and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.CrossRefPubMedPubMedCentralGoogle Scholar
  41. Yurkov, V., Stackebrandt, E., Buss, O., Vermeglio, A., Gorlenko, V., and Beatty, J.T. 1997. Reorganization of the genus Erythromicrobium: description of “Erythromicrobium sibiricum” as Sandaracinobacter sibiricus gen. nov., sp. nov., and of “Erythromicrobium ursincola” as Erythromonas ursincola gen. nov., sp. nov. Int. J. Syst. Bacteriol. 47, 1172–1178.CrossRefPubMedGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Hyosun Lee
    • 1
  • Dong-Uk Kim
    • 1
  • Sooyeon Park
    • 2
  • Jung-Hoon Yoon
    • 2
  • Jae-Hyung Ahn
    • 3
  • Jong-Ok Ka
    • 1
    Email author
  1. 1.Department of Agricultural Biotechnology and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
  2. 2.Department of Food Science and BiotechnologySungkyunkwan UniversitySuwonRepublic of Korea
  3. 3.Agricultural Microbiology Division, National Institute of Agricultural SciencesRural Development AdministrationWanjuRepublic of Korea

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