Antonie van Leeuwenhoek

, Volume 108, Issue 3, pp 517–524 | Cite as

Taibaiellayonginensis sp. nov., a bacterium isolated from soil of Yongin city

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

Abstract

A novel bacterial strain, designated as THG-SC4T, was isolated from a soil sample collected from Yongin city in South Korea. Cells of the strain were Gram-negative, aerobic, rod-shaped and non-motile. The strain grew optimally at 28–30 °C; at pH 7.0 and in the absence of NaCl. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-SC4T was shown to belong to the genus Taibaiella and shares high sequence similarity with Taibaiella smilacinae KCTC 32316T (95.4 %), followed by Taibaiella koreensis KACC 17171T (94.3 %) and Taibaiella chishuiensis JCM 19637T (94.2 %). The DNA G+C content of the novel isolate was determined to be 43.1 mol% and MK-7 was identified as the predominant isoprenoid quinone. The only polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified polar lipid. The predominant fatty acids were identified as iso-C15:0, iso-C15:1 G, C16:0 and iso-C17:03-OH. On the basis of data from this polyphasic taxonomic study, strain THG-SC4T is considered to represent a novel species of the genus Taibaiella, for which the name Taibaiella yonginensis sp. nov. is proposed. The type strain is THG-SC4T (=KACC 18372T = CCTCC AB 2014316T).

Keywords

Taibaiella yonginensis Gram-negative 16S rRNA Flexirubin-type pigments Homospermidine 

Notes

Acknowledgments

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_505_MOESM1_ESM.tif (185 kb)
Supplementary Fig. S1. The Maximum-likelihood tree based on 16S rRNA gene sequence analysis showing phylogenetic relationships of strain THG-SC4T and other related type species. Evolutionary distances were computed using Tamura-Nei model. Numbers at nodes represent percentages of bootstrap support based on a maximum-likelihood analysis of 1000 resampled datasets. Bootstrap values more than 50 % are shown at branching points. Burkholderia cepacia ATCC 25416T was used as an outgroup. Bar, 0.2 nucleotide substitutions per nucleotide position
10482_2015_505_MOESM2_ESM.tif (352 kb)
Supplementary Fig. S2. Transmission electron micrographs of Taibaiella yonginensis THG-SC4T after negative staining with uranyl acetate. Bar indicated 0.5 μm

References

  1. 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
  2. Busse HJ, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708CrossRefGoogle Scholar
  3. Busse HJ, Kämpfer P, Denner EBM (1999) Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 23:242–251PubMedCrossRefGoogle Scholar
  4. Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287Google Scholar
  5. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  6. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  7. Gomori G (1955) Preparation of buffers for use in enzyme studies. In: Colowick SP, Kaplan NO (eds) Methods in enzymology. Academic Press, New York, pp 138–146Google Scholar
  8. 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
  9. 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
  10. Kämpfer P, Lodders N, Falsen E (2011) Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61:518–523PubMedCrossRefGoogle Scholar
  11. 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
  12. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  13. 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
  14. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M (1977) Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 27:104–117CrossRefGoogle Scholar
  15. 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
  16. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  17. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, NewarkGoogle Scholar
  18. Schmidt K, Connor A, Britton G (1994) Chemical methods in prokaryotic systematics. In: Goodfellow M, O’Donnell AG (eds) Analysis of pigments: carotenoids and related polyenes. Wiley, Chichester, pp 403–461Google Scholar
  19. Skerman VBD (1967) A Guide to the Identification of the Genera of Bacteria, 2nd edn. Williams and Wilkins, BaltimoreGoogle Scholar
  20. Son HM, Kook MC, Kim JH, Yi TH (2014) Taibaiella koreensis sp. nov. isolated from soil of ginseng field. Int J Syst Evol Microbiol 64:1018–1023PubMedCrossRefGoogle Scholar
  21. Taibi G, Schiavo MR, Gueli MC, Calanni Rindina P, Muratore R, Nicotra CMA (2000) Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B 745:431–437CrossRefGoogle Scholar
  22. 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
  23. Tan X, Zhang RG, Meng TY, Liang HZ, Lv J (2014) Taibaiella chishuiensis sp. nov., isolated from freshwater. Int J Syst Evol Microbiol 64:1795–1801PubMedCrossRefGoogle Scholar
  24. 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
  25. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703PubMedCentralPubMedGoogle Scholar
  26. Zhang L, Wang Y, Wei L, Wang Y, Shen X, Li S (2013) Taibaiella smilacinae gen. nov., sp. nov., an endophytic member of the family Chitinophagaceae isolated from the stem of Smilacina japonica, and emended description of Flavihumibacter petaseus. Int J Syst Evol Microbiol 63:3769–3776PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Hina Singh
    • 1
  • Juan Du
    • 1
  • KyungHwa Won
    • 1
  • Jung-Eun Yang
    • 1
  • Shahina Akter
    • 1
  • Ki-Young Kim
    • 2
  • ChangShik Yin
    • 3
  • Tae-Hoo Yi
    • 1
  1. 1.Department of Oriental Medicine Biotechnology, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea
  2. 2.Department of Genetic Engineering, College of Life ScienceKyung Hee UniversityYongin-siRepublic of Korea
  3. 3.Acupuncture Meridian Science Research Center, College of Korean MedicineKyung Hee UniversityYongin-siRepublic of Korea

Personalised recommendations