Advertisement

Paenibacillus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter

  • Soo-Jin Kim
  • Hayoung Cho
  • Jae-Hyung Ahn
  • Hang-Yeon Weon
  • Jae-Ho Joa
  • Jeong-Seon Kim
  • Soon-Wo KwonEmail author
Article

Abstract

A Gram-stain-positive, rod-shaped, non-endospore-forming, motile by means of peritrichous flagella, facultatively anaerobic bacterium designated TI45-13arT was isolated from Nuruk, a Korean traditional Makgeolli fermentation starter. It grew at 4-35°C (optimum, 28-30°C), pH 5.0-9.0 (optimum, pH 7.0) and NaCl concentrations up to 5% (w/v). Phylogenetic trees generated using 16S rRNA gene sequences revealed that strain TI45-13arT belonged to the genus Paenibacillus and showed the highest sequence similarities with Paenibacillus kyungheensis DCY88T (98.5%), Paenibacillus hordei RH-N24T (98.4%) and Paenibacillus nicotianae YIM h-19T (98.1%). The major fatty acid was anteiso-C15:0. The DNA G+C content was 39.0 mol%, and MK-7 was the predominant isoprenoid quinone. The polar lipids were diphosphatidylglycerol, phos-phatidylglycerol, phosphatidylethanolamine, three unidentified glycolipids, and one unidentified aminoglycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. On the basis of polyphasic taxonomy study, it was suggested that strain TI45-13arT represents a novel species within the genus Paenibacillus for which the name Paenibacillus nuruki sp. nov. is proposed. The type strain was TI45-13arT (= KACC 18728T = NBRC 112013T).

Keywords

Korean traditional Makgeolli Paenibacillus nuruki sp. nov. novel species quinone 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Notes

Acknowledgments

This study was carried out with the support (Project no. PJ-011248) of the National Institute of Agricultural Sciences, Rural Development Administration, Republic of Korea.

Supplementary material

12275_2019_9118_MOESM1_ESM.pdf (7.3 mb)
Supplementary material, approximately 7.34 MB.

References

  1. Ash, C., Priest, F.G., and Collins, M.D. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 64, 253–260.CrossRefPubMedGoogle Scholar
  2. Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E.E., et al. 2013.Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569.CrossRefPubMedGoogle Scholar
  3. Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., Rooney, A.P., Yi, H., Xu, X.W., De Meyer, S., et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68, 461–466.CrossRefPubMedGoogle Scholar
  4. de Costa, M.S., Albuquerque, L., Nobre, M.F., and Wait, R. 2011. The identification of polar lipids in prokaryotes. Methods Mic-robiol. 38, 101–129.CrossRefGoogle Scholar
  5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.CrossRefPubMedGoogle Scholar
  6. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  7. Fitch, W.M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20, 406–416.CrossRefGoogle Scholar
  8. Kim, J.M., Lee, S.H., Lee, S.H., Choi, E.J., and Jeon, C.O. 2013. Pae-nibacillus hordei sp. nov., isolated from naked barley in Korea. Antonie van Leeuwenhoek 103, 3–9.CrossRefPubMedGoogle Scholar
  9. Kim, M., Oh, H.S., Park, S.C., and Chun, J. 2014. Towards a taxo-nomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of pro-karyotes. Int. J. Syst. Evol. Microbiol. 64, 346–351.CrossRefPubMedGoogle Scholar
  10. Lagesen, K., Hallin, P.F., Rødland, E., Stærfeldt, H.H., Rognes, T., and Ussery, D.W. 2007. RNAmmer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35, 3100–3108.CrossRefPubMedPubMedCentralGoogle Scholar
  11. 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, FL, USA.Google Scholar
  12. Li, Q.Q., Zhou, X.K., Dang, L.Z., Cheng, J., Hozzein, W.N., Liu, M.J., Hu, Q., Li, W.J., and Duan, Y.Q. 2014. Paenibacillus nicotianae sp. nov., isolated from a tobacco sample. Antonie van Leeuwen-hoek 106, 199–205.Google Scholar
  13. Logan, N.A., Berge, O., Bishop, A.H., Busse, H.J., De Vos, P., Fritze, D., Heyndrickx, M., Kämpfer, P., Rabinovitch, L., Salkinoja-Salonen, M.S., et al. 2009. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int. J. Syst. Evol. Microbiol. 59, 2114–2121.CrossRefPubMedGoogle Scholar
  14. 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
  15. Pednekar, P.B., Jain, R., Thakur, N.L., and Mahajan, G.B. 2010. Isolation of multi-drug resistant Paenibacillus sp. from fertile soil: an imminent menace of spreading resistance. J. Life Sci. 4, 7–12.Google Scholar
  16. 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
  17. Saha, P., Krishnamurthi, S., Bhattacharya, A., Sharma, R., and Chakrabarti, T. 2010. Fontibacillus aquaticus gen. nov., sp. nov., isolated from a warm spring. Int. J. Syst. Evol. Microbiol. 60, 422–428.CrossRefPubMedGoogle Scholar
  18. 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
  19. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Microbial ID Inc., Newark, DE, USA.Google Scholar
  20. Schaeffer, A.B. and Fulton, M.D. 1933. A simplified method of staining endospores. Science 77, 194.CrossRefPubMedGoogle Scholar
  21. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L.K., and Komagata, K. 1997. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int. J. Syst. Evol. Microbiol. 47, 289–298.Google Scholar
  22. Shin, S.K., Kim, E., and Yi, H. 2018. Paenibacillus crassostreae sp. nov., isolated from the pacific oyster Crassostrea gigas. Int. J. Syst. Evol. Microbiol. 68, 58–63.CrossRefPubMedGoogle Scholar
  23. Siddiqi, M.Z., Siddiqi, M.H., Im, W.T., Kim, Y.J., and Yang, D.C. 2015. Paenibacillus kyungheensis sp. nov., isolated from flowers of Magnolia. Int. J. Syst. Evol. Microbiol. 65, 3959–3964.CrossRefPubMedGoogle Scholar
  24. Staneck, J.L. and Roberts, G.D. 1974. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl. Microbiol. 28, 226–231.PubMedPubMedCentralGoogle Scholar
  25. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729.CrossRefPubMedPubMedCentralGoogle Scholar
  26. Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E.P., Zaslavsky, L., Lomsadze, A., Pruitt, K.D., Borodovsky, M., and Ostell, J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614–6624.CrossRefPubMedPubMedCentralGoogle Scholar
  27. 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 and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© The Microbiological Society of Korea 2019

Authors and Affiliations

  • Soo-Jin Kim
    • 1
  • Hayoung Cho
    • 1
  • Jae-Hyung Ahn
    • 1
  • Hang-Yeon Weon
    • 1
  • Jae-Ho Joa
    • 2
  • Jeong-Seon Kim
    • 1
  • Soon-Wo Kwon
    • 1
    Email author
  1. 1.Rural Development AdministrationAgricultural Microbiology Division, National Institute of Agricultural SciencesWanjuRepublic of Korea
  2. 2.Rural Development AdministrationNational Institute of Horticultural and Herbal ScienceJejuRepublic of Korea

Personalised recommendations