Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat

Abstract

Strain ML311-T8T was isolated from a glacial retreat area in Svalbard, Norway, and was taxonomically characterized by a polyphasic approach. Upon phylogenetic analysis, strain ML311-T8T was clustered with Paenibacillus arcticus MME2_ R6T and P. contaminans CKOBP-6T with 98.3-98.6 and 93.5-93.9% 16S rRNA gene sequence similarities, respectively. DNA-DNA hybridization values between strain ML311-T8T and P. arcticus MME2_R6T was 19.9%. The genomic DNA G+C content was 41.1 mol%. The isolated strain was Gram-stain-positive, strictly aerobic and rod-shaped, and grew in 0–0.5% (w/v) NaCl, at 4-23°C and pH 6.0-10.0, with optimal growth in 0% (w/v) NaCl, at 20°C and pH 7.0-8.0. The predominant respiratory quinone of strain ML311-T8T was MK-7 and the major fatty acids were anteiso-C15:0 and C16:0. The polar lipids of strain ML311-T8T were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three unidentified amino lipids, and three unidentified lipids. On the basis of polyphasic taxonomic analysis, the strain ML311-T8T is proposed to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus psychroresistens sp. nov. is proposed. The type strain is ML311-T8T (= KCCM 43190T = JCM 31243T).

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

References

  1. Ash, C., Farrow, J.A.E., Wallbanks, S., and Collinds, M.D. 1991. Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett. Appl. Microbiol. 13, 202–206.

    Article  CAS  Google Scholar 

  2. 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. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 64, 253–260.

    Article  CAS  PubMed  Google Scholar 

  3. Ash, C., Priest, F.G., and Collins, M.D. 1994. Paenibacillus gen. nov. and Paenibacillus polymyxa comb. nov. In validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 51. Int. J. Syst. Bacteriol. 44, 852.

    Article  Google Scholar 

  4. Bauer, A.W., Kirby, M.M., Sherris, J.C., and Truck, M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol. 45, 493–496.

    Article  CAS  Google Scholar 

  5. Benson, H.J. 2002. Microbiological applications: a laboratory manual in general microbiology. McGraw-Hill, New York, USA.

    Google Scholar 

  6. Cha, I.T., Cho, E.S., Yoo, Y., Seok, Y.J., Park, I., Lim, H.S., Park, J.M., Roh, S.W., Nam, Y.D., Choi, H.J., et al. 2017. Paenibacillus arcticus sp. nov., isolated from Arctic soil. Int. J. Syst. Evol. Microbiol. 67, 4385–4389.

    Article  CAS  PubMed  Google Scholar 

  7. Chou, J.H., Lee, J.H., Lin, M.C., Chang, P.S., Arun, A.B., Young, C.C., and Chen, W.M. 2009. Paenibacillus contaminans sp. nov., isolated from a contaminated laboratory plate. Int. J. Syst. Evol. Microbiol. 59, 125–129.

    Article  CAS  PubMed  Google Scholar 

  8. Collins, M.D. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev. 45, 316–354.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Ezaki, T., Hashimoto, Y., and 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. 38, 224–229.

    Article  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  11. Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. 1994. Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, USA.

    Google Scholar 

  12. Heyndrickx, M., Vandemeulebroecke, K., Scheldeman, P., Kersters, K., De Vos, P., Logan, N.A., Aziz, A.M., Ali, N., and Berkeley, R.C.W. 1996. A polyphasic reassessment of the genus Paenibacillus, reclassification of Bacillus lautus (Nakamura 1984) as Paenibacillus lautus comb. nov. and of Bacillus peoriae (Montefusco et al. 1993) as Paenibacillus peoriae comb. nov., and emended descriptions of P. lautus and of P. peoriae. Int. J. Syst. Bacteriol. 46, 988–1003.

    Article  CAS  PubMed  Google Scholar 

  13. Kämpfer, P., Rosselló-Mora, R., Falsen, E., Busse, H.J., and Tindall, B.J. 2006. Cohnella thermotolerans gen. nov., sp. nov., and classification of ‘Paenibacillus hongkongensis’ as Cohnella hongkon gensis sp. nov. Int. J. Syst. Evol. Microbiol. 56, 781–786.

    Article  CAS  PubMed  Google Scholar 

  14. 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.

    Article  CAS  Google Scholar 

  15. Kluge, A.G. and Farris, J.S. 1969. Quantitative phyletics and the evolution of anurans. Syst. Biol. 18, 1–32.

    Article  Google Scholar 

  16. Komagata, K. and Suzuki, K.I. 1987. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol. 19, 161–207.

    Article  CAS  Google Scholar 

  17. Kovacs, N. 1956. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178, 703.

    Article  CAS  PubMed  Google Scholar 

  18. 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.

    Article  CAS  PubMed  Google Scholar 

  19. Lagesen, K., Hallin, P.F., Rødland, E., Stærfeldt, H.H., Rognes, T., Ussery, D.W. 2007. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 35, 3100–3108.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Miller, L.T. 1982. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J. Clin. Microbiol. 16, 584–586.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Minnikin, D.E., O’Donnell, A.G., and Goodfellow, M. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2, 233–241.

    Article  CAS  Google Scholar 

  22. Montes, M.J., Mercadé, E., Bozal, N., and Guinea, J. 2004. Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. Int. J. Syst. Evol. Microbiol. 54, 1521–1526.

    Article  CAS  PubMed  Google Scholar 

  23. Pruesse, E., Peplies, J., and Glockner, F.O. 2012. SINA: accurate highthroughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Saitou, N. and Nei, M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    CAS  PubMed  Google Scholar 

  25. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI Inc, Newark, DE, USA.

    Google Scholar 

  26. 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. Bacteriol. 47, 289–298.

    Article  CAS  PubMed  Google Scholar 

  27. Tang, Q.Y., Yang, N., Wang, J., Xie, Y.Q., Ren, B., Zhou, Y.G., Gu, M.Y., Mao, J., Li, W.J., Shi, Y.H., et al. 2011. Paenibacillus algorifonticola sp. nov., isolated from a cold spring. Int. J. Syst. Evol. Microbiol. 61, 2167–2172.

    Article  CAS  PubMed  Google Scholar 

  28. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Tittsler, R.P. and Sandholzer, L.A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575–580.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Xiang, W., Wang, G., Wang, Y., Yao, R., Zhang, F., Wang, R., Wang, D., and Zheng, S. 2014. Paenibacillus selenii sp. nov., isolated from selenium mineral soil. Int. J. Syst. Evol. Microbiol. 64, 2662–2667.

    Article  CAS  PubMed  Google Scholar 

  31. Yao, R., Wang, R., Wang, D., Su, J., Zheng, S., and Wang, G. 2014. Paenibacillus selenitireducens sp. nov., a selenite-reducing bacterium isolated from a selenium mineral soil. Int. J. Syst. Evol. Microbiol. 64, 805–811.

    Article  CAS  PubMed  Google Scholar 

  32. Yokota, A., Ningsih, F., Nurlaili, D.G., Sakai, Y., Yabe, S., Oetari, A., Santoso, I., and Sjamsuridzal, W. 2016. Paenibacillus cisolokensis sp. nov., isolated from litter of a geyser. Int. J. Syst. Evol. Microbiol. 66, 1–7.

    Article  Google Scholar 

  33. 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 sequences and whole-genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Zhou, Y., Gao, S., Wei, D.Q., Yang, L.L., Huang, X., He, J., Zhang, Y.J., Tang, S.K., and Li, W.J. 2012. Paenibacillus thermophilus sp. nov., a novel bacterium isolated from a sediment of hot spring in Fujian province, China. Antonie van Leeuwenhoek 201, 601–609.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Incheon National University Research Grant in 2016. This field campaign was permitted by Svalbard Science Forum (Ris ID 6752).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Seong Woon Roh or Myung-Ji Seo.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cha, IT., Cho, ES., Lee, Y.K. et al. Paenibacillus psychroresistens sp. nov., isolated from the soil of an Arctic glacial retreat. J Microbiol. 57, 569–574 (2019). https://doi.org/10.1007/s12275-019-8666-x

Download citation

Keywords

  • Paenibacillus psychroresistens
  • arctic
  • isolation
  • polyphasic taxonomy