Skip to main content
SpringerLink
Log in

Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds

  • Microbial Systematics and Evolutionary Microbiology
  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

Strain ATSA2T was isolated from surface-sterilized kimchi cabbage (Brassica rapa subsp. pekinensis) seeds and represents a novel bacterium based on the polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ATSA2T formed a lineage within genus Saccharibacillus and was most closely to Saccharibacillus deserti WLG055T (98.1%) and Saccharibacillus qing-shengii H6T (97.9%). The whole-genome of ATSA2T comprised a 5,619,468 bp of circular chromosome with 58.4% G + C content. The DNA-DNA relatedness values between strain ATSA2T and its closely related type strains S. deserti WLJ055 and S. qingshengii H6T were 26.0% and 24.0%, respectively. Multiple gene clusters associated with plant growth promotion activities (stress response, nitrogen and phosphorus metabolism, and auxin biosynthesis) were annotated in the genome. Strain ATSA2T was Gram-positive, endospore-forming, facultatively anaerobic, and rod-shaped It grew at 15–37°C (optimum 25°C), pH 6.0–10.0 (optimum pH 8.0), and in the presence of 0–5% (w/v) NaCl (optimum 1%). The major cellular fatty acids (> 10%) of strain ATSA2T were anteiso-C15:0 and C16:0. MK-7 was the major isoprenoid quinone. The major polar lipids present were diphosphatidylglycerol, phosphatidylglycerol, and three unknown glycolipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxo-nomic features, strain ATSA2T is proposed to represent a novel species of genus Saccharibacillus, for which the name is Saccharibacillus brassicae sp. nov. The type strain is ATSA2T (KCTC 43072T = CCTCC AB 2019223T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Chin, C.S., Alexander, D.H., Marks, P., Hammer, 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. Methods10, 563–569.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Collins, M.D., Shah, H.N., and Minnikin, D.E. 1980. A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J. Appl. Bacteriol.48, 277–282.

    Article  CAS  Google Scholar 

  • 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.39, 224–229.

    Article  Google Scholar 

  • Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol.57, 81–91.

    Article  CAS  Google Scholar 

  • Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT. Nucleic Acids Symp. Ser.41, 95–98.

    CAS  Google Scholar 

  • Han, H., Gao, S., Wang, Q., He, L.Y., and Sheng, X.F. 2016. Saccharibacillus qingshengii sp. nov, isolated from a lead-cadmium tailing. Int. J. Syst. Evol. Microbiol.66, 4645–4649.

    Article  CAS  Google Scholar 

  • Hwang, S.H., Hwang, W.M., Kang, K. and Ahn, T.Y. 2019. Gramella fulva sp. nov, isolated from a dry surface of tidal flat. J. Microbiol.57, 23–29.

    Article  CAS  Google Scholar 

  • Jiang, L., Lim, C.J., Jeong, J.C., Kim, C.Y., Kim, D.H., Kim, S.W. and Lee, J. 2019. Whole-genome sequence data and analysis of Saccharibacillus sp. ATSA2 isolated from kimchi cabbage seeds. Data Brief26, 104465

    Article  Google Scholar 

  • Kämpfer, P., Busse, H.J., Kleinhagauer, T., Mclnroy, J.A., and Glaeser, S.P. 2016. Saccharibacillus endophyticus sp. nov., an endophyte of cotton. Int. J. Syst. Evol. Microbiol.66, 5134–5139.

    Article  Google Scholar 

  • Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y., and Morishima, K. 2016. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res.45, D353–D361.

    Article  Google Scholar 

  • Kim, I., Ghhetri, G., Kim, J., and Seo, T. 2019. Amnibacterium setariae sp. nov., an endophytic actinobacterium isolated from dried foxtail. Antonie van Leeuwenhoek DOI: 10.1007/sl0482-019-01302-7.

    Google Scholar 

  • Kim, M., Oh, H.S., Park, S.C., and Chun, J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol.64, 346–351.

    Article  CAS  Google Scholar 

  • 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  Google Scholar 

  • Lane, D.J. 1991. 16S/23S rRNA Sequencing. In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic Acid Techniques in Bacterial Systematic, pp. 115–175. John Wiley and Sons, New York, USA.

    Google Scholar 

  • Lee, Y. and Jeon, C.O. 2017. Cohnella algarum sp. nov, isolated from a freshwater green alga Paulinella chromatophora. Int. J. Syst. Evol. Microbiol.67, 4767–4772.

    Article  CAS  Google Scholar 

  • Lee, S.A., Kim, Y., Sang, M.K., Song, J., Kwon, S.W. and Weon, H.Y. 2019. Chryseolinea soli sp. nov., isolated from soil. J. Microbiol.57, 122–126.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Meier-Kolthoff, J.P., Auch, A.F., Klenk, H.P., and Goker, M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics14, 60.

    Article  Google Scholar 

  • 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. Methods2, 233–241.

    Article  CAS  Google Scholar 

  • Na, S.I., Kim, Y.O., Yoon, S.H., Ha, S.M., Back, I., and Chun, J. 2018. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol.56, 280–285.

    Article  CAS  Google Scholar 

  • Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., and Glöckner, F.O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res.41, D590–D596.

    Article  CAS  Google Scholar 

  • Rivas, R., García-Fraile, P., Zurdo-Piñeiro, J.L., Mateos, P.F., Martínez-Molina, E., Bedmar, E.J., Sánchez-Raya, J., and Velazquez, E. 2008. Saccharibacillus sacchari gen. nov, sp. nov, isolated from sugarcane. Int. J. Syst. Evol. Microbiol.58, 1850–1854.

    Article  CAS  Google Scholar 

  • Sasser, M. 2006. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI, Newark, DE, USA.

    Google Scholar 

  • Schumann, P. 2011. Peptidoglycan structure. Method Microbiol.38, 101–129.

    Article  CAS  Google Scholar 

  • Sun, J.Q., Wang, X.Y., Wang, L.J., Xu, L., Liu, M., and Wu, X.L. 2016. Saccharibacillus deserti sp. nov, isolated from desert soil. Int. J. Syst. Evol. Microbiol.66, 623–627.

    Article  CAS  Google Scholar 

  • Yang, S.Y., Liu, H., Liu, R., Zhang, K.Y., and Lai, R. 2009. Saccharibacillus kuerlensis sp. nov, isolated from a desert soil. Int. J. Syst. Evol. Microbiol.59, 953–957.

    Article  CAS  Google Scholar 

  • 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  Google Scholar 

Download references

Acknowledgments

This work was performed with the support of the KRIBB Research Initiative Program (KGM5281913).

Author information

Authors and Affiliations

  1. Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Republic of Korea

    Lingmin Jiang, Song-Gun Kim, Jae Cheol Jeong, Cha Young Kim, Suk Weon Kim & Jiyoung Lee

  2. Department of Bioactive Materials, Chonbuk National University, Jeonju, 54896, Republic of Korea

    Lingmin Jiang & Dae-Hyuk Kim

  3. Research Institute of Biotechnology Breeding, Asia Seed Co., Icheon, 17414, Republic of Korea

    Chan Ju Lim

Authors
  1. Lingmin Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chan Ju Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Song-Gun Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jae Cheol Jeong
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Cha Young Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dae-Hyuk Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Suk Weon Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jiyoung Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Suk Weon Kim or Jiyoung Lee.

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

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Jiang, L., Lim, C.J., Kim, SG. et al. Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds. J Microbiol. 58, 24–29 (2020). https://doi.org/10.1007/s12275-020-9346-6

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-020-9346-6

Keywords

Search

Navigation