Skip to main content
SpringerLink
Log in

Sulfitobacter profundi sp. nov., isolated from deep seawater

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

Abstract

A Gram-stain-negative, rod-shaped, obligately aerobic, chemoheterotrophic bacterium which is motile by means of a single polar flagellum, designated SAORIC-263T, was isolated from deep seawater of the Pacific Ocean. Phylogenetic analyses based on 16S rRNA gene sequences and genomebased phylogeny revealed that strain SAORIC-263T belonged to the genus Sulfitobacter and shared 96.1–99.9% 16S rRNA gene sequence similarities with Sulfitobacter species. Wholegenome sequencing of strain SAORIC-263T revealed a genome size of 3.9Mbp and DNA G+C content of 61.3 mol%. The SAORIC-263T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 79.1–88.5% and 18.9–35.0%, respectively, with other Sulfitobacter genomes. The SAORIC-263T genome contained the genes related to benzoate degradation, which are frequently found in deep-sea metagenome. The strain contained summed feature 8 (C18:1ω7c), C18:1ω7c 11-methyl, and C16:0 as the predominant cellular fatty acids as well as ubiquinone-10 (Q-10) as the major respiratory quinone. The major polar lipids of the strain were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and aminolipid. On the basis of taxonomic data obtained in this study, it is suggested that strain SAORIC-263T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter profundi sp. nov. is proposed. The type strain is SAORIC-263T (= KACC 21183T = NBRC 113428T).

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

  • Choo, Y.J., Lee, K., Song, J., and Cho, J.C. 2007. Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’. Int. J. Syst. Evol. Microbiol. 57, 532–537.

    Article  CAS  PubMed  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  PubMed  Google Scholar 

  • Curson, A.R., Rogers, R., Todd, J.D., Brearley, C.A., and Johnston, A.W. 2008. Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate–changing gas dimethylsulfide in several marine alpha–proteobacteria and Rhodobacter sphaeroides. Environ. Microbiol. 10, 757–767.

    Article  CAS  PubMed  Google Scholar 

  • Eloe, E.A., Malfatti, F., Gutierrez, J., Hardy, K., Schmidt, W.E., Pogliano, K., Pogliano, J., Azam, F., and Bartlett, D.H. 2011. Isolation and characterization of the first psychropiezophilic alphaproteobacterium. Appl. Environ. Microbiol. 77, 8145–8153.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.

    Article  Google Scholar 

  • Fukui, Y., Abe, M., Kobayashi, M., and Satomi, M. 2015. Sulfitobacter pacificus sp. nov., isolated from the red alga Pyropia yezoensis. Antonie van Leeuwenhoek 107, 1155–1163.

    Article  CAS  PubMed  Google Scholar 

  • Fukui, Y., Abe, M., Kobayashi, M., Shimada, Y., Saito, H., Oikawa, H., Yano, Y., and Satomi, M. 2014. Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis. Int. J. Syst. Evol. Microbiol. 64, 438–443.

    Article  CAS  PubMed  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  PubMed  Google Scholar 

  • Honda, M.C., Wakita, M., Matsumoto, K., Fujiki, T., Siswanto, E., Sasaoka, K., Kawakami, H., Mino, Y., Sukigara, C., and Kitamura, M. 2017. Comparison of carbon cycle between the western Pacific subarctic and subtropical time–series stations: highlights of the K2S1 project. J. Oceanogr. 73, 647–667.

    Article  CAS  Google Scholar 

  • Ivanova, E.P., Gorshkova, N.M., Sawabe, T., Zhukova, N.V., Hayashi, K., Kurilenko, V.V., Alexeeva, Y., Buljan, V., Nicolau, D.V., Mikhailov, V.V., et al. 2004. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina). Int. J. Syst. Evol. Microbiol. 54, 475–480.

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa, M., Sato, Y., and Morishima, K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome Sequences. J. Mol. Biol. 428, 726–731.

    Article  CAS  PubMed  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  PubMed  Google Scholar 

  • Kumari, P., Bhattacharjee, S., Poddar, A., and Das, S.K. 2016. Sulfitobacter faviae sp. nov., isolated from the coral Favia veroni. Int. J. Syst. Evol. Microbiol. 66, 3786–3792.

    Article  CAS  PubMed  Google Scholar 

  • Kwak, M.J., Lee, J.S., Lee, K.C., Kim, K.K., Eom, M.K., Kim, B.K., and Kim, J.F. 2014. Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater. Int. J. Syst. Evol. Microbiol. 64, 3760–3767.

    Article  CAS  PubMed  Google Scholar 

  • Labrenz, M., Tindall, B.J., Lawson, P.A., Collins, M.D., Schumann, P., and Hirsch, P. 2000. Staleya guttiformis gen. nov., sp. nov. and Sulfitobacter brevis sp. nov., α–3–Proteobacteria from hypersaline, heliothermal and meromictic Antarctic Ekho Lake. Int. J. Syst. Evol. Microbiol. 50, 303–313.

    Article  CAS  PubMed  Google Scholar 

  • Liu, Y., Lai, Q., and Shao, Z. 2017. Proposal for transfer of Oceanibulbus indolifex Wagner–Döbler et al. 2004 to the genus Sulfitobacter as Sulfitobacter indolifex comb. nov. Int. J. Syst. Evol. Microbiol. 67, 2328–2331.

    Article  CAS  PubMed  Google Scholar 

  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, Buchner, A., Lai, T., Steppi, S., Jobb, G., et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Markowitz, V.M., Mavromatis, K., Ivanova, N.N., Chen, I.M., Chu, K., and Kyrpides, N.C. 2009. IMG ER: a system for microbial ge nome annotation expert review and curation. Bioinformatics 25, 2271–2278.

    Article  CAS  PubMed  Google Scholar 

  • Martín–Cuadrado, A.B., López–García, P., Alba, J.C., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Rodríguez–Valera, F. 2007. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One 2, e914.

    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 Bioinformatics 14, 60.

    Article  PubMed  PubMed Central  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. Methods 2, 233–241.

    Article  CAS  Google Scholar 

  • Na, S.I., Kim, Y.O., Yoon, S.H., Ha, S.M., Baek, I., and Chun, J. 2018. UBCG: Up–to–date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol. 56, 281–285.

    Article  CAS  Google Scholar 

  • Park, A.Y., Teeravet, S., Pheng, S., Lee, J.R., Kim, S.G., and Suwannachart, C. 2018. Sulfitobacter aestuarii sp. nov., a marine bacterium isolated from a tidal flat of the Yellow Sea. Int. J. Syst. Evol. Microbiol. 68, 1771–1775.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pukall, R., Buntefuss, D., Fruhling, A., Rohde, M., Kroppenstedt, R.M., Burghardt, J., Lebaron, P., Bernard, L., and Stackebrandt, E. 1999. Sulfitobacter mediterraneus sp. nov., a new sulfite–oxidizing member of the alpha–Proteobacteria. Int. J. Syst. Evol. Microbiol. 49, 513–519.

    CAS  Google Scholar 

  • Richter, M. and Rossello–Mora, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106, 19126–19131.

    Article  PubMed  Google Scholar 

  • Rzhetsky, A. and Nei, M. 1993. Theoretical foundation of the minimum–evolution method of phylogenetic inference. Mol. Biol. Evol. 10, 1073–1095.

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, DE, USA.

    Google Scholar 

  • Song, J., Kang, I., Joung, Y., Yoshizawa, S., Kaneko, R., Oshima, K., Hattori, M., Hamasaki, K., Kogure, K., Kim, S., et al. 2019. Genome analysis of Rubritalea profundi SAORIC–165T, the first deep–sea verrucomicrobial isolate, from the northwestern Pacific Ocean. J. Microbiol. In press.

    Google Scholar 

  • Sorokin, D.Y. 1995. Sulfitobacter pontiacus gen. nov., sp. nov. a new heterotrophic bacterium from the Black Sea, specialized on sulfite oxidation. Mikrobiologiya 64, 295–295.

    Google Scholar 

  • Stothard, P. and Wishart D.S. 2005. Circular genome visualization and exploration using CGView. Bioinformatics 21, 537–539.

    Article  CAS  PubMed  Google Scholar 

  • Weisburg, W.G., Barns, S.M., Pelletier, D.A., and Lane, D.J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173, 697–703.

    CAS  PubMed  Google Scholar 

  • Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and Chun, J. 2017a. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole–genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613–1617.

    CAS  PubMed  Google Scholar 

  • Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., and Chun, J. 2017b. A largescale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 110, 1281–1286.

    CAS  Google Scholar 

  • Yoon, J.H., Kang, S.J., and Oh, T.K. 2007. Sulfitobacter marinus sp. nov., isolated from seawater of the East Sea in Korea. Int. J. Syst. Evol. Microbiol. 57, 302–305.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are grateful to the officer and crew of R/V Mirai (Japan Agency for Marine-Earth Science and Technology [JAMSTEC]) for their assistance and support with sample collection. We would also like to thank Dr. Kazuhiro Kogure for his support with the isolation of deep-sea bactrial strains.

This study was supported by Inha University Research Grant.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Inha University, Incheon, 22212, Republic of Korea

    Jaeho Song, Hye-Jin Jang, Yochan Joung, Ilnam Kang & Jang-Cheon Cho

Authors
  1. Jaeho Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hye-Jin Jang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yochan Joung
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ilnam Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jang-Cheon Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jang-Cheon Cho.

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

Song, J., Jang, HJ., Joung, Y. et al. Sulfitobacter profundi sp. nov., isolated from deep seawater. J Microbiol. 57, 661–667 (2019). https://doi.org/10.1007/s12275-019-9150-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-019-9150-3

Keywords

Search

Navigation