Skip to main content
SpringerLink
Log in

Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A taxonomic study was carried out on strain D104T, which was isolated from deep-sea subsurface sediment sample from the Arctic Ocean. The bacterium was found to be Gram-negative, oxidase negative and catalase weakly positive, rod shaped, motile by means of polar flagellum. The organism grows between 4 and 37 °C (optimum 25–28 °C) and 0.5–6 % NaCl (optimum 3 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D104T belongs to the genus Marinomonas, with highest sequence similarities of 97.7 % to Marinomonas ushuaiensis DSM 15871T, followed by M. dokdonensis DSW10-10T (96.9 %), M. arenicola KMM 3893T (96.7 %), M. arctica 328T (96.6 %) and other 18 species of the genus Marinomonas (94.4–96.5 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain D104T and M. ushuaiensis DSM 15871T were 84.24 % and 20.80 ± 2.33 % respectively. The principal fatty acids were C16:0, sum in feature 3 (C16:1 ω7c/C16:1 ω6c), sum in feature 8 (C18:1 ω7c/C18:1 ω6c) and C12:1 3OH. The G + C content of the chromosomal DNA was determined to be 44.8 mol%. The respiratory quinone was found to be Q8 (100 %). Polar lipids include phosphatidylglycerol and phosphatidylethanolamine as major phospholipids and aminolipid and phospholipid as minor components. The results of the genotypic and phenotypic analyses indicate that strain D104T represents a novel species of the genus Marinomonas, for which the name Marinomonas profundimaris sp. nov. is proposed, with the type strain D104T (=MCCC 1A07573T = LMG 27696T).

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

Fig. 1

Similar content being viewed by others

Abbreviations

MCCC:

Marine Culture Collection of China

References

  • Auch AF, Klenk HP, Goker M (2010a) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2:142–148

    Article  PubMed  PubMed Central  Google Scholar 

  • Auch AF, von Jan M, Klenk HP, Goker M (2010b) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134

    Article  PubMed  PubMed Central  Google Scholar 

  • Baumann L, Baumann P, Mandel M, Allen RD (1972) Taxonomy of aerobic marine eubacteria. J Bacteriol 110:402–429

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chimetto LA, Cleenwerck I, Brocchi M, Willems A, De Vos P, Thompson FL (2011) Marinomonas brasilensis sp. nov., isolated from the coral Mussismilia hispida, and reclassification of Marinomonas basaltis as a later heterotypic synonym of Marinomonas communis. Int J Syst Evol Microbiol 61:1170–1175

    Article  CAS  PubMed  Google Scholar 

  • Dong C, Bai X, Lai Q, Xie Y, Chen X, Shao Z (2014) Draft genome sequence of Marinomonas sp. strain D104, a polycyclic aromatic hydrocarbon-degrading bacterium from the deep-sea sediment of the Arctic Ocean. Genome Announc 2:e01211–e01213

    PubMed  PubMed Central  Google Scholar 

  • Espinosa E, Marco-Noales E, Gómez D, Lucas-Elío P, Ordax M, Garcías-Bonet N, Duarte CM, Sanchez-Amat A (2010) Taxonomic study of Marinomonas strains isolated from the seagrass Posidonia oceanica, with descriptions of Marinomonas balearica sp. nov. and Marinomonas pollencensis sp. nov. Int J Syst Evol Microbiol 60:93–98

    Article  CAS  PubMed  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 

  • Gupta P, Chaturvedi P, Pradhan S, Delille D, Shivaji S (2006) Marinomonas polaris sp. nov., a psychrohalotolerant strain isolated from coastal sea water off the subantarctic Kerguelen islands. Int J Syst Evol Microbiol 56:361–364

    Article  CAS  PubMed  Google Scholar 

  • Ivanova EP, Onyshchenko OM, Christen R, Lysenko AM, Zhukova NV, Shevchenko LS, Kiprianova EA (2005) Marinomonas pontica sp. nov., isolated from the Black Sea. Int J Syst Evol Microbiol 55:275–279

    Article  CAS  PubMed  Google Scholar 

  • Jung YT, Oh TK, Yoon JH (2012) Marinomonas hwangdonensis sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:2062–2067

    Article  CAS  PubMed  Google Scholar 

  • 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 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Lai Q, Yuan J, Wu C, Shao Z (2009) Oceanibaculum indicum gen. nov., sp. nov., isolated from deep seawater of the Indian Ocean. Int J Syst Evol Microbiol 59:1733–1737

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Shao Z (2005) Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 55:1181–1186

    Article  CAS  PubMed  Google Scholar 

  • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18

    Article  PubMed  PubMed Central  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, 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 

  • Prabagaran SR, Suresh K, Manorama R, Delille D, Shivaji S (2005) Marinomonas ushuaiensis sp. nov., isolated from coastal sea water in Ushuaia, Argentina, sub-Antarctica. Int J Syst Evol Microbiol 55:309–313

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rzhetsky A, 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, 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 (technical note no. 101)

  • Shieh WY, Chen YW, Chaw SM, Chiu HH (2003) Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int J Syst Evol Microbiol 53:479–484

    Article  PubMed  Google Scholar 

  • Solano F, Sanchez-Amat A (1999) Note: studies on the phylogenetic relationships of melanogenic marine bacteria: proposal of Marinomonas mediterranea sp. nov. Int J Syst Bacteriol 49:1241–1246

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van Landschoot A, De Ley J (1983) Intra-and intergeneric similarities of the rRNA cistrons of Alteromonas, Marinomonas (gen. nov.) and some other Gram-negative bacteria. J Gen Microbiol 129:3057–3074

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Yoon JH, Kang SJ, Oh TK (2005) Marinomonas dokdonensis sp. nov., isolated from sea water. Int J Syst Evol Microbiol 55:2303–2307

    Article  CAS  PubMed  Google Scholar 

  • Zhang DC, Li HR, Xin YH, Liu HC, Chen B, Chi ZM, Zhou PJ, Yu Y (2008) Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic. Int J Syst Evol Microbiol 58:1715–1718

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was financially supported by Public Welfare Project of SOA (201005032), COMRA program (No. DY125-15-R-01), National Natural Science Foundation of China (41206158), the China Polar Environment Investigation and Estimate Project (2012-2015) and National Infrastructure of Natural Resources for Science and Technology Program of China (No. NIMR-2013-9).

Author information

Authors and Affiliations

  1. State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China

    Xiuhua Bai, Qiliang Lai, Chunming Dong, Fuying Li & Zongze Shao

  2. Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China

    Xiuhua Bai, Qiliang Lai, Chunming Dong, Fuying Li & Zongze Shao

  3. Collaborative Innovation Center of Deep Sea Biology, Xiamen, China

    Xiuhua Bai, Qiliang Lai, Chunming Dong, Fuying Li & Zongze Shao

  4. Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, 361005, China

    Xiuhua Bai, Qiliang Lai, Chunming Dong, Fuying Li & Zongze Shao

Authors
  1. Xiuhua Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qiliang Lai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chunming Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fuying Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zongze Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zongze Shao.

Additional information

Xiuhua Bai and Qiliang Lai have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 357 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bai, X., Lai, Q., Dong, C. et al. Marinomonas profundimaris sp. nov., isolated from deep-sea sediment sample of the Arctic Ocean. Antonie van Leeuwenhoek 106, 449–455 (2014). https://doi.org/10.1007/s10482-014-0213-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0213-5

Keywords

Search

Navigation