Deinococcus petrolearius sp. nov. isolated from crude oil recovery water in China

Abstract

A Gram-stain positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain 6.1T, was isolated from a crude oil recovery water sample from the Huabei oil field in China. The novel strain exhibited tolerance of UV irradiation (> 1000 J m−2). Based on 16S rRNA gene sequence comparisons, strain 6.1T shows high similarity to Deinococcus citri DSM 24791T (98.1%) and Deinococcus gobiensis I-0T (97.8%), with less than 93.5% similarity to other closely related taxa. The major cellular fatty acids were identified as summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH), followed by iso-C17:1 ω9c and C16:0. The polar lipid profile was found to contain phospholipids, glycolipids, phosphoglycolipids and aminophospholipids. The predominant respiratory quinone was identified as MK-8. The DNA G + C content was determined to be 68.3 mol %. DNA–DNA hybridization between strain 6.1T and D. citri DSM 24791T was 45.6 ± 7.1% and with D. gobiensis I-OT was 36.6 ± 4.7%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, we conclude strain 6.1T represents a novel species of the genus Deinococcus, for which we propose the name Deinococcus petrolearius sp. nov. The type strain is 6.1T (= CGMCC 1.15053T = KCTC 33744T).

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

Fig. 1
Fig. 2

References

  1. Brooks BW, Murray RGE (1981) Nomenclature for “Micrococcus radiodurans” and other radiation-resistant Cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., including five species. Int J Sys Bacteriol 31(3):353–360

    Article  Google Scholar 

  2. Callegan RP, Nobre MF, McTernan PM, Battista JR, Navarro-Gonzalez R, McKay CP, da Costa MS, Rainey FA (2008) Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments. Int J Syst Evol Microbiol 58:1252–1258

    CAS  Article  PubMed  Google Scholar 

  3. Chun J, Goodfellow M (1995) A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45:240–245

    CAS  Article  PubMed  Google Scholar 

  4. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  Article  PubMed  Google Scholar 

  5. Collins MD, Goodfellow M, Minnikin DE, Alderson G (1985) Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 58:77–86

    CAS  Article  PubMed  Google Scholar 

  6. de Groot A, Chapon V, Servant P, Christen R, Saux MF, Sommer S, Heulin T (2005) Deinococcus deserti sp. nov., a gamma-radiation-tolerant bacterium isolated from the Sahara Desert. Int J Syst Evol Microbiol 55:2441–2446

    Article  PubMed  Google Scholar 

  7. Dong X, Cai M (2001) Manual of systematic and determinative bacteriology. Academic Press, Beijing

    Google Scholar 

  8. Ezaki T, Hashimoto Y, 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 Evol Microbiol 39:224–229

    Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  PubMed  Google Scholar 

  11. Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MS (1997) Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 47:939–947

    CAS  Article  PubMed  Google Scholar 

  12. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Sys Zool 20:406–416

    Article  Google Scholar 

  13. Hirsch P, Gallikowski CA, Siebert J, Peissl K, Kroppenstedt R, Schumann P, Stackebrandt E, Anderson R (2004) Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica. Sys Appl Microbiol 27:636–645

    CAS  Article  Google Scholar 

  14. Hussain F, Khan IU, Habib N, Xian WD, Hozzein WN, Zhang ZD, Zhi XY, Li WJ (2016) Deinococcus saudiensis sp. nov., isolated from desert. Int J Syst Evol Microbiol 66:5106–5111

    Article  PubMed  Google Scholar 

  15. 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

    CAS  Article  PubMed  Google Scholar 

  16. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Bio Evol 33:1870

    CAS  Article  Google Scholar 

  17. Küster E (1959) Outline of a comparative study of criteria used in characterization of the actinomycetes. Int Bull Bacteriol Nomencl Taxon 9:97–104

    Google Scholar 

  18. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt ER, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  19. Makk J, Toth EM, Anda D, Pal S, Schumann P, Kovacs AL, Madl-Szonyi J, Marialigeti K, Borsodi AK (2016) Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave. Int J Syst Evol Microbiol 66:5345–5351

    Article  PubMed  Google Scholar 

  20. Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5:109–118

    CAS  Article  PubMed  Google Scholar 

  21. Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF, Bagaley D, Rash BA, Park MJ, Earl AM, Shank NC, Small AM, Henk MC, Battista JR, Kampfer P, da Costa MS (2005) Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol 71:5225–5235

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Rong X, Huang Y (2010) Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 60:696–703

    CAS  Article  PubMed  Google Scholar 

  23. Rosselló-móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Syst Appl Microbiol 40:121–122

    Article  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  25. Sasser M (1990) Identification of bacteria by gaschromatography of cellular fatty acids, vol 101. Midi Technical Note Midi, Newark

    Google Scholar 

  26. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  27. Tamaoka J (1986) Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Method Enzymol 123:251–256

    CAS  Article  Google Scholar 

  28. Tindall BJ (1990a) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    CAS  Article  Google Scholar 

  29. Tindall BJ (1990b) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130

    CAS  Article  Google Scholar 

  30. Yuan ML, Zhang W, Dai SM, Wu J, Wang YD, Tao TS, Chen M, Lin M (2009) Deinococcus gobiensis sp nov., an extremely radiation-resistant bacterium. Int J Syst Evol Microbiol 59:1513–1517

    CAS  Article  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank Prof. Min Lin of Chinese Academy of Agricultural Sciences, Beijing, China for providing type strain D. gobiensis I-OT to us. This research was funded by the National Natural Science Foundation of China (No. 31400005 and No. 21473256), the Fundamental Research Funds for the Central Universities of China and the Key Research Project of Shandong Province (No. 2017GGX40114).

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Lijun Xi or Jing Li.

Ethics declarations

Conflict of interest

The authors declared that they have no conflicts of interest to this work. We declare that we do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 1739 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Xi, L., Qiao, N., Zhang, J. et al. Deinococcus petrolearius sp. nov. isolated from crude oil recovery water in China. Antonie van Leeuwenhoek 111, 353–360 (2018). https://doi.org/10.1007/s10482-017-0957-9

Download citation

Keywords

  • Deinococcaceae
  • Deinococcus petrolearius sp. nov.
  • New species
  • Oil field
  • Polyphasic